[1] "ofn"       "-oTGBM-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/GBM-TP/19775175/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/19791355/transformed.cor.cli.txt"

nPatients in clinical file=593, in cluster file=577, common to both=571
[1]  71 571
[1] "AMP PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            480 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            480 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          158                           413 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          158                           413 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         98                         473 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         98                         473 
[1] "AMP PEAK  4(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           49                           522 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           49                           522 
[1] "AMP PEAK  5(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            463 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            463 
[1] "AMP PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           523 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           523 
[1] "AMP PEAK  7(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         463 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         463 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          501                            70 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          501                            70 
[1] "AMP PEAK  9(7Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           459                            112 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           459                            112 
[1] "AMP PEAK 10(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          474                            97 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          474                            97 
[1] "AMP PEAK 11(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          467                           104 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          467                           104 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            501 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            501 
[1] "AMP PEAK 13(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          541 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          541 
[1] "AMP PEAK 14(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             84                             487 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             84                             487 
[1] "AMP PEAK 15(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           134                            437 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           134                            437 
[1] "AMP PEAK 16(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          92                          479 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          92                          479 
[1] "AMP PEAK 17(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          539 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          539 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          541 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          541 
[1] "AMP PEAK 19(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             535 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             535 
[1] "AMP PEAK 20(17P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            520 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            520 
[1] "AMP PEAK 21(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            83                            488 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            83                            488 
[1] "AMP PEAK 22(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           241                            330 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           241                            330 
[1] "AMP PEAK 23(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           246                            325 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           246                            325 
[1] "AMP PEAK 24(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         214                          357 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         214                          357 
[1] "AMP PEAK 25(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            69                            502 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            69                            502 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            475 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            475 
[1] "DEL PEAK  2(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           132                            439 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           132                            439 
[1] "DEL PEAK  3(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           511 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           511 
[1] "DEL PEAK  4(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           524 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           524 
[1] "DEL PEAK  5(1Q42.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            49                            522 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            49                            522 
[1] "DEL PEAK  6(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         537 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         537 
[1] "DEL PEAK  7(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           524 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           524 
[1] "DEL PEAK  8(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           516 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           516 
[1] "DEL PEAK  9(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           53                           518 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           53                           518 
[1] "DEL PEAK 10(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            515 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            515 
[1] "DEL PEAK 11(3Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           513 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           513 
[1] "DEL PEAK 12(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         506 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         506 
[1] "DEL PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           77                           494 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           77                           494 
[1] "DEL PEAK 14(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           92                           479 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           92                           479 
[1] "DEL PEAK 15(5Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                         69                         502 
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                         69                         502 
[1] "DEL PEAK 16(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           157                            414 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           157                            414 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        178                         393 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        178                         393 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           66                           505 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           66                           505 
[1] "DEL PEAK 19(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          418                           153 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          418                           153 
[1] "DEL PEAK 20(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           79                           492 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           79                           492 
[1] "DEL PEAK 21(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           464                            107 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           464                            107 
[1] "DEL PEAK 22(10P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         465                          106 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         465                          106 
[1] "DEL PEAK 23(10P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            470                             101 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            470                             101 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            508                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            508                              63 
[1] "DEL PEAK 25(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           509                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           509                             62 
[1] "DEL PEAK 26(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            442 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            442 
[1] "DEL PEAK 27(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           105                            466 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           105                            466 
[1] "DEL PEAK 28(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            475 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            475 
[1] "DEL PEAK 29(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            500 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            500 
[1] "DEL PEAK 30(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          76                          495 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          76                          495 
[1] "DEL PEAK 31(12Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          78                          493 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          78                          493 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           239                            332 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           239                            332 
[1] "DEL PEAK 33(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           227                            344 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           227                            344 
[1] "DEL PEAK 34(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           176                            395 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           176                            395 
[1] "DEL PEAK 35(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           171                            400 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           171                            400 
[1] "DEL PEAK 36(15Q14) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         152                          419 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         152                          419 
[1] "DEL PEAK 37(16P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            92                            479 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            92                            479 
[1] "DEL PEAK 38(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            99                            472 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            99                            472 
[1] "DEL PEAK 39(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                            86                            485 
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                            86                            485 
[1] "DEL PEAK 40(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                            96                            475 
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                            96                            475 
[1] "DEL PEAK 41(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            70                            501 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            70                            501 
[1] "DEL PEAK 42(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                            82                            489 
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                            82                            489 
[1] "DEL PEAK 43(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                             99                             472 
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                             99                             472 
[1] "DEL PEAK 44(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                            56                            515 
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                            56                            515 
[1] "DEL PEAK 45(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            212                             359 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            212                             359 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          118                           453 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          118                           453 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 571 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=377,	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=398,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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] "****** SUMMARY ***** "
Output Data has 571 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=72, 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
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P36.21) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  1(1P36.21) MUTATED    11  80
  AMP PEAK  1(1P36.21) WILD-TYPE  89 390
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            479 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            80                            390 
$`AMP PEAK  1(1P36.21) MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 
       11.77        42.74        12.59         2.50        11.67        92.65 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0332 TCGA-02-0451 TCGA-02-0456 TCGA-06-0130 
       17.72        10.75        25.71        16.21         3.35        12.95 
TCGA-06-0133 TCGA-06-0152 TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 
       14.30        12.33         4.47         4.18         3.65        27.22 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0213 
       44.58        38.96         7.40         7.66         7.63         0.53 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       24.16        13.64         4.70        35.11        12.62         5.75 
TCGA-06-0649 TCGA-06-2557 TCGA-06-5856 TCGA-06-6698 TCGA-08-0349 TCGA-08-0350 
        2.10         1.08         3.75         4.77         9.80        29.23 
TCGA-08-0386 TCGA-08-0520 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0769 
       18.02        10.75         7.56        34.92        38.17        15.06 
TCGA-12-0776 TCGA-12-0820 TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 
        9.73        18.48        27.78         7.59         3.98         4.14 
TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-12-5295 TCGA-14-0783 TCGA-14-0813 
       15.65        44.02        14.53        14.93         6.21         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1452 TCGA-14-1454 
        5.39         2.04        28.93        15.95         7.10        30.18 
TCGA-14-1794 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 TCGA-14-3477 TCGA-15-1449 
        0.99        17.85         5.88        17.49         3.78        13.28 
TCGA-16-1056 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 
       14.01         9.07        12.95        25.38        12.66         0.13 
TCGA-19-4065 TCGA-26-1440 TCGA-26-5132 TCGA-26-5136 TCGA-28-1752 TCGA-28-2509 
        7.04         9.73         9.40        18.97         8.48         4.77 
TCGA-28-5207 TCGA-28-5216 TCGA-28-6450 TCGA-32-1970 TCGA-32-1987 TCGA-32-2616 
       11.28        13.64         5.42        15.39        14.86         7.36 
TCGA-32-2638 TCGA-32-4210 TCGA-32-5222 TCGA-41-2575 TCGA-41-6646 TCGA-74-6584 
       25.18         3.72        19.23         9.53        12.46         7.50 
TCGA-76-4934 
        2.53 

$`AMP PEAK  1(1P36.21) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       15.09         6.54        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       47.11        11.34         9.27        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 
        6.94         3.98        22.72        33.67        25.35        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.29        13.12         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       20.25        69.90        73.84        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 
        5.56         0.39         8.42         7.40        11.84        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 
        9.01         0.26        72.36         9.57         3.16         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
        8.32        12.85         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56        14.60        17.72        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       12.16        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        58.68        19.33         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
        3.65        20.38        28.41        53.85        43.23         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        91.76        24.79        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 
       38.76         8.94        20.58       127.59         5.82        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       25.68        14.73         6.77        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       10.95        12.69        34.92         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1037 TCGA-14-1043 
        3.25         2.89        16.50        26.33        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        1.15         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1829 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
       17.79         7.63         7.17         7.96         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 
       16.37         4.31        29.03         4.57        10.29         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 
        0.66        14.27         3.39        10.75         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        3.65         7.17         3.25         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        7.53         0.16         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87        31.33         7.13         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       14.86         5.49         8.88         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 
        0.20         2.53         9.21         8.35         7.63         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.55         2.83         0.13         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-32-1973 
       23.44        11.01         5.16        22.68        10.49        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        22.78        21.14        12.59        19.86        10.85 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         8.22         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                          0.13                           0.10 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                         92.65                         127.59 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                         11.67                          12.23 
[1] "0.1 - 92.7 (11.7)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.3"
D1V2, continuous
D1V3, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED    39  52
  AMP PEAK  1(1P36.21) WILD-TYPE 185 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     39   52
  AMP PEAK  1(1P36.21) WILD-TYPE  185  295
        clus
vv       AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           39                            185
  MALE                             52                            295
[1] 2 2
[1] FALSE
D1V4, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED    17  72
  AMP PEAK  1(1P36.21) WILD-TYPE  57 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     17   72
  AMP PEAK  1(1P36.21) WILD-TYPE   57  402
     clus
vv    AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  NO                            17                             57
  YES                           72                            402
[1] 2 2
[1] FALSE
D1V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  1(1P36.21) MUTATED                               0
  AMP PEAK  1(1P36.21) WILD-TYPE                            28
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  1(1P36.21) MUTATED                     1
  AMP PEAK  1(1P36.21) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  1(1P36.21) MUTATED                                90
  AMP PEAK  1(1P36.21) WILD-TYPE                             435
D1V6, multiclass
                                 clus
vv                                AMP PEAK  1(1P36.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              0
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           90
                                 clus
vv                                AMP PEAK  1(1P36.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               28
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P36.21) MUTATED       0                         4    82
  AMP PEAK  1(1P36.21) WILD-TYPE    13                        46   403
D1V7, multiclass
                           clus
vv                          AMP PEAK  1(1P36.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               82
                           clus
vv                          AMP PEAK  1(1P36.21) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             46
  WHITE                                                403
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED     3  69
  AMP PEAK  1(1P36.21) WILD-TYPE   9 404
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED      3   69
  AMP PEAK  1(1P36.21) WILD-TYPE    9  404
                        clus
vv                       AMP PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            404
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q32.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q32.1) MUTATED    29 128
  AMP PEAK  2(1Q32.1) WILD-TYPE  71 342
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          157                           413 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          128                           342 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0014 TCGA-02-0024 TCGA-02-0028 TCGA-02-0052 
       11.77        23.18        82.59        53.10        90.58        12.59 
TCGA-02-0055 TCGA-02-0071 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 
        2.50         5.49        65.00        11.67        92.65        17.72 
TCGA-02-0269 TCGA-02-0330 TCGA-02-0333 TCGA-02-0422 TCGA-02-0430 TCGA-02-0451 
       10.75        15.91         4.37        14.50        10.55        16.21 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-06-0128 TCGA-06-0130 TCGA-06-0133 
        3.35        12.92        15.32        22.72        12.95        14.30 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 
       11.74         2.33         8.61        12.33        13.94         3.19 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0177 TCGA-06-0182 TCGA-06-0185 
        3.42         5.85        19.66         4.18         3.65        73.84 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0210 
       44.58        38.96         7.40         7.66         7.63         7.40 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0240 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       24.16        13.64        20.42        72.36         4.70         9.57 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0750 TCGA-06-1084 TCGA-06-1087 TCGA-06-1804 
       35.11         5.75         0.92        23.93         4.04        13.61 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2569 TCGA-06-5411 TCGA-06-5856 TCGA-06-6698 
       15.32         1.08         0.43         8.35         3.75         4.77 
TCGA-06-6699 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0349 TCGA-08-0350 
        1.55        26.79         3.12        22.68         9.80        29.23 
TCGA-08-0353 TCGA-08-0357 TCGA-08-0386 TCGA-08-0514 TCGA-08-0524 TCGA-08-0531 
        8.42        37.58        18.02        11.08         7.27         7.56 
TCGA-12-0615 TCGA-12-0619 TCGA-12-0670 TCGA-12-0692 TCGA-12-0769 TCGA-12-0773 
       15.35        34.92        25.97         3.65        15.06        43.23 
TCGA-12-0775 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1090 
        7.63        10.62        27.78        38.76        20.58         7.59 
TCGA-12-1092 TCGA-12-1096 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-3649 
       21.73         9.11         3.98         4.14        15.65        15.22 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
       14.53         6.21         2.24         1.35         5.39        16.50 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1401 TCGA-14-1452 TCGA-14-1454 
        2.04        28.93        19.30         3.75         7.10        30.18 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-15-1446 
       12.43         0.99        17.85         3.78        13.78        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-19-0962 TCGA-19-0963 
       13.28         3.91        17.59         4.31         0.66        14.27 
TCGA-19-1387 TCGA-19-1786 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2625 
        5.95         7.17         0.13         9.67         1.08         4.08 
TCGA-19-4065 TCGA-19-5952 TCGA-19-5954 TCGA-19-A6J4 TCGA-26-1440 TCGA-26-6173 
        7.04        18.90        12.10         3.98         9.73         7.92 
TCGA-27-1834 TCGA-27-2518 TCGA-27-2524 TCGA-27-2528 TCGA-28-1750 TCGA-28-1752 
       40.54        24.76         7.59        15.78         8.35         8.48 
TCGA-28-2509 TCGA-28-5207 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 
        4.77        11.28        13.64         5.16        10.49        15.39 
TCGA-32-1979 TCGA-32-1987 TCGA-32-1991 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 
       19.50        14.86        16.93         8.84        22.78         3.72 
TCGA-32-4213 TCGA-32-5222 TCGA-41-2573 TCGA-41-3392 TCGA-41-5651 TCGA-41-6646 
       19.86        19.23         8.94         0.99        15.12        12.46 
TCGA-4W-AA9S TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4934 TCGA-76-4935 
        1.45         4.34        14.33         7.50         2.53        36.85 
TCGA-76-6662 
       34.45 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 
        4.73        18.35        10.59        35.41        20.71        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 
        6.87        14.73         3.22        15.09         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       27.02        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-0440 
       25.71        25.12        10.59        12.39        47.11        11.34 
TCGA-02-0446 TCGA-02-2466 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
        9.27        16.80        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 
       20.38        47.61         6.94         3.98        33.67        25.35 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0155 
       20.09        17.79        10.09        19.46        46.59        10.45 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0169 
       10.82         9.44        11.80        56.91        10.65         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.12         4.47         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       20.25        69.90        27.22        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.56         0.39         8.42        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        19.82        13.32        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.26         3.16        12.62         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       16.57        20.78        26.76         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32        33.90        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.74         3.55         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        6.71         2.73         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.77         4.96         1.87         2.56        14.60        17.72 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       12.16        65.33         1.28        17.95        24.56        31.10 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56         4.27        42.15        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 
       19.33        10.75         4.80        15.98        18.41        14.73 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       12.99        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0776 
       26.66        12.13        20.38        28.41        53.85         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 
       14.93        14.86        91.76        24.79        18.48        23.51 
TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
        8.94       127.59         5.82        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       15.85        14.53        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       44.02        26.93        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
       11.24        13.78         3.25         2.89        26.33        15.95 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        0.79         1.38         1.12        32.05        58.78        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 
        1.15         0.92        40.96         6.67         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 
       50.53        53.19        26.07        16.37        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       11.77        21.90         8.61         3.39        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         3.65        12.66         3.25 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        4.87         7.53         0.16        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       17.19         8.02         4.73         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
        8.88        18.97         1.58         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        24.23        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       11.51        18.08        10.39        16.08         2.86        14.40 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
        0.20         2.53         9.21         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        2.83         0.13         0.66         6.74         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       14.93        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5219 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       11.01        22.68         5.42        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 
       15.85         1.18         4.67        12.69        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.02        15.95         7.36        25.18        21.14        12.59 
TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 
       10.85         0.85        13.35         9.53         4.44        11.84 
TCGA-41-4097 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6581 
        0.20         4.08        25.58         3.45        20.91         8.22 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-6191 
        4.80         4.54         3.09         3.65         9.17        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        4.83         5.03        23.90        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.13                          0.10 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        92.65                        127.59 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        11.67                         12.23 
[1] "0.1 - 92.7 (11.7)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    62  96
  AMP PEAK  2(1Q32.1) WILD-TYPE 162 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     62   96
  AMP PEAK  2(1Q32.1) WILD-TYPE  162  251
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          62                           162
  MALE                            96                           251
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    26 126
  AMP PEAK  2(1Q32.1) WILD-TYPE  48 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     26  126
  AMP PEAK  2(1Q32.1) WILD-TYPE   48  348
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           26                            48
  YES                         126                           348
[1] 2 2
[1] FALSE
D2V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  2(1Q32.1) MUTATED                               7
  AMP PEAK  2(1Q32.1) WILD-TYPE                            21
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  2(1Q32.1) MUTATED                     5
  AMP PEAK  2(1Q32.1) WILD-TYPE                  13
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  2(1Q32.1) MUTATED                               146
  AMP PEAK  2(1Q32.1) WILD-TYPE                             379
D2V6, multiclass
                                 clus
vv                                AMP PEAK  2(1Q32.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             7
  TREATED PRIMARY GBM                                       5
  UNTREATED PRIMARY (DE NOVO) GBM                         146
                                 clus
vv                                AMP PEAK  2(1Q32.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              21
  TREATED PRIMARY GBM                                        13
  UNTREATED PRIMARY (DE NOVO) GBM                           379
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED       3                        15   134
  AMP PEAK  2(1Q32.1) WILD-TYPE    10                        35   351
D2V7, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          15
  WHITE                                             134
                           clus
vv                          AMP PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            35
  WHITE                                               351
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED     2 130
  AMP PEAK  2(1Q32.1) WILD-TYPE  10 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      2  130
  AMP PEAK  2(1Q32.1) WILD-TYPE   10  343
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         130
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           343
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(1Q44) MUTATED    17  81
  AMP PEAK  3(1Q44) WILD-TYPE  83 389
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         98                         472 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         81                         389 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0028 TCGA-02-0052 TCGA-02-0055 TCGA-02-0104 
       11.77        53.10        90.58        12.59         2.50        65.00 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 TCGA-02-0269 TCGA-02-0290 TCGA-02-0330 
       11.67        92.65        17.72        10.75        15.95        15.91 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 TCGA-02-2485 TCGA-06-0133 TCGA-06-0152 
       16.21         3.35        15.32        15.45        14.30        12.33 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 
        3.42         5.85        19.66         4.47         4.18         3.65 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       44.58        38.96         7.40         7.66         7.63        24.16 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-1084 
       13.64        72.36         4.70        35.11         5.75        23.93 
TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-2561 TCGA-06-2569 TCGA-06-5856 
        4.04        11.84         1.08        17.65         0.43         3.75 
TCGA-06-6698 TCGA-06-A5U0 TCGA-08-0349 TCGA-08-0350 TCGA-08-0354 TCGA-08-0380 
        4.77        26.79         9.80        29.23        17.95        14.93 
TCGA-08-0386 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0619 TCGA-12-0657 
       18.02         7.27        18.41         7.56        34.92         0.10 
TCGA-12-0773 TCGA-12-0826 TCGA-12-0827 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 
       43.23        27.78        38.76         7.59         3.98         4.14 
TCGA-12-1598 TCGA-12-3653 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
       15.65        14.53         6.21         1.35         5.39        16.50 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1452 TCGA-14-1454 TCGA-14-1794 TCGA-14-1823 
        2.04        28.93         7.10        30.18         0.99        17.85 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1449 TCGA-19-0962 TCGA-19-1786 TCGA-19-1791 
        3.78        13.78        13.28         0.66         7.17         0.13 
TCGA-19-2625 TCGA-19-4065 TCGA-26-1440 TCGA-26-6173 TCGA-27-2524 TCGA-28-2509 
        4.08         7.04         9.73         7.92         7.59         4.77 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-32-1970 TCGA-32-1987 TCGA-32-2632 
       23.44        13.64         5.16        15.39        14.86         8.84 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4719 TCGA-32-5222 TCGA-41-5651 TCGA-74-6578 
       22.78         3.72        10.85        19.23        15.12        14.33 
TCGA-74-6584 TCGA-76-4934 
        7.50         2.53 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        6.54        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       26.43        28.70        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 
       57.76        16.96         3.48        27.02        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0271 
       99.98        15.65        48.95        16.54        16.93        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
        3.98        13.87        14.20        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
       10.62         7.33        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       16.80        12.92        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        46.59        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0169 
       10.82         9.44        11.80        56.91        10.65         3.29 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.12         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       69.90        73.84        27.22        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        5.56         0.39         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.82         9.01         0.26         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       26.76         6.84        26.79        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       15.32        12.49         4.93        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
       16.64         5.98         4.37        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        2.73         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16        65.33         1.28         8.42 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
       15.98        15.35        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       94.78        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 
       23.51         8.94        20.58       127.59         5.82        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        2.04        15.12        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
       11.24        13.78         3.25         2.89        26.33        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       58.78        23.11         1.15         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       17.49         7.96         3.42        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         8.61        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        3.65        12.66         3.25         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        7.53         0.16        24.23         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
       14.86         5.49         8.88        18.97         1.58         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.55         2.83         0.13         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 
       31.27        11.01        22.68        10.49         5.42        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-41-2571 
        7.36        25.18        21.14        12.59        19.86         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       20.91         4.34         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        0.1                         0.1 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      92.65                      127.59 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     11.805                      12.230 
[1] "0.1 - 92.7 (11.8)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    44  54
  AMP PEAK  3(1Q44) WILD-TYPE 180 293
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     44   54
  AMP PEAK  3(1Q44) WILD-TYPE  180  293
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        44                         180
  MALE                          54                         293
[1] 2 2
[1] FALSE
D3V4, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    17  78
  AMP PEAK  3(1Q44) WILD-TYPE  57 396
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     17   78
  AMP PEAK  3(1Q44) WILD-TYPE   57  396
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         17                          57
  YES                        78                         396
[1] 2 2
[1] FALSE
D3V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  3(1Q44) MUTATED                               1                   3
  AMP PEAK  3(1Q44) WILD-TYPE                            27                  15
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  3(1Q44) MUTATED                                94
  AMP PEAK  3(1Q44) WILD-TYPE                             431
D3V6, multiclass
                                 clus
vv                                AMP PEAK  3(1Q44) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           1
  TREATED PRIMARY GBM                                     3
  UNTREATED PRIMARY (DE NOVO) GBM                        94
                                 clus
vv                                AMP PEAK  3(1Q44) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            27
  TREATED PRIMARY GBM                                      15
  UNTREATED PRIMARY (DE NOVO) GBM                         431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       2                         9    80
  AMP PEAK  3(1Q44) WILD-TYPE    11                        41   405
D3V7, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                            80
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                          41
  WHITE                                             405
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED     3  76
  AMP PEAK  3(1Q44) WILD-TYPE   9 397
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      3   76
  AMP PEAK  3(1Q44) WILD-TYPE    9  397
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        76                         397
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P24.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P24.3) MUTATED     9  40
  AMP PEAK  4(2P24.3) WILD-TYPE  91 430
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           49                           521 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           40                           430 
$`AMP PEAK  4(2P24.3) MUTATED`
TCGA-02-0001 TCGA-02-0014 TCGA-02-0104 TCGA-02-0113 TCGA-02-0258 TCGA-02-0281 
       11.77        82.59        65.00        92.65        16.54         3.98 
TCGA-06-0133 TCGA-06-0151 TCGA-06-0192 TCGA-06-0216 TCGA-06-0221 TCGA-06-0649 
       14.30        46.59        38.96        24.16        19.82         2.10 
TCGA-06-0877 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-2557 TCGA-06-2569 
        5.65         6.84         4.04        15.32         1.08         0.43 
TCGA-06-5856 TCGA-06-6391 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 TCGA-08-0517 
        3.75         1.48         8.42        18.02         4.27        58.68 
TCGA-12-0619 TCGA-12-0773 TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0740 
       34.92        43.23        14.93         4.14        14.53        11.97 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1823 TCGA-14-3477 TCGA-16-0846 TCGA-16-0850 
        5.39        28.93        17.85         3.78         3.91        16.37 
TCGA-19-0957 TCGA-19-1786 TCGA-19-2629 TCGA-19-A60I TCGA-26-1439 TCGA-26-1442 
       21.90         7.17        24.23        17.79        13.87        31.33 
TCGA-26-5133 TCGA-27-1834 TCGA-27-1836 TCGA-28-5218 TCGA-32-4210 TCGA-41-2573 
       14.86        40.54        30.05         5.16         3.72         8.94 
TCGA-74-6584 
        7.50 

$`AMP PEAK  4(2P24.3) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       27.02        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       48.95        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        3.98        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 
       27.22        44.58        15.42        10.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
       11.84         0.53        15.02         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       26.79        11.84        13.61        33.90        15.32        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        6.15         4.57         5.23         7.79         5.39       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 
       12.56        42.15        11.08        19.59        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 
       28.41        15.06        53.85         7.63         9.73        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         3.98        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       34.92        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        1.35         2.89        16.50        26.33         2.04        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
       13.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 
        9.14        21.24        13.97         6.41        11.77         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         3.65        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       16.80        14.96         3.98        28.54        10.03         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
        9.86        24.23        21.30        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.95         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                        92.65                        127.59 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                        14.53                         12.13 
[1] "0.4 - 92.7 (14.5)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED    22  27
  AMP PEAK  4(2P24.3) WILD-TYPE 202 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     22   27
  AMP PEAK  4(2P24.3) WILD-TYPE  202  320
        clus
vv       AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  FEMALE                          22                           202
  MALE                            27                           320
[1] 2 2
[1] FALSE
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     6  41
  AMP PEAK  4(2P24.3) WILD-TYPE  68 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      6   41
  AMP PEAK  4(2P24.3) WILD-TYPE   68  433
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  NO                            6                            68
  YES                          41                           433
[1] 2 2
[1] FALSE
D4V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  4(2P24.3) MUTATED                               2
  AMP PEAK  4(2P24.3) WILD-TYPE                            26
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  4(2P24.3) MUTATED                     1
  AMP PEAK  4(2P24.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  4(2P24.3) MUTATED                                46
  AMP PEAK  4(2P24.3) WILD-TYPE                             479
D4V6, multiclass
                                 clus
vv                                AMP PEAK  4(2P24.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          46
                                 clus
vv                                AMP PEAK  4(2P24.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              26
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.3) MUTATED       1                         6    40
  AMP PEAK  4(2P24.3) WILD-TYPE    12                        44   445
D4V7, multiclass
                           clus
vv                          AMP PEAK  4(2P24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              40
                           clus
vv                          AMP PEAK  4(2P24.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     0  42
  AMP PEAK  4(2P24.3) WILD-TYPE  12 431
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      0   42
  AMP PEAK  4(2P24.3) WILD-TYPE   12  431
                        clus
vv                       AMP PEAK  4(2P24.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK  4(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           431
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3Q26.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(3Q26.33) MUTATED    20  88
  AMP PEAK  5(3Q26.33) WILD-TYPE  80 382
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            462 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                            88                            382 
$`AMP PEAK  5(3Q26.33) MUTATED`
TCGA-02-0001 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0047 TCGA-02-0048 
       11.77        10.59        87.06        77.65        14.73         3.22 
TCGA-02-0074 TCGA-02-0106 TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0332 
       10.19        11.67         3.98         7.73        10.62        25.71 
TCGA-06-0166 TCGA-06-0188 TCGA-06-0192 TCGA-06-0211 TCGA-06-0237 TCGA-06-0402 
        5.85        44.58        38.96        11.84        13.64         0.26 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0648 TCGA-06-0649 
        4.70         3.16        35.11        12.62         9.80         2.10 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-2557 
       14.20        26.40         7.86         7.17         4.04         1.08 
TCGA-06-2563 TCGA-06-5408 TCGA-06-5416 TCGA-06-5856 TCGA-06-6389 TCGA-06-6391 
       30.64        11.74         6.71         3.75         7.79         1.48 
TCGA-06-6694 TCGA-06-6695 TCGA-08-0345 TCGA-08-0346 TCGA-08-0353 TCGA-08-0358 
        7.36         8.32         1.74         8.42         8.42        22.29 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0618 
        0.72         4.27        10.75        15.98        15.35        12.99 
TCGA-12-0619 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 
       34.92         0.10        38.17        12.13         9.73        14.93 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1099 
       23.51        38.76        20.58       127.59         7.59         4.14 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 
       15.65         6.77        59.77        44.02        15.12         6.21 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1451 TCGA-14-1453 
        3.25         1.35         5.39         2.04        23.11         1.15 
TCGA-14-1794 TCGA-14-1825 TCGA-14-1829 TCGA-14-3477 TCGA-15-1449 TCGA-19-0963 
        0.99         7.63         7.17         3.78        13.28        14.27 
TCGA-19-1388 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 TCGA-26-6174 
       12.95         3.65        24.23         7.04         9.73         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-2521 TCGA-28-1752 
        5.06        16.60        40.54        21.30        10.39         8.48 
TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
        6.74         4.77        11.28        31.27        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1991 TCGA-32-2632 TCGA-41-2575 
       22.68        10.49         5.42        16.93         8.84         9.53 
TCGA-41-3915 TCGA-41-4097 TCGA-74-6577 TCGA-74-6584 TCGA-76-4934 TCGA-76-6285 
       11.84         0.20         4.34         7.50         2.53         8.35 

$`AMP PEAK  5(3Q26.33) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        4.73        18.35        23.18        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       20.61        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       18.31         6.87        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       28.70        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
        3.48        27.02        65.00        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        9.90         7.33        15.91         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 
       73.84        27.22        15.42        10.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.53        15.02        24.16         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 
       20.42        48.69        10.82         9.01        72.36         9.57 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 
        5.75         5.75        23.57        46.88         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         5.65        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90        15.32        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       17.65        12.56         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        31.50         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         6.15         4.57         5.23 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.39       120.56        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 
       17.72        22.68        37.84         4.18       115.86        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       12.16         9.80        29.23        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       24.56        31.10        37.58         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       19.59        58.68        19.33         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0670 
        7.56        14.73        10.45         7.59        94.78        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
       43.23         7.63        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 
       10.62        27.78         8.94         5.82        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       25.68        14.73        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0862 
        0.95        23.05         2.24        11.24        13.78         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
        1.38         1.12         3.75        32.05        58.78         7.10 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
       17.79        17.85         5.88        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 
       13.78        50.53        19.10        53.19         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         8.61         0.66         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95         4.64        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1832 
        8.88        18.97         1.58         7.92        19.33         9.86 
TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       24.23        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
        2.53         9.21         8.35         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         0.66         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-32-1970 
       17.88         2.53        11.77        23.44         5.16        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        14.86        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         7.36        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        8.94         0.99         4.44        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58         3.45        20.91        14.33         8.22 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 
       16.70         3.29         2.70        11.38        17.06        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                        127.59                         120.56 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                         9.765                         12.675 
[1] "0.1 - 127.6 (9.8)"  "0.1 - 120.6 (12.7)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    40  68
  AMP PEAK  5(3Q26.33) WILD-TYPE 184 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     40   68
  AMP PEAK  5(3Q26.33) WILD-TYPE  184  279
        clus
vv       AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  FEMALE                           40                            184
  MALE                             68                            279
[1] 2 2
[1] FALSE
D5V4, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    20  86
  AMP PEAK  5(3Q26.33) WILD-TYPE  54 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     20   86
  AMP PEAK  5(3Q26.33) WILD-TYPE   54  388
     clus
vv    AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  NO                            20                             54
  YES                           86                            388
[1] 2 2
[1] FALSE
D5V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  5(3Q26.33) MUTATED                               0
  AMP PEAK  5(3Q26.33) WILD-TYPE                            28
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  5(3Q26.33) MUTATED                     0
  AMP PEAK  5(3Q26.33) WILD-TYPE                  18
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  5(3Q26.33) MUTATED                               108
  AMP PEAK  5(3Q26.33) WILD-TYPE                             417
D5V6, multiclass
                                 clus
vv                                AMP PEAK  5(3Q26.33) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              0
  TREATED PRIMARY GBM                                        0
  UNTREATED PRIMARY (DE NOVO) GBM                          108
                                 clus
vv                                AMP PEAK  5(3Q26.33) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               28
  TREATED PRIMARY GBM                                         18
  UNTREATED PRIMARY (DE NOVO) GBM                            417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3Q26.33) MUTATED       0                         7    93
  AMP PEAK  5(3Q26.33) WILD-TYPE    13                        43   392
D5V7, multiclass
                           clus
vv                          AMP PEAK  5(3Q26.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               93
                           clus
vv                          AMP PEAK  5(3Q26.33) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                392
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED     1  82
  AMP PEAK  5(3Q26.33) WILD-TYPE  11 391
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED      1   82
  AMP PEAK  5(3Q26.33) WILD-TYPE   11  391
                        clus
vv                       AMP PEAK  5(3Q26.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       AMP PEAK  5(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            391
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(4P16.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(4P16.3) MUTATED     7  41
  AMP PEAK  6(4P16.3) WILD-TYPE  93 429
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           522 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           41                           429 
$`AMP PEAK  6(4P16.3) MUTATED`
TCGA-02-0011 TCGA-02-0021 TCGA-02-0055 TCGA-02-0074 TCGA-02-0075 TCGA-02-0086 
       20.71        77.65         2.50        10.19        20.84         8.81 
TCGA-02-0113 TCGA-06-0125 TCGA-06-0130 TCGA-06-0157 TCGA-06-0195 TCGA-06-0409 
       92.65        47.61        12.95         3.19         7.40        72.36 
TCGA-06-0410 TCGA-06-0744 TCGA-06-0879 TCGA-06-6388 TCGA-06-6697 TCGA-08-0246 
        4.70        46.88        40.41         5.23        12.85         4.18 
TCGA-08-0510 TCGA-08-0531 TCGA-12-0616 TCGA-12-0691 TCGA-12-0820 TCGA-12-0826 
        4.27         7.56        14.73        12.13        18.48        27.78 
TCGA-12-3650 TCGA-14-1795 TCGA-14-1821 TCGA-14-2554 TCGA-14-3477 TCGA-16-0846 
       10.95         1.97        17.79        17.49         3.78         3.91 
TCGA-16-1056 TCGA-19-1387 TCGA-19-1392 TCGA-19-5947 TCGA-19-5958 TCGA-19-A6J4 
       14.01         5.95         3.65         6.64        14.07         3.98 
TCGA-26-1439 TCGA-27-1835 TCGA-27-2521 TCGA-28-2506 TCGA-28-5215 TCGA-32-1982 
       13.87        21.30        10.39         6.74        11.01         4.67 
TCGA-32-1991 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-74-6578 TCGA-76-4925 
       16.93         9.53        11.84         0.20        14.33         4.80 

$`AMP PEAK  6(4P16.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       82.59        20.61        87.06        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 
       27.25        89.72        22.72        12.62        51.32        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        2.70         6.15        20.38         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       13.94        10.45        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42        38.96         4.67         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       20.42        48.69        10.82         9.01         0.26         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        26.40         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       18.02        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 
        7.27        15.98        18.41        15.35        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       24.79        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       26.93        15.22        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        5.39         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 
        0.92        40.96         6.67        12.43         0.99        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        7.63         5.88         7.17         7.96         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19        13.28        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 
       16.37         4.31        29.03         4.57        10.29         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
        0.66        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.00         7.04        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        22.49        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       17.79        28.54        10.03         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        40.54        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        2.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85        19.50         1.18        12.69        14.86 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 
       10.85        19.23         0.85        13.35         8.94         0.99 
TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
        3.45        20.91         4.34         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                          0.2                           0.1 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                        92.65                        127.59 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                        10.98                         12.23 
[1] "0.2 - 92.7 (11.0)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED    22  26
  AMP PEAK  6(4P16.3) WILD-TYPE 202 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED     22   26
  AMP PEAK  6(4P16.3) WILD-TYPE  202  321
        clus
vv       AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          22                           202
  MALE                            26                           321
[1] 2 2
[1] FALSE
D6V4, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED     5  41
  AMP PEAK  6(4P16.3) WILD-TYPE  69 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED      5   41
  AMP PEAK  6(4P16.3) WILD-TYPE   69  433
     clus
vv    AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  NO                            5                            69
  YES                          41                           433
[1] 2 2
[1] FALSE
D6V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  6(4P16.3) MUTATED                               1
  AMP PEAK  6(4P16.3) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  6(4P16.3) MUTATED                     1
  AMP PEAK  6(4P16.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  6(4P16.3) MUTATED                                46
  AMP PEAK  6(4P16.3) WILD-TYPE                             479
D6V6, multiclass
                                 clus
vv                                AMP PEAK  6(4P16.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          46
                                 clus
vv                                AMP PEAK  6(4P16.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4P16.3) MUTATED       0                         4    43
  AMP PEAK  6(4P16.3) WILD-TYPE    13                        46   442
D6V7, multiclass
                           clus
vv                          AMP PEAK  6(4P16.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              43
                           clus
vv                          AMP PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               442
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED     1  42
  AMP PEAK  6(4P16.3) WILD-TYPE  11 431
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED      1   42
  AMP PEAK  6(4P16.3) WILD-TYPE   11  431
                        clus
vv                       AMP PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           431
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(4Q12) MUTATED    19  89
  AMP PEAK  7(4Q12) WILD-TYPE  81 381
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         462 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         89                         381 
$`AMP PEAK  7(4Q12) MUTATED`
TCGA-02-0014 TCGA-02-0024 TCGA-02-0055 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 
       82.59        53.10         2.50        28.70        10.19        20.84 
TCGA-02-0079 TCGA-02-0113 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0339 
       27.25        92.65         3.98        13.87        14.20        12.39 
TCGA-02-0440 TCGA-02-0446 TCGA-02-2485 TCGA-06-0130 TCGA-06-0138 TCGA-06-0143 
       11.34         9.27        15.45        12.95        24.23        11.74 
TCGA-06-0155 TCGA-06-0166 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
       10.45         5.85        13.12         4.47         3.22         4.18 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0221 
       38.96         7.40         7.40        11.84        15.02        19.82 
TCGA-06-0241 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0649 
       48.69         0.26        72.36         4.70         9.57         2.10 
TCGA-06-0743 TCGA-06-0875 TCGA-06-0879 TCGA-06-1802 TCGA-06-2559 TCGA-06-5408 
       26.40        43.46        40.41        15.32         4.93        11.74 
TCGA-06-5856 TCGA-06-6695 TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0353 
        3.75         8.32        37.84         4.18        25.71         8.42 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0524 TCGA-08-0531 TCGA-12-0616 
        4.27        11.08        19.59         7.27         7.56        14.73 
TCGA-12-0692 TCGA-12-0828 TCGA-12-1096 TCGA-12-1097 TCGA-12-3646 TCGA-14-0740 
        3.65         8.94         9.11        14.53        44.02        11.97 
TCGA-14-0812 TCGA-14-0817 TCGA-14-0865 TCGA-14-1455 TCGA-14-1821 TCGA-14-1825 
        3.25         5.39        16.50         0.92        17.79         7.63 
TCGA-14-1829 TCGA-14-3477 TCGA-16-0846 TCGA-16-0848 TCGA-19-0957 TCGA-19-0960 
        7.17         3.78         3.91        17.59        21.90         8.61 
TCGA-19-0963 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-2631 
       14.27         5.95        12.95        25.38         3.65         7.00 
TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-5132 TCGA-26-5134 
       17.79         3.98        10.03        13.87         9.40         5.49 
TCGA-26-5135 TCGA-27-1830 TCGA-27-1834 TCGA-28-2506 TCGA-28-5211 TCGA-28-5215 
        8.88         5.06        40.54         6.74        11.77        11.01 
TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1991 TCGA-32-4210 
       13.64        21.07         0.49         0.10        16.93         3.72 
TCGA-32-4211 TCGA-32-5222 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9R 
       12.59        19.23         9.53        11.84         0.20         4.08 
TCGA-74-6575 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 TCGA-76-6193 TCGA-RR-A6KA 
       20.91         3.09         2.53        36.85         2.70         6.28 

$`AMP PEAK  7(4Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       20.71        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0080 
        6.02        19.73        26.43        25.05         5.49        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       10.75        14.47        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0451 TCGA-02-0456 
       10.59        14.50        10.55        47.11        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        12.92        15.32        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        14.30        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
        2.20         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        12.33        13.94         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.29         4.04        91.00        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        0.53        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       10.82         9.01         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80        23.57        14.20        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.70         0.92        46.19         5.65         7.17 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79        11.84        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       12.49        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37         0.43        31.50         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
      120.56         7.36        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       17.72        22.68       115.86         1.74         8.42        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       18.02        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 
       58.68        19.33        10.75         4.80        15.98        18.41 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       15.35        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 
        0.10        38.17        25.97        26.66        12.13        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        27.78        38.76        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       14.53        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        6.21        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        2.89        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15        30.18        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 
       12.43         0.99         1.97        17.85         5.88        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       13.28        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 
       11.77         0.66         3.39        10.75         9.07         4.64 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 
        1.08         7.53         0.16         4.08        24.23         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78        22.49        14.07        16.80        14.96        28.54 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5136 
        9.73        31.33         7.13         9.37        14.86        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33        19.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
        2.53        31.27        23.44         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        5.42        15.39        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 
        7.36         8.84        22.78        25.18        21.14        19.86 
TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       10.85         0.85        13.35         8.94         0.99         4.44 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 
       15.12        12.46         1.45        25.58         3.45         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 
       14.33         8.22         7.50         4.80         4.54         3.65 
TCGA-76-4931 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
        9.17        16.70         3.29        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
       36.20         1.61        17.72        26.30         5.92        20.55 

  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        0.1                         0.1 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      92.65                      127.59 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      10.73                       12.56 
[1] "0.1 - 92.7 (10.7)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    38  70
  AMP PEAK  7(4Q12) WILD-TYPE 186 277
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     38   70
  AMP PEAK  7(4Q12) WILD-TYPE  186  277
        clus
vv       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  FEMALE                        38                         186
  MALE                          70                         277
[1] 2 2
[1] FALSE
D7V4, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    20  84
  AMP PEAK  7(4Q12) WILD-TYPE  54 390
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     20   84
  AMP PEAK  7(4Q12) WILD-TYPE   54  390
     clus
vv    AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  NO                         20                          54
  YES                        84                         390
[1] 2 2
[1] FALSE
D7V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  7(4Q12) MUTATED                               4                   2
  AMP PEAK  7(4Q12) WILD-TYPE                            24                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  7(4Q12) MUTATED                               102
  AMP PEAK  7(4Q12) WILD-TYPE                             423
D7V6, multiclass
                                 clus
vv                                AMP PEAK  7(4Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           4
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                       102
                                 clus
vv                                AMP PEAK  7(4Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            24
  TREATED PRIMARY GBM                                      16
  UNTREATED PRIMARY (DE NOVO) GBM                         423
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q12) MUTATED       1                        11    93
  AMP PEAK  7(4Q12) WILD-TYPE    12                        39   392
D7V7, multiclass
                           clus
vv                          AMP PEAK  7(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                            93
                           clus
vv                          AMP PEAK  7(4Q12) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          39
  WHITE                                             392
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED     2  90
  AMP PEAK  7(4Q12) WILD-TYPE  10 383
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      2   90
  AMP PEAK  7(4Q12) WILD-TYPE   10  383
                        clus
vv                       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                        90                         383
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P11.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7P11.2) MUTATED    78 422
  AMP PEAK  8(7P11.2) WILD-TYPE  22  48
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          500                            70 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          422                            48 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 
       11.77         4.73        18.35        23.18        10.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 
       87.06        77.65        20.12        42.74        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 
       14.14         3.62        10.72        18.31         6.87         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 
       15.09        12.59         6.54         2.50        19.86         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       20.84        27.25        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       92.65        15.65        48.95        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
        4.37        25.12        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       13.94        10.45         3.19        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00         4.18        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 
        4.04        26.79        11.84        15.32        13.61        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.95        16.64         4.37        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        6.15         4.57         5.23         5.39       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 
        8.32        12.85         4.77         1.55         4.77         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        3.12         2.56        14.60        22.68        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
        0.72        12.56         4.27        11.08        19.33        10.75 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.86        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         5.39         2.89        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
        7.96         3.42        13.78        19.10        13.28         3.91 
TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 
       17.59         4.31        29.03         4.57        10.29         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 
       21.24        13.97        11.77        21.90         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 
        9.67         4.87         1.08         7.53         0.16        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        7.13         9.37         9.40         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
        2.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         5.42        15.39         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        2.53        36.85        16.70         3.29        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0024 TCGA-02-0026 TCGA-02-0028 
       35.41        20.71        82.59        53.10        24.59        90.58 
TCGA-02-0039 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 TCGA-02-0080 TCGA-02-0084 
       10.52        14.73         8.35         6.02        89.72        12.62 
TCGA-02-0104 TCGA-02-0114 TCGA-02-0258 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 
       65.00        99.98        16.54        10.59        12.39        47.11 
TCGA-02-2483 TCGA-06-0129 TCGA-06-0146 TCGA-06-0160 TCGA-06-0165 TCGA-06-0178 
       15.32        33.67        20.09        11.80        10.65        88.14 
TCGA-06-0221 TCGA-06-0410 TCGA-06-1805 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       19.82         4.70        33.90         5.98         0.43        31.50 
TCGA-06-5416 TCGA-06-6389 TCGA-06-6391 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TL 
        6.71         7.79         1.48         4.96        26.79        17.72 
TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
      115.86        29.23        65.33        42.15        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0818 TCGA-12-0827 TCGA-14-0740 TCGA-14-0865 
        4.80         7.27        91.76        38.76        11.97        16.50 
TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 
       17.79         3.78        50.53        53.19        26.07        16.37 
TCGA-16-1056 TCGA-16-1460 TCGA-19-0960 TCGA-19-2625 TCGA-19-5956 TCGA-26-1442 
       14.01         6.41         8.61         4.08        22.49        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-27-2521 TCGA-28-1756 TCGA-28-5216 TCGA-32-1973 
       14.86         5.49        10.39         2.83        13.64        21.07 
TCGA-32-2634 TCGA-32-4208 TCGA-41-4097 TCGA-76-6193 
       22.78        21.14         0.20         2.70 

  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          0.1                           0.2 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                       127.59                        115.86 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                        11.77                         17.13 
[1] "0.1 - 127.6 (11.8)" "0.2 - 115.9 (17.1)"
[1] "hr=" "2.1"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED   192 309
  AMP PEAK  8(7P11.2) WILD-TYPE  32  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED    192  309
  AMP PEAK  8(7P11.2) WILD-TYPE   32   38
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                         192                            32
  MALE                           309                            38
[1] 2 2
[1] FALSE
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    69 412
  AMP PEAK  8(7P11.2) WILD-TYPE   5  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     69  412
  AMP PEAK  8(7P11.2) WILD-TYPE    5   62
     clus
vv    AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  NO                           69                             5
  YES                         412                            62
[1] 2 2
[1] FALSE
D8V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  8(7P11.2) MUTATED                              23
  AMP PEAK  8(7P11.2) WILD-TYPE                             5
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  8(7P11.2) MUTATED                    13
  AMP PEAK  8(7P11.2) WILD-TYPE                   5
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  8(7P11.2) MUTATED                               465
  AMP PEAK  8(7P11.2) WILD-TYPE                              60
D8V6, multiclass
                                 clus
vv                                AMP PEAK  8(7P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            23
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         465
                                 clus
vv                                AMP PEAK  8(7P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               5
  TREATED PRIMARY GBM                                         5
  UNTREATED PRIMARY (DE NOVO) GBM                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P11.2) MUTATED      10                        44   425
  AMP PEAK  8(7P11.2) WILD-TYPE     3                         6    60
D8V7, multiclass
                           clus
vv                          AMP PEAK  8(7P11.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          44
  WHITE                                             425
                           clus
vv                          AMP PEAK  8(7P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED     8 413
  AMP PEAK  8(7P11.2) WILD-TYPE   4  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      8  413
  AMP PEAK  8(7P11.2) WILD-TYPE    4   60
                        clus
vv                       AMP PEAK  8(7P11.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         413
                        clus
vv                       AMP PEAK  8(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            60
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7Q11.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(7Q11.21) MUTATED    74 384
  AMP PEAK  9(7Q11.21) WILD-TYPE  26  86
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           458                            112 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           384                             86 
$`AMP PEAK  9(7Q11.21) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 
       11.77         4.73        18.35        23.18        10.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 
       87.06        77.65        20.12        42.74        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       14.14         3.62        10.72         6.87         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 
       12.59         6.54         2.50        19.86         9.57        19.73 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0085 
       25.05         5.49        10.19        20.84        27.25        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 
        8.81        57.76        16.96         3.48        27.02        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       17.65        23.18        92.65        15.65        48.95        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0430 TCGA-02-0440 
       15.91        25.71         4.37        25.12        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 
        9.27        16.21         3.35        16.80        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       22.72        12.95        25.35        14.30        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.20        10.29        11.74         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        46.59        12.33        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       10.82         9.44        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        69.90        73.84        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
       15.02        24.16        13.64        13.32        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26        72.36         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40        46.88         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 
        4.93        17.65        12.56        30.64         5.95         4.37 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        2.73         3.75         6.15         4.57         5.23         5.39 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0345 TCGA-08-0346 
        1.87         2.56        14.60        22.68         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
       25.71        12.16         9.80         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       18.02        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       19.33        10.75        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.93        14.86        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       14.53        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        1.35        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       23.11         7.10         1.15        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 
        7.17        17.49         7.96         3.42        13.78        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       13.28         3.91        17.59         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       10.29        21.24        13.97        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.66        14.27        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 
        4.64        25.38         3.65         7.17        12.66         0.13 
TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        9.67         7.53         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-5132 TCGA-26-5135 
       10.03        13.87         9.73         7.13         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 
       16.60         9.86        24.23        40.54        21.30        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        18.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 
        7.30         5.26        14.93        11.28        17.88        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 
       20.78        15.95         7.36         8.84        25.18         3.72 
TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       12.59        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.80         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        2.53        36.85        16.70         3.29        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

$`AMP PEAK  9(7Q11.21) WILD-TYPE`
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0024 TCGA-02-0026 TCGA-02-0028 
       35.41        20.71        82.59        53.10        24.59        90.58 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 TCGA-02-0068 
       10.52        18.31        14.73         8.35         6.02        26.43 
TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0104 TCGA-02-0114 
       28.70        89.72        22.72        12.62        65.00        99.98 
TCGA-02-0258 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-2483 
       16.54        10.59        12.39        14.50        47.11        15.32 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0137 TCGA-06-0142 TCGA-06-0146 TCGA-06-0154 
        3.98        33.67        26.70         2.20        20.09        13.94 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0178 TCGA-06-0187 TCGA-06-0219 
       11.80         3.42        10.65        88.14        27.22         0.72 
TCGA-06-0221 TCGA-06-0240 TCGA-06-0410 TCGA-06-0747 TCGA-06-1805 TCGA-06-2565 
       19.82        20.42         4.70         2.70        33.90        16.64 
TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 TCGA-06-6389 
        5.98         0.43        31.50        11.74         6.71         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TL 
        1.48       120.56         4.96        26.79         3.12        17.72 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 
       37.84         4.18       115.86        29.23        65.33         8.42 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       42.15        11.08        19.59        58.68         4.80         7.27 
TCGA-12-0688 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 TCGA-12-3652 TCGA-14-0740 
       26.66        91.76        24.79        38.76        34.92        11.97 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 
        5.39         2.89        16.50        40.96        17.79         3.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 
       50.53        53.19        26.07        16.37        14.01         9.14 
TCGA-16-1460 TCGA-19-0964 TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        6.41         3.39         3.25         4.87         1.08         4.08 
TCGA-19-5951 TCGA-19-5956 TCGA-26-1442 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 
        8.02        22.49        31.33         9.37        14.86         5.49 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 TCGA-27-2523 TCGA-28-1756 TCGA-28-5209 
       30.05        14.04        10.39        16.08         2.83         2.53 
TCGA-28-5216 TCGA-32-1973 TCGA-32-2495 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 
       13.64        21.07        15.02        22.78        21.14        19.86 
TCGA-32-4719 TCGA-41-4097 TCGA-76-4926 TCGA-76-6193 
       10.85         0.20         4.54         2.70 

  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           0.1                            0.2 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                        127.59                         120.56 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                         11.77                          15.17 
[1] "0.1 - 127.6 (11.8)" "0.2 - 120.6 (15.2)"
[1] "hr=" "1.7"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED   174 285
  AMP PEAK  9(7Q11.21) WILD-TYPE  50  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED    174  285
  AMP PEAK  9(7Q11.21) WILD-TYPE   50   62
        clus
vv       AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  FEMALE                          174                             50
  MALE                            285                             62
[1] 2 2
[1] FALSE
D9V4, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED    63 376
  AMP PEAK  9(7Q11.21) WILD-TYPE  11  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED     63  376
  AMP PEAK  9(7Q11.21) WILD-TYPE   11   98
     clus
vv    AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  NO                            63                             11
  YES                          376                             98
[1] 2 2
[1] FALSE
D9V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  9(7Q11.21) MUTATED                              20
  AMP PEAK  9(7Q11.21) WILD-TYPE                             8
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  9(7Q11.21) MUTATED                    10
  AMP PEAK  9(7Q11.21) WILD-TYPE                   8
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  9(7Q11.21) MUTATED                               429
  AMP PEAK  9(7Q11.21) WILD-TYPE                              96
D9V6, multiclass
                                 clus
vv                                AMP PEAK  9(7Q11.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             20
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          429
                                 clus
vv                                AMP PEAK  9(7Q11.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                8
  TREATED PRIMARY GBM                                          8
  UNTREATED PRIMARY (DE NOVO) GBM                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7Q11.21) MUTATED       8                        41   388
  AMP PEAK  9(7Q11.21) WILD-TYPE     5                         9    97
D9V7, multiclass
                           clus
vv                          AMP PEAK  9(7Q11.21) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           41
  WHITE                                              388
                           clus
vv                          AMP PEAK  9(7Q11.21) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED     7 377
  AMP PEAK  9(7Q11.21) WILD-TYPE   5  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED      7  377
  AMP PEAK  9(7Q11.21) WILD-TYPE    5   96
                        clus
vv                       AMP PEAK  9(7Q11.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          377
                        clus
vv                       AMP PEAK  9(7Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q21.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7Q21.2) MUTATED    75 398
  AMP PEAK 10(7Q21.2) WILD-TYPE  25  72
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          473                            97 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          398                            72 
$`AMP PEAK 10(7Q21.2) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 
       11.77         4.73        18.35        10.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       77.65        20.12        42.74        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
        3.62        10.72        18.31         6.87         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 
       12.59         6.54         2.50        19.86         9.57        19.73 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        20.84        89.72        22.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0422 
       10.62         7.33        15.91        25.71        25.12        14.50 
TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       10.55        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 
       12.92        15.45        20.32         2.70        20.38        47.61 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        6.94        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90         0.20        10.29        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       13.94        10.45         3.19        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00         4.18        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
       24.16        19.82        13.64        13.32        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26        72.36         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79        11.84        15.32        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.23         5.39         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        1.55         4.77         1.87         3.12         2.56        14.60 
TCGA-08-0244 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       22.68         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
        0.72        12.56         4.27        11.08        19.33        10.75 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       27.78         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
        3.98         4.14        15.65        25.68        14.73        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 
       44.02        26.93        15.22        10.95        12.69        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
       14.93         3.22         2.04         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18         0.92         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
        7.96         3.42        13.78        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91        17.59         4.31        29.03         4.57        10.29 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       21.24        13.97         6.41        11.77        21.90         0.66 
TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
       14.27        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        9.67         7.53         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        9.40         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59         2.86         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        8.35         7.63         8.48         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         4.77         7.30        14.93        11.28 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
        2.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 
       22.68        10.49         5.42        15.39         0.49        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       25.18         3.72        12.59        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 
        8.94         9.53         0.99         4.44        11.84        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

$`AMP PEAK 10(7Q21.2) WILD-TYPE`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0024 TCGA-02-0026 
       23.18        35.41        20.71        82.59        53.10        24.59 
TCGA-02-0028 TCGA-02-0039 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 TCGA-02-0068 
       90.58        10.52        14.73         8.35         6.02        26.43 
TCGA-02-0069 TCGA-02-0079 TCGA-02-0084 TCGA-02-0104 TCGA-02-0114 TCGA-02-0333 
       28.70        27.25        12.62        65.00        99.98         4.37 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2483 TCGA-06-0122 TCGA-06-0127 
       10.59        12.39        47.11        15.32         6.15         3.98 
TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0160 TCGA-06-0165 TCGA-06-0178 
       33.67         2.20        20.09        11.80        10.65        88.14 
TCGA-06-0219 TCGA-06-0240 TCGA-06-0410 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 
        0.72        20.42         4.70        33.90        16.64         5.98 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 
        0.43        31.50         6.71         7.79         1.48       120.56 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        4.96        26.79        17.72        37.84         4.18       115.86 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       29.23        65.33         8.42        42.15        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0827 TCGA-12-1091 TCGA-12-1602 TCGA-12-3652 
        4.80         7.27        38.76        33.21         6.77        34.92 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1452 TCGA-14-1456 
       15.12        11.97         2.89        16.50         7.10        40.96 
TCGA-14-1821 TCGA-14-3477 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 
       17.79         3.78        53.19        26.07        16.37        14.01 
TCGA-16-1060 TCGA-19-0960 TCGA-19-0964 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        9.14         8.61         3.39         4.87         1.08         4.08 
TCGA-19-5951 TCGA-19-5956 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 
        8.02        22.49        14.86         5.49        30.05        14.40 
TCGA-27-2528 TCGA-28-1756 TCGA-28-2514 TCGA-28-5208 TCGA-28-5216 TCGA-32-1973 
       15.78         2.83         5.26        17.88        13.64        21.07 
TCGA-32-1977 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 
        0.10        22.78        21.14        19.86        10.85         0.20 
TCGA-76-6193 
        2.70 

  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                       127.59                        120.56 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                        11.84                         15.12 
[1] "0.1 - 127.6 (11.8)" "0.1 - 120.6 (15.1)"
[1] "hr=" "1.7"
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED   182 292
  AMP PEAK 10(7Q21.2) WILD-TYPE  42  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED    182  292
  AMP PEAK 10(7Q21.2) WILD-TYPE   42   55
        clus
vv       AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  FEMALE                         182                            42
  MALE                           292                            55
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED    64 392
  AMP PEAK 10(7Q21.2) WILD-TYPE  10  82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED     64  392
  AMP PEAK 10(7Q21.2) WILD-TYPE   10   82
     clus
vv    AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  NO                           64                            10
  YES                         392                            82
[1] 2 2
[1] FALSE
D10V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 10(7Q21.2) MUTATED                              22
  AMP PEAK 10(7Q21.2) WILD-TYPE                             6
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK 10(7Q21.2) MUTATED                    12
  AMP PEAK 10(7Q21.2) WILD-TYPE                   6
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 10(7Q21.2) MUTATED                               440
  AMP PEAK 10(7Q21.2) WILD-TYPE                              85
D10V6, multiclass
                                 clus
vv                                AMP PEAK 10(7Q21.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            22
  TREATED PRIMARY GBM                                      12
  UNTREATED PRIMARY (DE NOVO) GBM                         440
                                 clus
vv                                AMP PEAK 10(7Q21.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               6
  TREATED PRIMARY GBM                                         6
  UNTREATED PRIMARY (DE NOVO) GBM                            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q21.2) MUTATED       7                        42   403
  AMP PEAK 10(7Q21.2) WILD-TYPE     6                         8    82
D10V7, multiclass
                           clus
vv                          AMP PEAK 10(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          42
  WHITE                                             403
                           clus
vv                          AMP PEAK 10(7Q21.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED     7 392
  AMP PEAK 10(7Q21.2) WILD-TYPE   5  81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED      7  392
  AMP PEAK 10(7Q21.2) WILD-TYPE    5   81
                        clus
vv                       AMP PEAK 10(7Q21.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         392
                        clus
vv                       AMP PEAK 10(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            81
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q31.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q31.2) MUTATED    76 390
  AMP PEAK 11(7Q31.2) WILD-TYPE  24  80
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          466                           104 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          390                            80 
$`AMP PEAK 11(7Q31.2) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0015 
       11.77         4.73        18.35        10.59        35.41        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 
       87.06        77.65        20.12        53.10        42.74        12.16 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 
        2.83        14.14         3.62        10.72        18.31         6.87 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 
       15.09        12.59         6.54         2.50        19.86         9.57 
TCGA-02-0064 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       19.73        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       89.72        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 
       27.02        11.67        17.65        23.18        92.65        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 
        7.73        10.62         7.33        15.91        25.71        25.12 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 
       16.80        12.92        15.45        20.32         2.70        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
       47.61         6.94        22.72        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       26.70        24.23        11.90         0.20        10.29        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0164 
       12.33        13.94        10.45         3.19         9.44        56.91 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        4.04        91.00         4.18        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.64        13.32        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79        11.84        15.32        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2567 TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37         0.43        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 
        4.57         5.23         5.39         1.48         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 
       12.85         4.77         1.55         4.77         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        2.56        14.60        22.68         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 
       12.16         9.80         1.28        17.95        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 
       13.97         0.72        12.56         4.27        19.33        10.75 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       24.79        18.48        10.62        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82         7.59        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
        2.04         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 
       13.78         3.25         1.35         5.39        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
        3.75        58.78        23.11        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.42        13.78 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 
       19.10        13.28         3.91        17.59         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
        4.57        10.29        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       21.90         0.66        14.27        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1791 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        0.13         7.53         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        9.40         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59         2.86         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        8.35         7.63         8.48         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         4.77         7.30        14.93        11.28 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
        2.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 
        5.16        22.68         5.42        15.39         0.49        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 
       12.23        20.78        15.02         7.36         8.84        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
        3.72        12.59        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44        11.84        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

$`AMP PEAK 11(7Q31.2) WILD-TYPE`
TCGA-02-0007 TCGA-02-0011 TCGA-02-0014 TCGA-02-0026 TCGA-02-0028 TCGA-02-0039 
       23.18        20.71        82.59        24.59        90.58        10.52 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0058 TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 
       14.73         3.22         8.35         6.02        26.43        28.70 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0104 TCGA-02-0114 TCGA-02-0333 TCGA-02-0338 
       22.72        12.62        65.00        99.98         4.37        10.59 
TCGA-02-0339 TCGA-02-0432 TCGA-02-2483 TCGA-06-0122 TCGA-06-0127 TCGA-06-0129 
       12.39        47.11        15.32         6.15         3.98        33.67 
TCGA-06-0142 TCGA-06-0146 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        2.20        20.09        10.82        11.80         3.42        10.65 
TCGA-06-0178 TCGA-06-0219 TCGA-06-0240 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 
       88.14         0.72        20.42        33.90        16.64         5.98 
TCGA-06-2570 TCGA-06-5416 TCGA-06-6389 TCGA-06-6693 TCGA-06-6701 TCGA-06-A5U0 
       31.50         6.71         7.79       120.56         4.96        26.79 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
       17.72        37.84         4.18       115.86        29.23        65.33 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        8.42        24.56        42.15        11.08        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0615 TCGA-12-0691 TCGA-12-0827 TCGA-12-1091 
        4.80         7.27        15.35        12.13        38.76        33.21 
TCGA-12-1602 TCGA-12-3652 TCGA-14-0736 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 
        6.77        34.92        15.12        11.97         2.89        16.50 
TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 
       32.05         7.10         1.15        17.79         3.78        50.53 
TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 TCGA-19-0960 
       53.19        26.07        16.37        14.01         9.14         8.61 
TCGA-19-0964 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        3.39         3.25         9.67         4.87         1.08         4.08 
TCGA-19-5951 TCGA-19-5956 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 
        8.02        22.49        14.86         5.49        30.05        14.40 
TCGA-27-2528 TCGA-28-1756 TCGA-28-2514 TCGA-28-5208 TCGA-28-5220 TCGA-32-1973 
       15.78         2.83         5.26        17.88        10.49        21.07 
TCGA-32-1977 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 
        0.10        15.95        22.78        21.14        19.86        10.85 
TCGA-41-4097 TCGA-76-6193 
        0.20         2.70 

  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                       127.59                        120.56 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                       11.840                        14.795 
[1] "0.1 - 127.6 (11.8)" "0.1 - 120.6 (14.8)"
[1] "hr=" "1.5"
D11V2, continuous
D11V3, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   178 289
  AMP PEAK 11(7Q31.2) WILD-TYPE  46  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    178  289
  AMP PEAK 11(7Q31.2) WILD-TYPE   46   58
        clus
vv       AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  FEMALE                         178                            46
  MALE                           289                            58
[1] 2 2
[1] FALSE
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED    65 383
  AMP PEAK 11(7Q31.2) WILD-TYPE   9  91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED     65  383
  AMP PEAK 11(7Q31.2) WILD-TYPE    9   91
     clus
vv    AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  NO                           65                             9
  YES                         383                            91
[1] 2 2
[1] FALSE
D11V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 11(7Q31.2) MUTATED                              21
  AMP PEAK 11(7Q31.2) WILD-TYPE                             7
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK 11(7Q31.2) MUTATED                    13
  AMP PEAK 11(7Q31.2) WILD-TYPE                   5
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 11(7Q31.2) MUTATED                               433
  AMP PEAK 11(7Q31.2) WILD-TYPE                              92
D11V6, multiclass
                                 clus
vv                                AMP PEAK 11(7Q31.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            21
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         433
                                 clus
vv                                AMP PEAK 11(7Q31.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               7
  TREATED PRIMARY GBM                                         5
  UNTREATED PRIMARY (DE NOVO) GBM                            92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q31.2) MUTATED       7                        42   397
  AMP PEAK 11(7Q31.2) WILD-TYPE     6                         8    88
D11V7, multiclass
                           clus
vv                          AMP PEAK 11(7Q31.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          42
  WHITE                                             397
                           clus
vv                          AMP PEAK 11(7Q31.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED     7 387
  AMP PEAK 11(7Q31.2) WILD-TYPE   5  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED      7  387
  AMP PEAK 11(7Q31.2) WILD-TYPE    5   86
                        clus
vv                       AMP PEAK 11(7Q31.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         387
                        clus
vv                       AMP PEAK 11(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            86
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    13  57
  AMP PEAK 12(8Q24.21) WILD-TYPE  87 413
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            500 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            57                            413 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-02-0010 TCGA-02-0014 TCGA-02-0024 TCGA-02-0037 TCGA-02-0055 TCGA-02-0074 
       35.41        82.59        53.10         3.62         2.50        10.19 
TCGA-02-0075 TCGA-02-0084 TCGA-02-0104 TCGA-02-0325 TCGA-02-2483 TCGA-06-0128 
       20.84        12.62        65.00        10.62        15.32        22.72 
TCGA-06-0146 TCGA-06-0177 TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 TCGA-06-0211 
       20.09         4.18        44.58        38.96         7.63        11.84 
TCGA-06-0409 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-2557 TCGA-06-2569 
       72.36        35.11         2.10        14.20         1.08         0.43 
TCGA-06-5856 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-06-6701 TCGA-08-0350 
        3.75         7.79       120.56         7.36         4.96        29.23 
TCGA-08-0351 TCGA-08-0516 TCGA-12-0616 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 
       65.33        19.59        14.73        91.76        24.79        38.76 
TCGA-12-1092 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       21.73         4.14        15.65         6.77        44.02        14.53 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1456 
        5.39        16.50         2.04        28.93         1.15        40.96 
TCGA-14-1825 TCGA-14-3477 TCGA-19-1388 TCGA-19-1392 TCGA-19-2619 TCGA-19-A6J4 
        7.63         3.78        12.95         3.65         9.67         3.98 
TCGA-19-A6J5 TCGA-26-5133 TCGA-27-1834 TCGA-27-2521 TCGA-28-1746 TCGA-28-5204 
       28.54        14.86        40.54        10.39         0.20        14.93 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1976 TCGA-32-1978 TCGA-32-2632 
       11.01         5.16        22.68         0.49        15.85         8.84 
TCGA-32-4210 TCGA-41-2573 TCGA-41-4097 TCGA-41-5651 
        3.72         8.94         0.20        15.12 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58         2.83        14.14        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        6.54        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 
       26.43        28.70        25.05         5.49        27.25        89.72 
TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       27.22        15.42        10.42         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        0.39         7.66         8.42         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
        3.16        12.62         5.75         5.75         9.80        23.57 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       11.84        15.32        13.61        33.90        15.32        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6695 
        6.15         4.57         5.23         5.39         1.48         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        9.80         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        15.35        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        27.78         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 
       15.85         9.11        14.53         3.98        25.68        14.73 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        7.10        30.18         0.92         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79        17.85         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
       25.38         7.17        12.66         3.25         0.13         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       17.79        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.37         9.40         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       18.08        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       31.27        23.44        13.64        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        7.36        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23         0.85        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        11.84        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        120.56                         127.59 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        13.575                         12.145 
[1] "0.2 - 120.6 (13.6)" "0.1 - 127.6 (12.1)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    30  40
  AMP PEAK 12(8Q24.21) WILD-TYPE 194 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     30   40
  AMP PEAK 12(8Q24.21) WILD-TYPE  194  307
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           30                            194
  MALE                             40                            307
[1] 2 2
[1] FALSE
D12V4, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    11  52
  AMP PEAK 12(8Q24.21) WILD-TYPE  63 422
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     11   52
  AMP PEAK 12(8Q24.21) WILD-TYPE   63  422
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            11                             63
  YES                           52                            422
[1] 2 2
[1] FALSE
D12V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 12(8Q24.21) MUTATED                               2
  AMP PEAK 12(8Q24.21) WILD-TYPE                            26
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 12(8Q24.21) MUTATED                     2
  AMP PEAK 12(8Q24.21) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 12(8Q24.21) MUTATED                                66
  AMP PEAK 12(8Q24.21) WILD-TYPE                             459
D12V6, multiclass
                                 clus
vv                                AMP PEAK 12(8Q24.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           66
                                 clus
vv                                AMP PEAK 12(8Q24.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               26
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            459
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       1                        10    59
  AMP PEAK 12(8Q24.21) WILD-TYPE    12                        40   426
D12V7, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               59
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                426
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED     1  59
  AMP PEAK 12(8Q24.21) WILD-TYPE  11 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      1   59
  AMP PEAK 12(8Q24.21) WILD-TYPE   11  414
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            414
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(11P13) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 13(11P13) MUTATED     3  27
  AMP PEAK 13(11P13) WILD-TYPE  97 443
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          540 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          27                          443 
$`AMP PEAK 13(11P13) MUTATED`
TCGA-02-0025 TCGA-02-0037 TCGA-02-0054 TCGA-02-0099 TCGA-02-0106 TCGA-02-0115 
       42.74         3.62         6.54         3.48        11.67        15.65 
TCGA-02-0258 TCGA-02-0290 TCGA-06-0130 TCGA-06-0160 TCGA-06-0221 TCGA-06-0743 
       16.54        15.95        12.95        11.80        19.82        26.40 
TCGA-06-1087 TCGA-06-2557 TCGA-08-0386 TCGA-08-0517 TCGA-12-0616 TCGA-12-0670 
        4.04         1.08        18.02        58.68        14.73        25.97 
TCGA-12-0826 TCGA-12-1093 TCGA-12-1598 TCGA-14-0871 TCGA-19-1388 TCGA-19-4065 
       27.78        15.98        15.65        28.93        12.95         7.04 
TCGA-19-5958 TCGA-19-A60I TCGA-27-1838 TCGA-27-2521 TCGA-27-2526 TCGA-28-5207 
       14.07        17.79        11.51        10.39         2.86        11.28 

$`AMP PEAK 13(11P13) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 
       51.32         8.81        57.76        16.96        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       17.65        23.18        92.65        99.98        48.95        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       13.94        10.45         3.19        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       94.78         0.10        38.17        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        21.73        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98         4.14        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33         2.04        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
       10.75         9.07         5.95         4.64        25.38         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78        22.49        16.80        14.96         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 
       24.23        40.54        21.30        30.05        14.04        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       18.08        16.08         7.59        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                        1.08                         0.10 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       58.68                       127.59 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                      14.400                       12.115 
[1] "1.1 - 58.7 (14.4)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED    12  18
  AMP PEAK 13(11P13) WILD-TYPE 212 329
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED     12   18
  AMP PEAK 13(11P13) WILD-TYPE  212  329
        clus
vv       AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  FEMALE                         12                          212
  MALE                           18                          329
[1] 2 2
[1] FALSE
D13V4, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     2  27
  AMP PEAK 13(11P13) WILD-TYPE  72 447
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      2   27
  AMP PEAK 13(11P13) WILD-TYPE   72  447
     clus
vv    AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  NO                           2                           72
  YES                         27                          447
[1] 2 2
[1] FALSE
D13V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 13(11P13) MUTATED                               2
  AMP PEAK 13(11P13) WILD-TYPE                            26
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 13(11P13) MUTATED                     1
  AMP PEAK 13(11P13) WILD-TYPE                  17
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 13(11P13) MUTATED                                27
  AMP PEAK 13(11P13) WILD-TYPE                             498
D13V6, multiclass
                                 clus
vv                                AMP PEAK 13(11P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 13(11P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             26
  TREATED PRIMARY GBM                                       17
  UNTREATED PRIMARY (DE NOVO) GBM                          498
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11P13) MUTATED       1                         2    27
  AMP PEAK 13(11P13) WILD-TYPE    12                        48   458
D13V7, multiclass
                           clus
vv                          AMP PEAK 13(11P13) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             27
                           clus
vv                          AMP PEAK 13(11P13) WILD-TYPE
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                           48
  WHITE                                              458
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     1  27
  AMP PEAK 13(11P13) WILD-TYPE  11 446
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      1   27
  AMP PEAK 13(11P13) WILD-TYPE   11  446
                        clus
vv                       AMP PEAK 13(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         27
                        clus
vv                       AMP PEAK 13(11P13) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          446
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12P13.32) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 14(12P13.32) MUTATED    16  68
  AMP PEAK 14(12P13.32) WILD-TYPE  84 402
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             84                             486 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             68                             402 
$`AMP PEAK 14(12P13.32) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0051 TCGA-02-0054 TCGA-02-0070 TCGA-02-0074 
       11.77        53.10        15.09         6.54        25.05        10.19 
TCGA-02-0084 TCGA-02-0087 TCGA-02-0266 TCGA-02-0271 TCGA-02-0324 TCGA-02-2466 
       12.62        57.76        17.72        14.47         7.73        16.80 
TCGA-06-0129 TCGA-06-0146 TCGA-06-0151 TCGA-06-0157 TCGA-06-0162 TCGA-06-0164 
       33.67        20.09        46.59         3.19         3.42        56.91 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0192 TCGA-06-0216 
        4.18        69.90        27.22        44.58        38.96        24.16 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0649 TCGA-06-0743 TCGA-06-0877 
       19.82        13.32        72.36         2.10        26.40         5.65 
TCGA-06-1086 TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-5856 TCGA-06-5859 
        6.84         4.04        17.65         8.55         3.75         4.57 
TCGA-06-6389 TCGA-06-6694 TCGA-06-6699 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 
        7.79         7.36         1.55        14.60        17.72        37.84 
TCGA-08-0246 TCGA-08-0352 TCGA-08-0392 TCGA-08-0516 TCGA-12-0691 TCGA-12-0776 
        4.18         1.28         0.72        19.59        12.13         9.73 
TCGA-12-0778 TCGA-12-0820 TCGA-12-1090 TCGA-12-1098 TCGA-12-1602 TCGA-12-3653 
       14.93        18.48         7.59         3.98         6.77        14.53 
TCGA-14-0740 TCGA-14-0790 TCGA-14-1396 TCGA-14-1453 TCGA-14-1458 TCGA-14-1821 
       11.97        13.78         1.12         1.15         6.67        17.79 
TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 TCGA-16-0850 TCGA-16-1460 TCGA-19-1786 
       17.85        17.49        13.28        16.37         6.41         7.17 
TCGA-19-1787 TCGA-19-5954 TCGA-26-1438 TCGA-26-1442 TCGA-26-5132 TCGA-27-1838 
       12.66        12.10        10.03        31.33         9.40        11.51 
TCGA-28-1756 TCGA-28-2506 TCGA-28-5207 TCGA-28-5218 TCGA-32-1979 TCGA-32-1991 
        2.83         6.74        11.28         5.16        19.50        16.93 
TCGA-32-2615 TCGA-32-4208 TCGA-32-4210 TCGA-32-5222 TCGA-74-6577 TCGA-76-4928 
       15.95        21.14         3.72        19.23         4.34         3.09 

$`AMP PEAK 14(12P13.32) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       19.73        26.43        28.70         5.49        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 
       89.72        22.72        51.32         8.81        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 
       99.98        15.65        48.95        16.54        16.93        10.75 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        9.27        16.21         3.35        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 
        2.33        17.79        10.09         8.61        19.46        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 
       13.94        10.45        10.82         9.44        11.80        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.04        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       15.02         0.72        13.64        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       12.62         5.75         5.75         9.80        23.57        14.20 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       23.93        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        6.71         2.73         6.15         5.23         5.39         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
      120.56         8.32        12.85         4.77         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 
       26.79         1.87         3.12         2.56        22.68       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       65.33         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
       13.97        12.56         4.27        42.15        11.08        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
        7.63        14.86        91.76        24.79        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       14.53         4.14        15.65        25.68        14.73        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        15.12         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       19.30         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
       23.11         7.10        30.18         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 
        0.99         1.97         7.63         5.88         7.17         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91        17.59        26.07         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 
       10.29        14.01         9.14        21.24        13.97        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.65 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 
       17.19         8.02        18.90         4.73         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 
       13.87         9.73         7.13         9.37        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        24.76        18.08        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         4.77         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        15.85         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       14.86        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       22.78        25.18        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                           0.72                            0.10 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                          72.36                          127.59 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                         12.375                          12.195 
[1] "0.7 - 72.4 (12.4)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED    33  51
  AMP PEAK 14(12P13.32) WILD-TYPE 191 296
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED     33   51
  AMP PEAK 14(12P13.32) WILD-TYPE  191  296
        clus
vv       AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  FEMALE                            33                             191
  MALE                              51                             296
[1] 2 2
[1] FALSE
D14V4, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED     7  73
  AMP PEAK 14(12P13.32) WILD-TYPE  67 401
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED      7   73
  AMP PEAK 14(12P13.32) WILD-TYPE   67  401
     clus
vv    AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  NO                              7                              67
  YES                            73                             401
[1] 2 2
[1] FALSE
D14V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 14(12P13.32) MUTATED                               3
  AMP PEAK 14(12P13.32) WILD-TYPE                            25
                                 vv
clus                              TREATED PRIMARY GBM
  AMP PEAK 14(12P13.32) MUTATED                     2
  AMP PEAK 14(12P13.32) WILD-TYPE                  16
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 14(12P13.32) MUTATED                                79
  AMP PEAK 14(12P13.32) WILD-TYPE                             446
D14V6, multiclass
                                 clus
vv                                AMP PEAK 14(12P13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               3
  TREATED PRIMARY GBM                                         2
  UNTREATED PRIMARY (DE NOVO) GBM                            79
                                 clus
vv                                AMP PEAK 14(12P13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                25
  TREATED PRIMARY GBM                                          16
  UNTREATED PRIMARY (DE NOVO) GBM                             446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12P13.32) MUTATED       3                         6    71
  AMP PEAK 14(12P13.32) WILD-TYPE    10                        44   414
D14V7, multiclass
                           clus
vv                          AMP PEAK 14(12P13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                71
                           clus
vv                          AMP PEAK 14(12P13.32) WILD-TYPE
  ASIAN                                                  10
  BLACK OR AFRICAN AMERICAN                              44
  WHITE                                                 414
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED     2  68
  AMP PEAK 14(12P13.32) WILD-TYPE  10 405
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED      2   68
  AMP PEAK 14(12P13.32) WILD-TYPE   10  405
                        clus
vv                       AMP PEAK 14(12P13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            68
                        clus
vv                       AMP PEAK 14(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             405
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(12Q14.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(12Q14.1) MUTATED    20 113
  AMP PEAK 15(12Q14.1) WILD-TYPE  80 357
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           133                            437 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           113                            357 
$`AMP PEAK 15(12Q14.1) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0024 TCGA-02-0046 TCGA-02-0051 
       11.77         4.73        18.35        53.10         6.87        15.09 
TCGA-02-0054 TCGA-02-0060 TCGA-02-0070 TCGA-02-0074 TCGA-02-0099 TCGA-02-0102 
        6.54         6.02        25.05        10.19         3.48        27.02 
TCGA-02-0107 TCGA-02-0266 TCGA-02-0271 TCGA-02-0324 TCGA-02-0332 TCGA-02-2485 
       17.65        17.72        14.47         7.73        25.71        15.45 
TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 TCGA-06-0138 TCGA-06-0145 TCGA-06-0151 
       20.32        22.72        33.67        24.23         2.33        46.59 
TCGA-06-0152 TCGA-06-0157 TCGA-06-0162 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
       12.33         3.19         3.42        56.91         4.47         3.22 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 
        4.18         3.65        44.58        38.96         7.63        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0402 TCGA-06-0409 
       24.16         0.72        19.82        13.32         0.26        72.36 
TCGA-06-0412 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0875 TCGA-06-0877 
        9.57         2.10        14.20        26.40        43.46         5.65 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
        6.84         4.04        33.90        12.49         4.93        17.65 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5415 TCGA-06-5856 TCGA-06-5859 TCGA-06-6390 
        0.43        31.50         8.55         3.75         4.57         5.39 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-A7TK TCGA-08-0245 TCGA-08-0246 
        1.48         7.36         8.32        14.60        37.84         4.18 
TCGA-08-0352 TCGA-08-0380 TCGA-08-0518 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
        1.28        14.93        19.33        14.73        12.99        10.45 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 
        0.10        25.97        12.13         9.73        14.93        18.48 
TCGA-12-0826 TCGA-12-1089 TCGA-12-1090 TCGA-12-1098 TCGA-12-1598 TCGA-12-1602 
       27.78         5.82         7.59         3.98        15.65         6.77 
TCGA-12-3653 TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 TCGA-14-1451 TCGA-14-1821 
       14.53        13.78         1.12        58.78        23.11        17.79 
TCGA-14-1823 TCGA-14-2554 TCGA-15-1444 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       17.85        17.49        50.53        13.28         3.91        17.59 
TCGA-16-0850 TCGA-16-1056 TCGA-19-0957 TCGA-19-0960 TCGA-19-1786 TCGA-19-1787 
       16.37        14.01        21.90         8.61         7.17        12.66 
TCGA-19-1791 TCGA-19-2624 TCGA-19-5950 TCGA-19-5960 TCGA-26-1438 TCGA-26-5135 
        0.13         0.16        17.19        14.96        10.03         8.88 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2526 TCGA-28-1746 
       24.23        21.30        11.51        24.76         2.86         0.20 
TCGA-28-2506 TCGA-28-5207 TCGA-28-5209 TCGA-28-5214 TCGA-28-5218 TCGA-32-1979 
        6.74        11.28         2.53        23.44         5.16        19.50 
TCGA-32-2615 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 
       15.95        21.14        12.59        19.23         0.85         8.94 
TCGA-41-4097 TCGA-41-5651 TCGA-74-6577 TCGA-76-4928 TCGA-76-4935 TCGA-76-6193 
        0.20        15.12         4.34         3.09        36.85         2.70 
TCGA-RR-A6KA 
        6.28 

$`AMP PEAK 15(12Q14.1) WILD-TYPE`
TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
       23.18        10.59        35.41        20.71        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 
       18.31        14.73         3.22        12.59         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 
        8.35         9.57        19.73        26.43        28.70         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0104 TCGA-02-0106 TCGA-02-0111 
        8.81        57.76        16.96        65.00        11.67        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 
        9.90        10.62         7.33        15.91         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        14.30        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
       10.29         2.20        11.74        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 
        8.61        19.46        13.94        10.45        10.82         9.44 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       11.80        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 
        4.04        91.00        88.14        20.25        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       27.22        15.42        10.42         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0410 
       13.64        20.42        48.69        10.82         9.01         4.70 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       23.57        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 
       23.93        26.79        11.84        15.32        13.61        15.32 
TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        1.08        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 
        8.98         6.71         2.73         6.15         5.23         7.79 
TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
      120.56        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0244 
       26.79         1.87         3.12         2.56        17.72        22.68 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 
       37.58        22.29         3.39        12.23        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       19.59        58.68        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0619 TCGA-12-0654 TCGA-12-0656 
       18.41         7.56        15.35        34.92         7.59        94.78 
TCGA-12-0662 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       38.17        26.66         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       53.85        43.23         7.63        14.86        91.76        24.79 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
       14.53         4.14        25.68        14.73        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        11.24         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1452 
       19.30         0.79         1.38         3.75        32.05         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 
        0.99         1.97         7.63         5.88         7.17         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 
        3.78         3.42        13.78        19.10        53.19        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 
        4.31        29.03         4.57        10.29         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       13.97         6.41        11.77         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.65         3.25         9.67         4.87         1.08         7.53 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5951 
        4.08        24.23         7.00         7.04         6.64         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 
       16.80        17.79         3.98        28.54        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-2519 
       16.60         9.86        40.54        30.05        14.04        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       10.39        16.08         7.59        14.40        15.78         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        2.83         0.13         0.66         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       14.93        17.88        11.77        31.27        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 
       22.78        25.18         3.72        19.86        10.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R 
        9.53         0.99         4.44        11.84        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58         3.45        20.91        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        7.50         4.80         4.54         3.65         9.17         2.53 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92        20.55 

  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                         72.36                         127.59 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                         12.59                          12.10 
[1] "0.1 - 72.4 (12.6)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    57  77
  AMP PEAK 15(12Q14.1) WILD-TYPE 167 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     57   77
  AMP PEAK 15(12Q14.1) WILD-TYPE  167  270
        clus
vv       AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  FEMALE                           57                            167
  MALE                             77                            270
[1] 2 2
[1] FALSE
D15V4, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    21 108
  AMP PEAK 15(12Q14.1) WILD-TYPE  53 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     21  108
  AMP PEAK 15(12Q14.1) WILD-TYPE   53  366
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  NO                            21                             53
  YES                          108                            366
[1] 2 2
[1] FALSE
D15V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 15(12Q14.1) MUTATED                               5
  AMP PEAK 15(12Q14.1) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 15(12Q14.1) MUTATED                     3
  AMP PEAK 15(12Q14.1) WILD-TYPE                  15
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 15(12Q14.1) MUTATED                               126
  AMP PEAK 15(12Q14.1) WILD-TYPE                             399
D15V6, multiclass
                                 clus
vv                                AMP PEAK 15(12Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          126
                                 clus
vv                                AMP PEAK 15(12Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            399
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q14.1) MUTATED       4                        12   112
  AMP PEAK 15(12Q14.1) WILD-TYPE     9                        38   373
D15V7, multiclass
                           clus
vv                          AMP PEAK 15(12Q14.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              112
                           clus
vv                          AMP PEAK 15(12Q14.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             38
  WHITE                                                373
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED     1 114
  AMP PEAK 15(12Q14.1) WILD-TYPE  11 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED      1  114
  AMP PEAK 15(12Q14.1) WILD-TYPE   11  359
                        clus
vv                       AMP PEAK 15(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       AMP PEAK 15(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            359
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12Q15) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(12Q15) MUTATED    13  79
  AMP PEAK 16(12Q15) WILD-TYPE  87 391
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          92                          478 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          79                          391 
$`AMP PEAK 16(12Q15) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0024 TCGA-02-0039 TCGA-02-0051 TCGA-02-0052 
       11.77        18.35        53.10        10.52        15.09        12.59 
TCGA-02-0054 TCGA-02-0060 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0099 
        6.54         6.02        25.05         5.49        10.19         3.48 
TCGA-02-0102 TCGA-02-0271 TCGA-02-0321 TCGA-02-0324 TCGA-02-0330 TCGA-02-0337 
       27.02        14.47         9.90         7.73        15.91        25.12 
TCGA-06-0138 TCGA-06-0140 TCGA-06-0151 TCGA-06-0152 TCGA-06-0162 TCGA-06-0164 
       24.23         0.20        46.59        12.33         3.42        56.91 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 TCGA-06-0188 
        4.47         3.22         4.18         3.65        27.22        44.58 
TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 TCGA-06-0409 TCGA-06-0648 
       38.96         7.63        15.02        24.16        72.36         9.80 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0877 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 
       14.20        26.40         5.65        26.76         6.84         4.04 
TCGA-06-2561 TCGA-06-2569 TCGA-06-5415 TCGA-06-5856 TCGA-06-6390 TCGA-06-6391 
       17.65         0.43         8.55         3.75         5.39         1.48 
TCGA-06-6695 TCGA-06-6700 TCGA-06-A7TK TCGA-08-0246 TCGA-12-0616 TCGA-12-0670 
        8.32         4.77        14.60         4.18        14.73        25.97 
TCGA-12-0691 TCGA-12-0772 TCGA-12-0778 TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 
       12.13        53.85        14.93        27.78         7.59         3.98 
TCGA-12-1602 TCGA-12-3653 TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 TCGA-14-1451 
        6.77        14.53        13.78         1.12        58.78        23.11 
TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 TCGA-19-0957 TCGA-19-1786 
       17.79        17.85        17.49        13.28        21.90         7.17 
TCGA-19-1787 TCGA-19-2624 TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-27-2518 
       12.66         0.16        10.03         9.40         8.88        24.76 
TCGA-27-2526 TCGA-28-2506 TCGA-28-5207 TCGA-28-5214 TCGA-28-5218 TCGA-32-1978 
        2.86         6.74        11.28        23.44         5.16        15.85 
TCGA-32-1979 TCGA-32-2615 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 
       19.50        15.95        21.14        12.59        19.23         0.85 
TCGA-74-6577 TCGA-74-6584 
        4.34         7.50 

$`AMP PEAK 16(12Q15) WILD-TYPE`
TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        4.73        23.18        10.59        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0055 TCGA-02-0057 
       18.31         6.87        14.73         3.22         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0075 
        8.35         9.57        19.73        26.43        28.70        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       57.76        16.96        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        10.75         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 
       12.23        10.62         7.33        25.71         4.37        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       26.70        11.90        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 
       20.09        17.79        10.09         8.61        19.46        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 
       10.45         3.19        10.82         9.44        11.80        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 
        5.85        19.66         3.29        13.12         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 
       88.14        20.25        69.90        73.84        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        7.40        11.84         0.53         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        5.75         2.10        23.57        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       16.57        20.78        23.93        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.98         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        7.79       120.56         7.36        12.85         4.77         1.55 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL 
        4.96        26.79         1.87         3.12         2.56        17.72 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
       94.78         0.10        38.17        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 
       28.41        15.06        43.23         7.63         9.73        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
       91.76        24.79        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 
        8.94        20.58       127.59         5.82        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       15.98        12.23        15.85         9.11        14.53         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 
        0.79         1.38         3.75        32.05         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 
        1.97         7.63         5.88         7.17         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 
        3.42        13.78        50.53        19.10        53.19         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.65 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.37        14.86 
TCGA-26-5134 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        11.51        18.08        10.39        16.08 
TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         4.77         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       17.88         2.53        11.77        31.27        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
        0.10         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2573 
       25.18         3.72        19.86        10.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                        0.16                         0.10 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       72.36                       127.59 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       12.46                        12.16 
[1] "0.2 - 72.4 (12.5)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    32  60
  AMP PEAK 16(12Q15) WILD-TYPE 192 287
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     32   60
  AMP PEAK 16(12Q15) WILD-TYPE  192  287
        clus
vv       AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  FEMALE                         32                          192
  MALE                           60                          287
[1] 2 2
[1] FALSE
D16V4, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    12  76
  AMP PEAK 16(12Q15) WILD-TYPE  62 398
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     12   76
  AMP PEAK 16(12Q15) WILD-TYPE   62  398
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  NO                          12                           62
  YES                         76                          398
[1] 2 2
[1] FALSE
D16V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 16(12Q15) MUTATED                               3
  AMP PEAK 16(12Q15) WILD-TYPE                            25
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 16(12Q15) MUTATED                     2
  AMP PEAK 16(12Q15) WILD-TYPE                  16
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 16(12Q15) MUTATED                                87
  AMP PEAK 16(12Q15) WILD-TYPE                             438
D16V6, multiclass
                                 clus
vv                                AMP PEAK 16(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            3
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         87
                                 clus
vv                                AMP PEAK 16(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             25
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          438
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q15) MUTATED       3                         6    79
  AMP PEAK 16(12Q15) WILD-TYPE    10                        44   406
D16V7, multiclass
                           clus
vv                          AMP PEAK 16(12Q15) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             79
                           clus
vv                          AMP PEAK 16(12Q15) WILD-TYPE
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           44
  WHITE                                              406
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED     0  78
  AMP PEAK 16(12Q15) WILD-TYPE  12 395
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED      0   78
  AMP PEAK 16(12Q15) WILD-TYPE   12  395
                        clus
vv                       AMP PEAK 16(12Q15) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         78
                        clus
vv                       AMP PEAK 16(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          395
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(13Q34) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(13Q34) MUTATED     3  29
  AMP PEAK 17(13Q34) WILD-TYPE  97 441
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          538 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          29                          441 
$`AMP PEAK 17(13Q34) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0025 TCGA-02-0114 TCGA-02-0281 TCGA-02-0289 
       11.77        53.10        42.74        99.98         3.98        14.20 
TCGA-02-0338 TCGA-06-0146 TCGA-06-0210 TCGA-06-0221 TCGA-06-1087 TCGA-06-5856 
       10.59        20.09         7.40        19.82         4.04         3.75 
TCGA-08-0386 TCGA-12-0769 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-0817 
       18.02        15.06        21.73         6.77        14.53         5.39 
TCGA-14-0871 TCGA-14-1453 TCGA-14-4157 TCGA-16-0849 TCGA-16-1063 TCGA-19-1388 
       28.93         1.15         3.42        26.07        13.97        12.95 
TCGA-19-1390 TCGA-19-1787 TCGA-19-A6J4 TCGA-28-1752 TCGA-28-5207 TCGA-32-1970 
       25.38        12.66         3.98         8.48        11.28        15.39 
TCGA-32-2615 TCGA-41-3392 
       15.95         0.99 

$`AMP PEAK 17(13Q34) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 
       82.59        20.61        87.06        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 
       65.00        11.67        17.65        23.18        92.65        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       13.87        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0339 
        7.33        15.91        25.71         4.37        25.12        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        2.73         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        2.56        14.60        17.72        22.68        37.84         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         2.89        16.50        26.33         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.78        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91        17.59        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 
       10.29        14.01         9.14        21.24         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
        9.07         5.95         4.64         3.65         7.17         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26        14.93        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         5.42        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                        0.99                         0.10 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                       99.98                       127.59 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                      13.460                       12.145 
[1] "1.0 - 100.0 (13.5)" "0.1 - 127.6 (12.1)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED    10  22
  AMP PEAK 17(13Q34) WILD-TYPE 214 325
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED     10   22
  AMP PEAK 17(13Q34) WILD-TYPE  214  325
        clus
vv       AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  FEMALE                         10                          214
  MALE                           22                          325
[1] 2 2
[1] FALSE
D17V4, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED     5  26
  AMP PEAK 17(13Q34) WILD-TYPE  69 448
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED      5   26
  AMP PEAK 17(13Q34) WILD-TYPE   69  448
     clus
vv    AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  NO                           5                           69
  YES                         26                          448
[1] 2 2
[1] FALSE
D17V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 17(13Q34) MUTATED                               1
  AMP PEAK 17(13Q34) WILD-TYPE                            27
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 17(13Q34) MUTATED                     2
  AMP PEAK 17(13Q34) WILD-TYPE                  16
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 17(13Q34) MUTATED                                29
  AMP PEAK 17(13Q34) WILD-TYPE                             496
D17V6, multiclass
                                 clus
vv                                AMP PEAK 17(13Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            1
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         29
                                 clus
vv                                AMP PEAK 17(13Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             27
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          496
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(13Q34) MUTATED       0                         3    29
  AMP PEAK 17(13Q34) WILD-TYPE    13                        47   456
D17V7, multiclass
                           clus
vv                          AMP PEAK 17(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             29
                           clus
vv                          AMP PEAK 17(13Q34) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           47
  WHITE                                              456
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED     0  26
  AMP PEAK 17(13Q34) WILD-TYPE  12 447
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED      0   26
  AMP PEAK 17(13Q34) WILD-TYPE   12  447
                        clus
vv                       AMP PEAK 17(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         26
                        clus
vv                       AMP PEAK 17(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          447
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED     3  27
  AMP PEAK 18(13Q34) WILD-TYPE  97 443
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          540 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          27                          443 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0114 TCGA-02-0281 TCGA-02-0289 TCGA-02-0338 
       11.77        42.74        99.98         3.98        14.20        10.59 
TCGA-06-0221 TCGA-06-1087 TCGA-08-0354 TCGA-08-0386 TCGA-08-0389 TCGA-12-0616 
       19.82         4.04        17.95        18.02        15.35        14.73 
TCGA-12-0769 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-0817 TCGA-14-0871 
       15.06        21.73         6.77        14.53         5.39        28.93 
TCGA-14-1453 TCGA-14-4157 TCGA-19-1388 TCGA-19-1390 TCGA-19-1787 TCGA-19-A60I 
        1.15         3.42        12.95        25.38        12.66        17.79 
TCGA-19-A6J4 TCGA-28-1752 TCGA-28-5207 TCGA-32-1970 TCGA-32-2615 TCGA-41-3392 
        3.98         8.48        11.28        15.39        15.95         0.99 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       14.47        13.87        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28         8.42        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        3.39        12.23        14.93        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       15.35        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       14.73        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         1.35         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
        2.04        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.78        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65         7.17         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 
       13.64         5.16        22.68        10.49         5.42        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
        7.36         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        8.94         9.53         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.99                         0.10 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                       99.98                       127.59 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      14.365                       12.115 
[1] "1.0 - 100.0 (14.4)" "0.1 - 127.6 (12.1)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    10  20
  AMP PEAK 18(13Q34) WILD-TYPE 214 327
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     10   20
  AMP PEAK 18(13Q34) WILD-TYPE  214  327
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         10                          214
  MALE                           20                          327
[1] 2 2
[1] FALSE
D18V4, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     4  25
  AMP PEAK 18(13Q34) WILD-TYPE  70 449
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      4   25
  AMP PEAK 18(13Q34) WILD-TYPE   70  449
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           4                           70
  YES                         25                          449
[1] 2 2
[1] FALSE
D18V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 18(13Q34) MUTATED                               2
  AMP PEAK 18(13Q34) WILD-TYPE                            26
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 18(13Q34) MUTATED                     1
  AMP PEAK 18(13Q34) WILD-TYPE                  17
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 18(13Q34) MUTATED                                27
  AMP PEAK 18(13Q34) WILD-TYPE                             498
D18V6, multiclass
                                 clus
vv                                AMP PEAK 18(13Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 18(13Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             26
  TREATED PRIMARY GBM                                       17
  UNTREATED PRIMARY (DE NOVO) GBM                          498
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       0                         4    25
  AMP PEAK 18(13Q34) WILD-TYPE    13                        46   460
D18V7, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             25
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           46
  WHITE                                              460
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     0  24
  AMP PEAK 18(13Q34) WILD-TYPE  12 449
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      0   24
  AMP PEAK 18(13Q34) WILD-TYPE   12  449
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         24
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          449
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(14Q32.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(14Q32.33) MUTATED     3  33
  AMP PEAK 19(14Q32.33) WILD-TYPE  97 437
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             534 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             33                             437 
$`AMP PEAK 19(14Q32.33) MUTATED`
TCGA-02-0059 TCGA-02-0075 TCGA-02-0102 TCGA-06-0148 TCGA-06-0151 TCGA-06-0159 
        9.57        20.84        27.02        10.09        46.59         9.44 
TCGA-06-0177 TCGA-06-0195 TCGA-06-0237 TCGA-06-0397 TCGA-06-0414 TCGA-06-0747 
        4.18         7.40        13.64         9.01        35.11         2.70 
TCGA-06-1087 TCGA-06-2563 TCGA-06-2569 TCGA-06-5415 TCGA-08-0244 TCGA-08-0246 
        4.04        30.64         0.43         8.55        22.68         4.18 
TCGA-08-0351 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-1600 
       65.33        18.02         4.27        11.08        34.92        14.73 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0867 TCGA-16-0846 TCGA-19-0962 
       44.02        14.53        11.97         2.04         3.91         0.66 
TCGA-19-2620 TCGA-26-1439 TCGA-32-2495 TCGA-32-2632 TCGA-41-2575 TCGA-76-6286 
        4.87        13.87        15.02         8.84         9.53        20.98 

$`AMP PEAK 19(14Q32.33) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         8.35         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       65.00        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       17.79         8.61        19.46        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        4.04        91.00        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 
       19.82        13.32        20.42        48.69        10.82         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       46.88         7.86         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       12.56         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 
        1.87         3.12         2.56        14.60        17.72        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       13.97         0.72        12.56        42.15        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
        4.14        15.65        25.68         6.77        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        15.12         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
       13.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         8.61        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 
       12.66         3.25         0.13         9.67         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.95         7.36        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
       13.35         8.94         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                           0.43                            0.10 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                          65.33                          127.59 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                         10.585                          12.230 
[1] "0.4 - 65.3 (10.6)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D19V2, continuous
D19V3, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED    12  24
  AMP PEAK 19(14Q32.33) WILD-TYPE 212 323
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED     12   24
  AMP PEAK 19(14Q32.33) WILD-TYPE  212  323
        clus
vv       AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  FEMALE                            12                             212
  MALE                              24                             323
[1] 2 2
[1] FALSE
D19V4, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED     4  30
  AMP PEAK 19(14Q32.33) WILD-TYPE  70 444
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED      4   30
  AMP PEAK 19(14Q32.33) WILD-TYPE   70  444
     clus
vv    AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  NO                              4                              70
  YES                            30                             444
[1] 2 2
[1] FALSE
D19V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 19(14Q32.33) MUTATED                               2
  AMP PEAK 19(14Q32.33) WILD-TYPE                            26
                                 vv
clus                              TREATED PRIMARY GBM
  AMP PEAK 19(14Q32.33) MUTATED                     2
  AMP PEAK 19(14Q32.33) WILD-TYPE                  16
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 19(14Q32.33) MUTATED                                32
  AMP PEAK 19(14Q32.33) WILD-TYPE                             493
D19V6, multiclass
                                 clus
vv                                AMP PEAK 19(14Q32.33) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               2
  TREATED PRIMARY GBM                                         2
  UNTREATED PRIMARY (DE NOVO) GBM                            32
                                 clus
vv                                AMP PEAK 19(14Q32.33) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                26
  TREATED PRIMARY GBM                                          16
  UNTREATED PRIMARY (DE NOVO) GBM                             493
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(14Q32.33) MUTATED       0                         2    34
  AMP PEAK 19(14Q32.33) WILD-TYPE    13                        48   451
D19V7, multiclass
                           clus
vv                          AMP PEAK 19(14Q32.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                34
                           clus
vv                          AMP PEAK 19(14Q32.33) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                              48
  WHITE                                                 451
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED     0  34
  AMP PEAK 19(14Q32.33) WILD-TYPE  12 439
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED      0   34
  AMP PEAK 19(14Q32.33) WILD-TYPE   12  439
                        clus
vv                       AMP PEAK 19(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            34
                        clus
vv                       AMP PEAK 19(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             439
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(17P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17P13.2) MUTATED     5  46
  AMP PEAK 20(17P13.2) WILD-TYPE  95 424
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            519 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            46                            424 
$`AMP PEAK 20(17P13.2) MUTATED`
TCGA-02-0051 TCGA-02-0266 TCGA-02-0281 TCGA-02-2466 TCGA-06-0151 TCGA-06-0166 
       15.09        17.72         3.98        16.80        46.59         5.85 
TCGA-06-0173 TCGA-06-0195 TCGA-06-0216 TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 
        4.47         7.40        24.16        72.36        35.11        14.20 
TCGA-06-0743 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-A5U1 TCGA-08-0347 
       26.40         4.04        11.84         1.08         1.87        25.71 
TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
       12.16        29.23        65.33         8.42        24.56        31.10 
TCGA-08-0375 TCGA-08-0389 TCGA-08-0392 TCGA-08-0510 TCGA-12-0821 TCGA-12-0822 
       12.23        15.35         0.72         4.27        10.62        23.51 
TCGA-12-0827 TCGA-12-1096 TCGA-12-1600 TCGA-12-1602 TCGA-14-0813 TCGA-14-0865 
       38.76         9.11        14.73         6.77         1.35        16.50 
TCGA-15-1447 TCGA-16-0849 TCGA-19-1388 TCGA-19-1390 TCGA-19-A6J4 TCGA-27-2521 
       53.19        26.07        12.95        25.38         3.98        10.39 
TCGA-28-1746 TCGA-28-2506 TCGA-28-5207 TCGA-28-5218 TCGA-32-2615 TCGA-32-4210 
        0.20         6.74        11.28         5.16        15.95         3.72 
TCGA-41-2575 TCGA-41-4097 TCGA-RR-A6KA 
        9.53         0.20         6.28 

$`AMP PEAK 20(17P13.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 
       47.11        11.34         9.27        16.21         3.35        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 
       10.65        19.66         3.29        13.12         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80         2.10        23.57        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        6.84        26.79        15.32        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0349 TCGA-08-0352 
        4.18       115.86         1.74         8.42         9.80         1.28 
TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 
       17.95        37.58        22.29         3.39        14.93        18.02 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       13.97        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        18.48        27.78         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       15.85        14.53         3.98         4.14        15.65        25.68 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 
       13.78         3.25         5.39         2.89        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 
       19.10        13.28         3.91        17.59        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        18.08        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        14.40        15.78         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         4.77         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
       26.30         5.92        20.55 

  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                         72.36                         127.59 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                         12.16                          12.23 
[1] "0.2 - 72.4 (12.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    16  35
  AMP PEAK 20(17P13.2) WILD-TYPE 208 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     16   35
  AMP PEAK 20(17P13.2) WILD-TYPE  208  312
        clus
vv       AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  FEMALE                           16                            208
  MALE                             35                            312
[1] 2 2
[1] FALSE
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    10  39
  AMP PEAK 20(17P13.2) WILD-TYPE  64 435
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     10   39
  AMP PEAK 20(17P13.2) WILD-TYPE   64  435
     clus
vv    AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  NO                            10                             64
  YES                           39                            435
[1] 2 2
[1] FALSE
D20V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 20(17P13.2) MUTATED                               4
  AMP PEAK 20(17P13.2) WILD-TYPE                            24
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 20(17P13.2) MUTATED                     1
  AMP PEAK 20(17P13.2) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 20(17P13.2) MUTATED                                46
  AMP PEAK 20(17P13.2) WILD-TYPE                             479
D20V6, multiclass
                                 clus
vv                                AMP PEAK 20(17P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           46
                                 clus
vv                                AMP PEAK 20(17P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17P13.2) MUTATED       0                         5    42
  AMP PEAK 20(17P13.2) WILD-TYPE    13                        45   443
D20V7, multiclass
                           clus
vv                          AMP PEAK 20(17P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               42
                           clus
vv                          AMP PEAK 20(17P13.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             45
  WHITE                                                443
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED     1  43
  AMP PEAK 20(17P13.2) WILD-TYPE  11 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED      1   43
  AMP PEAK 20(17P13.2) WILD-TYPE   11  430
                        clus
vv                       AMP PEAK 20(17P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 20(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            430
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(17Q25.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(17Q25.1) MUTATED     8  75
  AMP PEAK 21(17Q25.1) WILD-TYPE  92 395
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            83                            487 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            75                            395 
$`AMP PEAK 21(17Q25.1) MUTATED`
TCGA-02-0003 TCGA-02-0047 TCGA-02-0051 TCGA-02-0104 TCGA-02-0106 TCGA-02-0266 
        4.73        14.73        15.09        65.00        11.67        17.72 
TCGA-02-0281 TCGA-02-0325 TCGA-02-0456 TCGA-02-2466 TCGA-06-0151 TCGA-06-0152 
        3.98        10.62         3.35        16.80        46.59        12.33 
TCGA-06-0166 TCGA-06-0173 TCGA-06-0188 TCGA-06-0195 TCGA-06-0216 TCGA-06-0237 
        5.85         4.47        44.58         7.40        24.16        13.64 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 
       72.36         4.70        35.11         2.10        14.20        26.40 
TCGA-06-0744 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 
       46.88        23.93         4.04        11.84         1.08         7.36 
TCGA-06-6700 TCGA-06-A5U1 TCGA-08-0346 TCGA-08-0350 TCGA-08-0353 TCGA-08-0510 
        4.77         1.87         8.42        29.23         8.42         4.27 
TCGA-08-0514 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0818 TCGA-12-0821 
       11.08         7.56        34.92        38.17        91.76        10.62 
TCGA-12-0827 TCGA-12-1090 TCGA-12-1092 TCGA-12-1096 TCGA-12-1098 TCGA-12-1600 
       38.76         7.59        21.73         9.11         3.98        14.73 
TCGA-12-1602 TCGA-12-5301 TCGA-14-0813 TCGA-14-0865 TCGA-14-1453 TCGA-14-1794 
        6.77         2.04         1.35        16.50         1.15         0.99 
TCGA-14-1827 TCGA-14-1829 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 TCGA-16-1063 
        5.88         7.17         3.78        13.28         3.91        13.97 
TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-A60I TCGA-19-A6J4 TCGA-27-1835 
       12.95        25.38         3.65        17.79         3.98        21.30 
TCGA-27-2521 TCGA-28-1746 TCGA-28-1757 TCGA-28-2506 TCGA-28-5207 TCGA-28-5215 
       10.39         0.20         0.13         6.74        11.28        11.01 
TCGA-28-5218 TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-41-2575 
        5.16        16.93        15.02        15.95         7.36         9.53 
TCGA-41-3915 TCGA-41-4097 TCGA-74-6573 TCGA-76-6280 TCGA-RR-A6KA 
       11.84         0.20         3.45        11.38         6.28 

$`AMP PEAK 21(17Q25.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 
        3.62        10.72        10.52        18.31         6.87         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       17.65        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90         7.73         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.21        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       10.09         8.61        19.46        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       27.22        15.42        10.42        38.96         4.67         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       48.69        10.82         9.01         0.26         9.57         3.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0745 
       12.62         5.75         5.75         9.80        23.57         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 
        7.17        40.41        16.57        20.78        26.76         6.84 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       26.79        15.32        13.61        33.90        15.32        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48       120.56         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        1.55         4.96        26.79         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       25.71        12.16         9.80        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41        15.35        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       10.45         7.59        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       43.23         7.63         9.73        14.93        14.86        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        23.51        27.78         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
        5.82        33.21        15.98        12.23        15.85        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        4.14        15.65        25.68        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         3.25         5.39         2.89 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-2554 TCGA-14-2555 
        1.97        17.79        17.85         7.63        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 
        3.42        13.78        50.53        19.10        53.19        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
       14.01         9.14        21.24         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        5.95         4.64         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       16.80        14.96        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 
        5.06        16.60         9.86        24.23        40.54        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
        2.86        14.40        15.78         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 
        7.63         8.48         1.22         1.55         2.83         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26        14.93        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       11.77        31.27        23.44        13.64        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
       19.50         1.18         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       20.78         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        8.94         0.99         4.44        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KC 
       20.55 

  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                          0.13                           0.10 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                         91.76                         127.59 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                         10.62                          12.56 
[1] "0.1 - 91.8 (10.6)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    27  56
  AMP PEAK 21(17Q25.1) WILD-TYPE 197 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     27   56
  AMP PEAK 21(17Q25.1) WILD-TYPE  197  291
        clus
vv       AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  FEMALE                           27                            197
  MALE                             56                            291
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    15  65
  AMP PEAK 21(17Q25.1) WILD-TYPE  59 409
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     15   65
  AMP PEAK 21(17Q25.1) WILD-TYPE   59  409
     clus
vv    AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  NO                            15                             59
  YES                           65                            409
[1] 2 2
[1] FALSE
D21V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 21(17Q25.1) MUTATED                               5
  AMP PEAK 21(17Q25.1) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 21(17Q25.1) MUTATED                     2
  AMP PEAK 21(17Q25.1) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 21(17Q25.1) MUTATED                                76
  AMP PEAK 21(17Q25.1) WILD-TYPE                             449
D21V6, multiclass
                                 clus
vv                                AMP PEAK 21(17Q25.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           76
                                 clus
vv                                AMP PEAK 21(17Q25.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(17Q25.1) MUTATED       0                        10    69
  AMP PEAK 21(17Q25.1) WILD-TYPE    13                        40   416
D21V7, multiclass
                           clus
vv                          AMP PEAK 21(17Q25.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               69
                           clus
vv                          AMP PEAK 21(17Q25.1) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                416
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED     2  69
  AMP PEAK 21(17Q25.1) WILD-TYPE  10 404
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED      2   69
  AMP PEAK 21(17Q25.1) WILD-TYPE   10  404
                        clus
vv                       AMP PEAK 21(17Q25.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK 21(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            404
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(19P13.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(19P13.3) MUTATED    42 199
  AMP PEAK 22(19P13.3) WILD-TYPE  58 271
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           241                            329 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           199                            271 
$`AMP PEAK 22(19P13.3) MUTATED`
TCGA-02-0007 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       23.18        10.59        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0028 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0051 
       20.12        90.58         3.62        10.72        18.31        15.09 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        6.54        19.86        19.73        26.43        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 
       10.19        20.84        27.02        11.67        23.18        92.65 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 TCGA-02-2466 
       13.87        14.20        15.95         4.37        10.55        16.80 
TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       15.45         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0137 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        3.98        33.67        26.70         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
        3.19        10.82         9.44        56.91         4.47         3.22 
TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 
        4.04         4.18        20.25        73.84        10.42        38.96 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 
        0.39         7.66         8.42         7.63        11.84        24.16 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       19.82        13.64        10.82         0.26        72.36         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.11         5.75        23.57        26.40        46.88         2.70 
TCGA-06-0877 TCGA-06-0879 TCGA-06-1086 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
        5.65        40.41         6.84        15.32        15.32        30.64 
TCGA-06-2565 TCGA-06-2570 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
       16.64        31.50         8.98         8.55         6.71         3.75 
TCGA-06-6388 TCGA-06-6693 TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 TCGA-08-0246 
        5.23       120.56         8.32         1.55         3.12         4.18 
TCGA-08-0347 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       25.71         1.28         8.42        24.56        31.10        37.58 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       12.23        18.02        13.97         0.72        12.56         4.27 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 
       11.08        19.33        18.41         7.56        94.78         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       25.97        26.66        20.38        28.41        15.06        53.85 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 
       14.93        14.86        24.79        18.48        27.78        20.58 
TCGA-12-1094 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       12.23         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 
        6.21        23.05        11.24        13.78         5.39        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 
        2.04        15.95        32.05        58.78         7.10        30.18 
TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 
       17.85         7.17        17.49         7.96         3.42        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 
        3.91        17.59         4.31        10.29        14.01        21.24 
TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
       11.77         9.07        12.95        25.38         3.65         7.17 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2629 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 
        3.25         4.87        24.23        17.19         8.02         4.73 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1799 
        1.78        14.07        16.80        17.79        28.54         9.37 
TCGA-26-5139 TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
        1.58        24.23        24.76        10.39        16.08         7.59 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
       15.78         0.20         9.21         7.63         8.48         1.22 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 
        0.66         6.74         7.30         5.26        17.88         2.53 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 TCGA-32-1970 
       23.44        11.01        13.64         5.16         5.42        15.39 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 TCGA-32-2495 
        0.10        15.85        19.50         4.67        14.86        15.02 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 
        8.84        25.18        21.14        12.59        19.23        13.35 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9T 
        9.53         4.44        11.84        15.12         4.08        25.58 
TCGA-74-6578 TCGA-76-4925 TCGA-76-4934 TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 
       14.33         4.80         2.53        11.38         4.83        23.90 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA 
       18.64        36.20         1.61        17.72        26.30         6.28 
TCGA-RR-A6KC 
       20.55 

$`AMP PEAK 22(19P13.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0024 
       11.77         4.73        18.35        35.41        20.71        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 
       42.74        24.59        12.16         2.83        14.14        10.52 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 
        6.87        14.73         3.22        12.59         2.50         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        9.57         6.02        28.70        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 
       65.00        17.65        99.98        14.47         3.98        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 
       25.12        10.59        12.39        14.50        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 
        9.27        16.21         3.35        12.92        15.32        20.32 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       22.72        12.95        25.35        14.30        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0149 TCGA-06-0160 
        0.20        10.29         2.20        11.74         8.61        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 
       91.00        88.14         3.65        69.90        27.22        44.58 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 
       15.42         4.67         7.40         5.56         7.40         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
       15.02         0.72        13.32        20.42        48.69         9.01 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        9.57         3.16        12.62         5.75         9.80         2.10 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       14.20         7.86         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        7.17        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.79        11.84        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93        17.65        12.56         5.95         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        2.73         6.15         4.57         7.79         5.39         1.48 
TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
        7.36        12.85         4.77         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        1.87         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
      115.86         1.74         8.42        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 
       65.33        17.95        22.29         3.39        14.93        15.35 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       42.15        19.59        58.68        10.75         4.80         7.27 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 
        7.59        38.17        12.13         3.65        43.23         7.63 
TCGA-12-0776 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
        9.73        91.76        10.62        23.51        38.76         8.94 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 
       15.85         9.11        14.53         3.98        59.77        44.02 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 
        2.24         3.25         1.35         2.89        16.50        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 
       19.30         0.79         1.38         1.12         3.75        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 TCGA-15-0742 
        1.97        17.79         7.63         5.88         3.78        13.78 
TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 
       50.53        53.19        13.28        26.07        16.37        29.03 
TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
        4.57         9.14        13.97         6.41        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 
        0.66        14.27         3.39        10.75         5.95         4.64 
TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
       12.66         0.13         9.67         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 
        4.08         7.00         7.04         6.64        18.90        12.10 
TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       22.49        14.96         3.98        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       31.33         7.13         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
       18.97         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2519 TCGA-27-2526 TCGA-27-2527 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 
       18.08         2.86        14.40         2.53         8.35         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 
        2.83         0.13         4.77        14.93        11.28        11.77 
TCGA-28-5213 TCGA-28-5219 TCGA-28-5220 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
       31.27        22.68        10.49        21.07         0.49         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 
       12.69        16.93        12.23        20.78        15.95         7.36 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 
       22.78         3.72        19.86        10.85         0.85         8.94 
TCGA-41-3392 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6573 TCGA-74-6575 
        0.99         0.20        12.46         1.45         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        4.34         8.22         7.50         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        9.17        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-OX-A56R 
        8.35        20.98         5.03        34.45         5.92 

  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                          0.10                           0.13 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                        120.56                         127.59 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                         14.01                          11.28 
[1] "0.1 - 120.6 (14.0)" "0.1 - 127.6 (11.3)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED    95 146
  AMP PEAK 22(19P13.3) WILD-TYPE 129 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED     95  146
  AMP PEAK 22(19P13.3) WILD-TYPE  129  201
        clus
vv       AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  FEMALE                           95                            129
  MALE                            146                            201
[1] 2 2
[1] FALSE
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED    27 204
  AMP PEAK 22(19P13.3) WILD-TYPE  47 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED     27  204
  AMP PEAK 22(19P13.3) WILD-TYPE   47  270
     clus
vv    AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  NO                            27                             47
  YES                          204                            270
[1] 2 2
[1] FALSE
D22V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 22(19P13.3) MUTATED                              12
  AMP PEAK 22(19P13.3) WILD-TYPE                            16
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 22(19P13.3) MUTATED                    10
  AMP PEAK 22(19P13.3) WILD-TYPE                   8
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 22(19P13.3) MUTATED                               219
  AMP PEAK 22(19P13.3) WILD-TYPE                             306
D22V6, multiclass
                                 clus
vv                                AMP PEAK 22(19P13.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             12
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          219
                                 clus
vv                                AMP PEAK 22(19P13.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               16
  TREATED PRIMARY GBM                                          8
  UNTREATED PRIMARY (DE NOVO) GBM                            306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(19P13.3) MUTATED       8                        21   206
  AMP PEAK 22(19P13.3) WILD-TYPE     5                        29   279
D22V7, multiclass
                           clus
vv                          AMP PEAK 22(19P13.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           21
  WHITE                                              206
                           clus
vv                          AMP PEAK 22(19P13.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             29
  WHITE                                                279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED     6 199
  AMP PEAK 22(19P13.3) WILD-TYPE   6 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED      6  199
  AMP PEAK 22(19P13.3) WILD-TYPE    6  274
                        clus
vv                       AMP PEAK 22(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          199
                        clus
vv                       AMP PEAK 22(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            274
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(19P13.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(19P13.2) MUTATED    44 202
  AMP PEAK 23(19P13.2) WILD-TYPE  56 268
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           246                            324 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           202                            268 
$`AMP PEAK 23(19P13.2) MUTATED`
TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0028 
       10.59        20.61        87.06        77.65        20.12        90.58 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 
        3.62        10.72        18.31        15.09         6.54        19.86 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0080 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       89.72        27.02        11.67        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 
       14.47        13.87        14.20        15.95         4.37        10.55 
TCGA-02-2466 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       16.80        15.45         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        6.94         3.98        26.70         2.33        17.79        10.09 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 
       19.46        46.59        12.33        13.94        10.45        10.82 
TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
        9.44        56.91         4.47         3.22         4.04         4.18 
TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 
       20.25        73.84        10.42        38.96         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 
        8.42         7.63        11.84        24.16        19.82        13.64 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 
       10.82         0.26        72.36         4.70        35.11         5.75 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0875 TCGA-06-0877 
       23.57        26.40        46.88         2.70        43.46         5.65 
TCGA-06-0879 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
       40.41         6.84        26.79        15.32        15.32        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 
        5.95        16.64         8.98         8.55         6.71         5.23 
TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0347 
        8.32         4.77         1.55         3.12         4.18        25.71 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 
        1.28         8.42        24.56        31.10        37.58        12.23 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       18.02        13.97         0.72        12.56         4.27        11.08 
TCGA-08-0518 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0656 
       19.33        15.98        18.41         7.56        14.73        94.78 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
        0.10        25.97        26.66        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 
       53.85        14.86        24.79        18.48        27.78        20.58 
TCGA-12-1094 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 
       12.23         4.14        15.65        25.68        14.73        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5299 TCGA-14-0783 
       15.22        10.95        34.92        14.53         3.22         6.21 
TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 
       23.05        11.24        13.78         5.39        26.33         2.04 
TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 TCGA-14-1823 
       15.95        32.05        58.78         7.10        30.18        17.85 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-15-1449 
        7.17        17.49         7.96         3.42        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
        3.91        17.59        10.29        14.01        21.24        13.97 
TCGA-19-0955 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 
       11.77         9.07         5.95        12.95        25.38         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 TCGA-19-2624 TCGA-19-2629 TCGA-19-5950 
        7.17         3.25         4.87         0.16        24.23        17.19 
TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I 
        8.02         4.73         1.78        14.07        16.80        17.79 
TCGA-26-1799 TCGA-26-5139 TCGA-27-1831 TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 
        9.37         1.58        16.60        24.23        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 
       16.08         7.59         2.86        15.78         0.20         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        7.63         8.48         1.22         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        5.26        17.88         2.53        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       22.68         5.42        15.39         0.10        15.85        19.50 
TCGA-32-1982 TCGA-32-1987 TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 
        4.67        14.86        15.02         8.84        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
        3.72        12.59        19.23        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6578 
        4.44        11.84        15.12         4.08        25.58        14.33 
TCGA-76-4925 TCGA-76-4934 TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 
        4.80         2.53        11.38         4.83        23.90        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       36.20         1.61        17.72        26.30         6.28        20.55 

$`AMP PEAK 23(19P13.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 
       82.59        53.10        42.74        24.59        12.16         2.83 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       14.14        10.52         6.87        14.73         3.22        12.59 
TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 TCGA-02-0079 
        2.50         8.35         9.57         6.02        28.70        27.25 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 
        3.48        65.00        17.65         3.98        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 
        7.73        10.62         7.33        15.91        25.71        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        12.39        14.50        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 
       16.21         3.35        12.92        15.32        20.32        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       33.67        12.95        25.35        14.30        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 
        0.20        10.29         2.20        11.74        20.09         8.61 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
        3.19        11.80         3.42        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 
        3.29        13.12        91.00        88.14         3.65        69.90 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       27.22        44.58        15.42         4.67         7.40         5.56 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 
        7.40         0.53        15.02         0.72        13.32        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       48.69         9.01         9.57         3.16        12.62         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.80         2.10        14.20         7.86         2.70         0.92 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17        16.57        20.78        26.76        23.93 
TCGA-06-1087 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        4.04        11.84        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
        4.93        17.65        12.56         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 
        2.73         3.75         6.15         4.57         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6700 TCGA-06-6701 
        1.48       120.56         7.36        12.85         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
       26.79         1.87         2.56        14.60        17.72        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 
       37.84       115.86         1.74         8.42        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 
       29.23        65.33        17.95        22.29         3.39        14.93 
TCGA-08-0389 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 
       15.35        42.15        19.59        58.68        10.75         4.80 
TCGA-08-0524 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.27        15.35        12.99        34.92        10.45         7.59 
TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       38.17        12.13         3.65        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       14.93        91.76        10.62        23.51        38.76         8.94 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1602 TCGA-12-3644 
       15.85         9.11        14.53         3.98         6.77        59.77 
TCGA-12-3646 TCGA-12-3651 TCGA-12-5295 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       44.02        12.69        14.93         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
        0.95         2.24         3.25         1.35         2.89        16.50 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       28.93        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
       23.11         1.15         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 
        0.99         1.97        17.79         7.63         5.88         3.78 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.78        50.53        53.19        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
       29.03         4.57         9.14         6.41        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1389 TCGA-19-1787 
        0.66        14.27         3.39        10.75         4.64        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2631 
        0.13         9.67         1.08         7.53         4.08         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 
        7.04         6.64        18.90        12.10        22.49        14.96 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.40        14.86         5.49         8.88        18.97 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 
        7.92         2.33        19.33         5.06         9.86        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2527 
       21.30        30.05        14.04        11.51        18.08        14.40 
TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2509 
        2.53         8.35         1.55         2.83         0.13         4.77 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5220 
       14.93        11.28        11.77        31.27        11.01        10.49 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
       21.07         0.49         1.18        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-4213 TCGA-32-4719 
       20.78        15.95         7.36        22.78        19.86        10.85 
TCGA-41-2571 TCGA-41-2573 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6573 
        0.85         8.94         0.20        12.46         1.45         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
       20.91         4.34         8.22         7.50         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-OX-A56R 
       17.06         8.35        20.98         5.03        34.45         5.92 

  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                          0.10                           0.13 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                         99.98                         127.59 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                         13.97                          11.31 
[1] "0.1 - 100.0 (14.0)" "0.1 - 127.6 (11.3)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.2) MUTATED    96 150
  AMP PEAK 23(19P13.2) WILD-TYPE 128 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED     96  150
  AMP PEAK 23(19P13.2) WILD-TYPE  128  197
        clus
vv       AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  FEMALE                           96                            128
  MALE                            150                            197
[1] 2 2
[1] FALSE
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.2) MUTATED    28 207
  AMP PEAK 23(19P13.2) WILD-TYPE  46 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED     28  207
  AMP PEAK 23(19P13.2) WILD-TYPE   46  267
     clus
vv    AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  NO                            28                             46
  YES                          207                            267
[1] 2 2
[1] FALSE
D23V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 23(19P13.2) MUTATED                              11
  AMP PEAK 23(19P13.2) WILD-TYPE                            17
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 23(19P13.2) MUTATED                    10
  AMP PEAK 23(19P13.2) WILD-TYPE                   8
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 23(19P13.2) MUTATED                               225
  AMP PEAK 23(19P13.2) WILD-TYPE                             300
D23V6, multiclass
                                 clus
vv                                AMP PEAK 23(19P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             11
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          225
                                 clus
vv                                AMP PEAK 23(19P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               17
  TREATED PRIMARY GBM                                          8
  UNTREATED PRIMARY (DE NOVO) GBM                            300
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(19P13.2) MUTATED       7                        21   210
  AMP PEAK 23(19P13.2) WILD-TYPE     6                        29   275
D23V7, multiclass
                           clus
vv                          AMP PEAK 23(19P13.2) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           21
  WHITE                                              210
                           clus
vv                          AMP PEAK 23(19P13.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             29
  WHITE                                                275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.2) MUTATED     6 203
  AMP PEAK 23(19P13.2) WILD-TYPE   6 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED      6  203
  AMP PEAK 23(19P13.2) WILD-TYPE    6  270
                        clus
vv                       AMP PEAK 23(19P13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       AMP PEAK 23(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(19Q12) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(19Q12) MUTATED    37 177
  AMP PEAK 24(19Q12) WILD-TYPE  63 293
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         214                          356 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         177                          293 
$`AMP PEAK 24(19Q12) MUTATED`
TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       23.18        10.59        20.61        77.65        20.12        42.74 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0054 TCGA-02-0057 TCGA-02-0064 
        3.62        10.72        18.31         6.54        19.86        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 
       26.43        25.05         5.49        10.19        20.84        89.72 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0116 
       16.96        27.02        11.67        23.18        92.65        48.95 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        17.72        10.75        13.87        14.20        15.95 
TCGA-02-0333 TCGA-02-0430 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
        4.37        10.55        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 
       47.61         6.94         3.98        26.70         2.33        17.79 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 
       10.09        19.46        46.59        12.33        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
       10.82         9.44        56.91         4.47         3.22         4.18 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 
       20.25         3.65        73.84        10.42        38.96         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 
        7.66         8.42         7.63        11.84        24.16        13.64 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 
       10.82         0.26        72.36         4.70        35.11         5.75 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 
       23.57        26.40        46.88         2.70         5.65        40.41 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 TCGA-06-2565 
        6.84         4.04        15.32        15.32        30.64        16.64 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 TCGA-06-6695 TCGA-06-6699 
        8.98         8.55         6.71         5.23         8.32         1.55 
TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0352 TCGA-08-0355 
        3.12         4.18        25.71         9.80         1.28        24.56 
TCGA-08-0356 TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       31.10        12.23        18.02        13.97        12.56         4.27 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       11.08        19.33         7.27        15.98        18.41         7.56 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       25.97        26.66        20.38        28.41        15.06        53.85 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 
       14.93        14.86        24.79        27.78        20.58        12.23 
TCGA-12-1095 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.85         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
       11.24        13.78         5.39        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1454 TCGA-14-1823 TCGA-14-1829 
       15.95        32.05        58.78        30.18        17.85         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       17.49         7.96        19.10        13.28         3.91        17.59 
TCGA-16-1055 TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1392 TCGA-19-1786 
       10.29        21.24        11.77         9.07         3.65         7.17 
TCGA-19-1789 TCGA-19-2620 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 
        3.25         4.87        17.19         8.02         4.73         1.78 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1799 TCGA-26-5139 TCGA-27-1833 TCGA-27-2518 
        3.98        28.54         9.37         1.58        24.23        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 
       18.08        10.39         7.59        15.78         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        8.48         1.22         0.66         6.74         7.30         5.26 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-32-1970 
       17.88         2.53        23.44        13.64         5.16        15.39 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 TCGA-32-2495 
        0.10        15.85        19.50         4.67        14.86        15.02 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-5222 TCGA-41-2572 TCGA-41-3393 
        8.84        25.18        21.14        19.23        13.35         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12         4.08         1.45        25.58 
TCGA-74-6578 TCGA-76-4934 TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 
       14.33         2.53        11.38         4.83        23.90        18.64 
TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         6.28        20.55 

$`AMP PEAK 24(19Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        18.35        35.41        20.71        82.59 
TCGA-02-0016 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       87.06        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       14.14        10.52         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 
       12.59         2.50         8.35         9.57         6.02        28.70 
TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0258 
        3.48        65.00        17.65        99.98        15.65        16.54 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.47         3.98        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 
       16.80        12.92        15.32        20.32        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        14.30        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 TCGA-06-0154 
       10.29         2.20        11.74        20.09         8.61        13.94 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 
       13.12         4.04        91.00        88.14        69.90        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 
       44.58        15.42         4.67         7.40         5.56         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       48.69         9.01         9.57         3.16        12.62         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.80         2.10        14.20         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       43.46        46.19         7.17        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       23.93        26.79        11.84        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 
       12.49         4.93        17.65        12.56         5.95         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        4.54         8.81         2.73         3.75         6.15         4.57 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 
        7.79         5.39         1.48       120.56         7.36        12.85 
TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 
        4.77         4.77         4.96        26.79         1.87         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
       14.60        17.72        22.68        37.84       115.86         1.74 
TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 
        8.42        12.16        29.23        65.33         8.42        17.95 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 
       37.58        22.29         3.39        14.93        15.35         0.72 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-12-0615 
       42.15        19.59        58.68        10.75         4.80        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 
        0.10        38.17        12.13         3.65        43.23         7.63 
TCGA-12-0776 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
        9.73        91.76        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 
       15.98         9.11        14.53         3.98        59.77        44.02 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        6.21        23.05         2.24         3.25         1.35         2.89 
TCGA-14-0865 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       16.50        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 
        3.78         3.42        13.78        50.53        53.19        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 
       16.37         4.31        29.03         4.57        14.01         9.14 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       13.97         6.41        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         5.95        12.95         4.64        25.38 
TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
       12.66         0.13         9.67         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        4.08        24.23         7.00         7.04         6.64        18.90 
TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
       12.10        22.49        14.07        16.80        14.96        17.79 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 
       10.03        13.87         9.73        31.33         7.13         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 TCGA-26-6174 
       14.86         5.49         8.88        18.97         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
       19.33         5.06        16.60         9.86        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       30.05        14.04        11.51        16.08         2.86        14.40 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        0.20         2.53         8.35         1.55         2.83         0.13 
TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
        4.77        14.93        11.28        11.77        31.27        11.01 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
       22.68        10.49         5.42        21.07         0.49         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 
       12.69        16.93        12.23        20.78        15.95         7.36 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       22.78         3.72        12.59        19.86        10.85         0.85 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        8.94         9.53         0.99        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-76-6664 
       17.06         8.35        20.98         5.03        34.45        36.20 
TCGA-81-5910 TCGA-OX-A56R 
        1.61         5.92 

  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                       92.65                       127.59 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                       13.71                        11.77 
[1] "0.1 - 92.7 (13.7)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                              cls
clus                             0   1
  AMP PEAK 24(19Q12) MUTATED    87 127
  AMP PEAK 24(19Q12) WILD-TYPE 137 220
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED     87  127
  AMP PEAK 24(19Q12) WILD-TYPE  137  220
        clus
vv       AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  FEMALE                         87                          137
  MALE                          127                          220
[1] 2 2
[1] FALSE
D24V4, binary
                              cls
clus                             0   1
  AMP PEAK 24(19Q12) MUTATED    21 182
  AMP PEAK 24(19Q12) WILD-TYPE  53 292
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED     21  182
  AMP PEAK 24(19Q12) WILD-TYPE   53  292
     clus
vv    AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  NO                          21                           53
  YES                        182                          292
[1] 2 2
[1] FALSE
D24V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 24(19Q12) MUTATED                              13
  AMP PEAK 24(19Q12) WILD-TYPE                            15
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 24(19Q12) MUTATED                     8
  AMP PEAK 24(19Q12) WILD-TYPE                  10
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 24(19Q12) MUTATED                               193
  AMP PEAK 24(19Q12) WILD-TYPE                             332
D24V6, multiclass
                                 clus
vv                                AMP PEAK 24(19Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           13
  TREATED PRIMARY GBM                                      8
  UNTREATED PRIMARY (DE NOVO) GBM                        193
                                 clus
vv                                AMP PEAK 24(19Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             15
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          332
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19Q12) MUTATED       6                        20   180
  AMP PEAK 24(19Q12) WILD-TYPE     7                        30   305
D24V7, multiclass
                           clus
vv                          AMP PEAK 24(19Q12) MUTATED
  ASIAN                                              6
  BLACK OR AFRICAN AMERICAN                         20
  WHITE                                            180
                           clus
vv                          AMP PEAK 24(19Q12) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           30
  WHITE                                              305
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(19Q12) MUTATED     6 179
  AMP PEAK 24(19Q12) WILD-TYPE   6 294
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED      6  179
  AMP PEAK 24(19Q12) WILD-TYPE    6  294
                        clus
vv                       AMP PEAK 24(19Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        179
                        clus
vv                       AMP PEAK 24(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          294
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(21Q21.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(21Q21.1) MUTATED     9  60
  AMP PEAK 25(21Q21.1) WILD-TYPE  91 410
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            69                            501 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            60                            410 
$`AMP PEAK 25(21Q21.1) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0025 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
       11.77        18.35        42.74         2.50         9.57        28.70 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0113 TCGA-02-0333 TCGA-02-0337 
       20.84        27.25        89.72        92.65         4.37        25.12 
TCGA-06-0130 TCGA-06-0140 TCGA-06-0149 TCGA-06-0151 TCGA-06-0159 TCGA-06-0164 
       12.95         0.20         8.61        46.59         9.44        56.91 
TCGA-06-0168 TCGA-06-0176 TCGA-06-0177 TCGA-06-0188 TCGA-06-0189 TCGA-06-0197 
       19.66        91.00         4.18        44.58        15.42         5.56 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0644 TCGA-06-0743 TCGA-06-1086 TCGA-06-1087 
       24.16        13.64        12.62        26.40         6.84         4.04 
TCGA-06-1806 TCGA-06-2565 TCGA-06-2567 TCGA-06-5856 TCGA-06-6698 TCGA-08-0246 
       15.32        16.64         4.37         3.75         4.77         4.18 
TCGA-08-0386 TCGA-08-0510 TCGA-12-0619 TCGA-12-0822 TCGA-12-1095 TCGA-12-1602 
       18.02         4.27        34.92        23.51        15.85         6.77 
TCGA-12-3646 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1454 TCGA-16-0846 
       44.02         2.04        28.93        15.95        30.18         3.91 
TCGA-19-1392 TCGA-19-1787 TCGA-19-5954 TCGA-19-A6J4 TCGA-27-1832 TCGA-27-2526 
        3.65        12.66        12.10         3.98         9.86         2.86 
TCGA-27-2527 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 
       14.40         6.74         4.77        11.28        11.01        13.64 
TCGA-28-5218 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-41-2575 
        5.16        15.95         8.84        22.78         3.72         9.53 
TCGA-41-3915 TCGA-4W-AA9S TCGA-76-6657 
       11.84         1.45         5.03 

$`AMP PEAK 25(21Q21.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        4.73        23.18        10.59        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 
       20.61        87.06        77.65        20.12        53.10        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0083 TCGA-02-0084 
       26.43        25.05         5.49        10.19        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       65.00        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0338 
        7.73        10.62         7.33        15.91        25.71        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        33.67        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       20.09        17.79        10.09        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
       10.45         3.19        10.82        11.80         3.42        10.65 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
        5.85         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         4.67         7.40         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       35.11         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       12.56        30.64         5.95         5.98         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
       12.85         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97         0.72        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        18.48        10.62        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       21.73        15.98        12.23         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
        4.14        15.65        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1037 TCGA-14-1043 
        5.39         2.89        16.50        26.33        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19        13.28        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1789 
        5.95        12.95         4.64        25.38         7.17         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
        8.02        18.90         4.73         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
       19.33         5.06        16.60        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        0.13         0.66         7.30         5.26        14.93        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 
        2.53        11.77        31.27        23.44        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 
       12.23        20.78        15.02         7.36        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        8.94         0.99         4.44         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.08        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 
       11.38        17.06         8.35        20.98         4.83        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                         92.65                         127.59 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                         12.10                          12.23 
[1] "0.2 - 92.7 (12.1)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                                cls
clus                               0   1
  AMP PEAK 25(21Q21.1) MUTATED    27  42
  AMP PEAK 25(21Q21.1) WILD-TYPE 197 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED     27   42
  AMP PEAK 25(21Q21.1) WILD-TYPE  197  305
        clus
vv       AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE
  FEMALE                           27                            197
  MALE                             42                            305
[1] 2 2
[1] FALSE
D25V4, binary
                                cls
clus                               0   1
  AMP PEAK 25(21Q21.1) MUTATED    10  56
  AMP PEAK 25(21Q21.1) WILD-TYPE  64 418
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED     10   56
  AMP PEAK 25(21Q21.1) WILD-TYPE   64  418
     clus
vv    AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE
  NO                            10                             64
  YES                           56                            418
[1] 2 2
[1] FALSE
D25V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 25(21Q21.1) MUTATED                               6
  AMP PEAK 25(21Q21.1) WILD-TYPE                            22
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 25(21Q21.1) MUTATED                     1
  AMP PEAK 25(21Q21.1) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 25(21Q21.1) MUTATED                                62
  AMP PEAK 25(21Q21.1) WILD-TYPE                             463
D25V6, multiclass
                                 clus
vv                                AMP PEAK 25(21Q21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           62
                                 clus
vv                                AMP PEAK 25(21Q21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               22
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(21Q21.1) MUTATED       4                         4    60
  AMP PEAK 25(21Q21.1) WILD-TYPE     9                        46   425
D25V7, multiclass
                           clus
vv                          AMP PEAK 25(21Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               60
                           clus
vv                          AMP PEAK 25(21Q21.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             46
  WHITE                                                425
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                                cls
clus                               0   1
  AMP PEAK 25(21Q21.1) MUTATED     0  61
  AMP PEAK 25(21Q21.1) WILD-TYPE  12 412
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED      0   61
  AMP PEAK 25(21Q21.1) WILD-TYPE   12  412
                        clus
vv                       AMP PEAK 25(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       AMP PEAK 25(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            412
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED    17  79
  DEL PEAK  1(1P36.32) WILD-TYPE  83 391
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            474 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            79                            391 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-02-0015 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 
       20.61        20.12        53.10        42.74        24.59        90.58 
TCGA-02-0051 TCGA-02-0064 TCGA-02-0069 TCGA-02-0114 TCGA-02-0115 TCGA-02-0281 
       15.09        19.73        28.70        99.98        15.65         3.98 
TCGA-02-0446 TCGA-02-2483 TCGA-06-0126 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
        9.27        15.32         6.94         3.42        56.91         5.85 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 TCGA-06-0195 TCGA-06-0208 TCGA-06-0402 
       13.12         4.04        69.90         7.40         8.42         0.26 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 TCGA-06-0879 TCGA-06-1084 
       26.40         7.86         2.70         7.17        40.41        23.93 
TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-2562 TCGA-06-5411 TCGA-06-5859 
        4.04        11.84        15.32        12.56         8.35         4.57 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
      120.56        22.68       115.86        15.35        13.97         0.72 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0517 TCGA-08-0520 TCGA-08-0531 TCGA-12-0688 
        4.27        11.08        58.68        10.75         7.56        26.66 
TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-3649 TCGA-12-3651 
       18.48        15.98        12.23        15.85        15.22        12.69 
TCGA-12-3653 TCGA-14-0786 TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
       14.53        23.05         2.24         2.89        16.50         1.12 
TCGA-14-1453 TCGA-14-1458 TCGA-14-1821 TCGA-15-1449 TCGA-16-0861 TCGA-16-1056 
        1.15         6.67        17.79        13.28         4.31        14.01 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1387 TCGA-19-2619 TCGA-19-2629 TCGA-19-5947 
        0.66        14.27         5.95         9.67        24.23         6.64 
TCGA-19-5950 TCGA-19-5958 TCGA-27-1833 TCGA-27-2521 TCGA-27-2524 TCGA-28-1747 
       17.19        14.07        24.23        10.39         7.59         2.53 
TCGA-28-1750 TCGA-28-1752 TCGA-28-1756 TCGA-28-2502 TCGA-28-5211 TCGA-28-6450 
        8.35         8.48         2.83         0.66        11.77         5.42 
TCGA-32-1977 TCGA-32-2638 TCGA-32-4208 TCGA-41-2575 TCGA-41-4097 TCGA-74-6575 
        0.10        25.18        21.14         9.53         0.20        20.91 
TCGA-76-4931 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-87-5896 TCGA-OX-A56R 
        9.17         8.35        20.98         5.03        26.30         5.92 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0027 TCGA-02-0033 
       20.71        82.59        87.06        77.65        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        8.35         9.57         6.02        26.43        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0116 
       65.00        11.67        17.65        23.18        92.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0451 
       12.39        14.50        10.55        47.11        11.34        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        16.80        12.92        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        6.15        20.38        47.61         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       10.65        19.66         3.29         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
        4.18        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       44.58        15.42        10.42        38.96         4.67         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 
       20.42        48.69        10.82         9.01        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 
        9.80         2.10        23.57        14.20        46.88         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0881 TCGA-06-0882 
        0.92        43.46        46.19         5.65        16.57        20.78 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.76         6.84        26.79        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49         4.93        17.65        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        3.55         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        2.73         3.75         6.15         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
       14.60        17.72        37.84         4.18         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0509 TCGA-08-0512 
        3.39        12.23        14.93        18.02        12.56        42.15 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.59        19.33         4.80         7.27        15.98        18.41 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 
       94.78         0.10        38.17        25.97        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
        9.73        14.93        14.86        91.76        24.79        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1096 TCGA-12-1097 
        5.82         7.59        33.21        21.73         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 
       59.77        44.02        26.93        10.95        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 
       11.24        13.78         3.25         1.35         5.39        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 
        0.92        40.96        12.43         0.99         1.97        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 
        3.42        13.78        50.53        19.10        53.19         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       17.59        26.07        16.37        29.03         4.57        10.29 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 
        8.61         3.39        10.75         9.07        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-4065 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        7.04         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       22.49        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       18.08        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2506 
        9.21         7.63         1.22         1.55         0.13         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
        2.53        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 
       22.68        10.49        15.39        21.07         0.49        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       22.78         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 
        2.70        11.38        17.06         4.83        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-RR-A6KA TCGA-RR-A6KC 
       18.64        36.20         1.61        17.72         6.28        20.55 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        12.395                         12.160 
[1] "0.1 - 120.6 (12.4)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    28  68
  DEL PEAK  1(1P36.32) WILD-TYPE 196 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     28   68
  DEL PEAK  1(1P36.32) WILD-TYPE  196  279
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           28                            196
  MALE                             68                            279
[1] 2 2
[1] FALSE
D26V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    14  79
  DEL PEAK  1(1P36.32) WILD-TYPE  60 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     14   79
  DEL PEAK  1(1P36.32) WILD-TYPE   60  395
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            14                             60
  YES                           79                            395
[1] 2 2
[1] FALSE
D26V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  1(1P36.32) MUTATED                               1
  DEL PEAK  1(1P36.32) WILD-TYPE                            27
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK  1(1P36.32) MUTATED                     4
  DEL PEAK  1(1P36.32) WILD-TYPE                  14
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  1(1P36.32) MUTATED                                91
  DEL PEAK  1(1P36.32) WILD-TYPE                             434
D26V6, multiclass
                                 clus
vv                                DEL PEAK  1(1P36.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        4
  UNTREATED PRIMARY (DE NOVO) GBM                           91
                                 clus
vv                                DEL PEAK  1(1P36.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         14
  UNTREATED PRIMARY (DE NOVO) GBM                            434
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       5                         6    83
  DEL PEAK  1(1P36.32) WILD-TYPE     8                        44   402
D26V7, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               83
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             44
  WHITE                                                402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     1  81
  DEL PEAK  1(1P36.32) WILD-TYPE  11 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      1   81
  DEL PEAK  1(1P36.32) WILD-TYPE   11  392
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            392
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  2(1P36.23) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.23) MUTATED    21 111
  DEL PEAK  2(1P36.23) WILD-TYPE  79 359
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           132                            438 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           111                            359 
$`DEL PEAK  2(1P36.23) MUTATED`
TCGA-02-0015 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0051 
       20.61        20.12        53.10        42.74        90.58        15.09 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0106 TCGA-02-0115 TCGA-02-0281 
       19.73        26.43        28.70        11.67        15.65         3.98 
TCGA-02-0285 TCGA-02-0290 TCGA-02-0446 TCGA-02-2483 TCGA-06-0124 TCGA-06-0137 
       13.87        15.95         9.27        15.32        20.38        26.70 
TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       10.82         3.42        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 
       13.12         4.04        69.90        10.42        38.96         7.40 
TCGA-06-0208 TCGA-06-0219 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 
        8.42         0.72        26.40         7.86         2.70         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       40.41        20.78        23.93         4.04        11.84        15.32 
TCGA-06-1804 TCGA-06-2562 TCGA-06-2565 TCGA-06-5411 TCGA-06-5414 TCGA-06-5415 
       13.61        12.56        16.64         8.35         8.98         8.55 
TCGA-06-5859 TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0375 
        4.57       120.56        22.68       115.86         1.74        12.23 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 TCGA-08-0514 
       18.02        15.35        13.97         0.72         4.27        11.08 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 
       19.33        10.75         7.56        94.78        25.97        26.66 
TCGA-12-0769 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 
       15.06         9.73        14.93        18.48        15.98        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1599 TCGA-12-3649 TCGA-12-3652 TCGA-14-0736 
       15.85        14.53        25.68        15.22        34.92        15.12 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 TCGA-14-1458 
       23.05         2.24         2.89        16.50         1.12         6.67 
TCGA-14-1827 TCGA-14-1829 TCGA-16-0861 TCGA-16-1045 TCGA-16-1056 TCGA-19-0962 
        5.88         7.17         4.31        29.03        14.01         0.66 
TCGA-19-0963 TCGA-19-1386 TCGA-19-1387 TCGA-19-2619 TCGA-19-2620 TCGA-19-2629 
       14.27         9.07         5.95         9.67         4.87        24.23 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5959 TCGA-26-1439 TCGA-26-6173 TCGA-27-1833 
        6.64        17.19        16.80        13.87         7.92        24.23 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 TCGA-28-5211 
       10.39         7.59         8.35         8.48         0.66        11.77 
TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-2634 TCGA-32-2638 TCGA-32-5222 
        5.42         0.10        15.85        22.78        25.18        19.23 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-4W-AA9S TCGA-74-6575 
       13.35         9.53         4.44         0.20         1.45        20.91 
TCGA-76-4928 TCGA-76-4931 TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 
        3.09         9.17        16.70         8.35        20.98         5.03 
TCGA-76-6661 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       23.90         1.61        26.30         5.92         6.28        20.55 

$`DEL PEAK  2(1P36.23) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0026 TCGA-02-0027 
       20.71        82.59        87.06        77.65        24.59        12.16 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73         3.22        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0070 TCGA-02-0071 
       19.86         8.35         9.57         6.02        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 
       65.00        17.65        23.18        92.65        99.98        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0289 
       16.54        16.93        17.72        10.75        14.47        14.20 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       10.55        47.11        11.34        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0125 
       12.92        15.45        20.32         2.70         6.15        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.30        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
        9.44        11.80        10.65         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
        4.18        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       44.58        15.42         4.67         5.56         0.39         7.66 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       23.57        14.20        46.88         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0881 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 
       46.19         5.65        16.57        26.76         6.84        26.79 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5416 TCGA-06-5418 
       11.74         3.55         4.54         8.81         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        3.75         6.15         5.23         7.79         5.39         1.48 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       17.72        37.84         4.18         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 
       24.56        31.10        37.58        22.29         3.39        14.93 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       12.56        42.15        19.59        58.68         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 
       10.45         7.59         0.10        38.17        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 
       20.38        28.41        53.85        43.23         7.63        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1096 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 
       21.73         9.11         3.98         4.14        15.65        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        44.02        26.93        10.95        12.69 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0783 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        6.21        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.38         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18         0.92        40.96        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-2554 TCGA-14-2555 
        1.97        17.79        17.85         7.63        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 
       13.28         3.91        17.59        26.07        16.37         4.57 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       10.29         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0964 TCGA-19-1385 TCGA-19-1388 TCGA-19-1389 
       21.90         8.61         3.39        10.75        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16         4.08         7.00         7.04 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       14.07        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88        18.97         1.58         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 
       14.04        11.51        24.76        18.08        16.08         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       14.40        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         2.83         0.13         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1979 TCGA-32-1980 
       10.49        15.39        21.07         0.49        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-4208 TCGA-32-4210 
       15.02        15.95         7.36         8.84        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 
       12.59        19.86        10.85         0.85         8.94         0.99 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 
       11.84        15.12        12.46         4.08        25.58         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        3.65         2.53        36.85         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 
       17.06         4.83        34.45        18.64        36.20        17.72 

  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                        13.480                         11.935 
[1] "0.1 - 120.6 (13.5)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    39  93
  DEL PEAK  2(1P36.23) WILD-TYPE 185 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     39   93
  DEL PEAK  2(1P36.23) WILD-TYPE  185  254
        clus
vv       DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  FEMALE                           39                            185
  MALE                             93                            254
[1] 2 2
[1] FALSE
D27V4, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    18 111
  DEL PEAK  2(1P36.23) WILD-TYPE  56 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     18  111
  DEL PEAK  2(1P36.23) WILD-TYPE   56  363
     clus
vv    DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  NO                            18                             56
  YES                          111                            363
[1] 2 2
[1] FALSE
D27V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  2(1P36.23) MUTATED                               4
  DEL PEAK  2(1P36.23) WILD-TYPE                            24
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK  2(1P36.23) MUTATED                     3
  DEL PEAK  2(1P36.23) WILD-TYPE                  15
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  2(1P36.23) MUTATED                               125
  DEL PEAK  2(1P36.23) WILD-TYPE                             400
D27V6, multiclass
                                 clus
vv                                DEL PEAK  2(1P36.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          125
                                 clus
vv                                DEL PEAK  2(1P36.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            400
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.23) MUTATED       6                        11   111
  DEL PEAK  2(1P36.23) WILD-TYPE     7                        39   374
D27V7, multiclass
                           clus
vv                          DEL PEAK  2(1P36.23) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              111
                           clus
vv                          DEL PEAK  2(1P36.23) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                374
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED     1 111
  DEL PEAK  2(1P36.23) WILD-TYPE  11 362
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED      1  111
  DEL PEAK  2(1P36.23) WILD-TYPE   11  362
                        clus
vv                       DEL PEAK  2(1P36.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       DEL PEAK  2(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            362
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  3(1P32.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P32.3) MUTATED    11  49
  DEL PEAK  3(1P32.3) WILD-TYPE  89 421
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           510 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           49                           421 
$`DEL PEAK  3(1P32.3) MUTATED`
TCGA-02-0028 TCGA-02-0059 TCGA-02-0074 TCGA-02-0115 TCGA-02-0269 TCGA-02-0281 
       90.58         9.57        10.19        15.65        10.75         3.98 
TCGA-02-0333 TCGA-02-0446 TCGA-02-2483 TCGA-02-2486 TCGA-06-0188 TCGA-06-0194 
        4.37         9.27        15.32        20.32        44.58         4.67 
TCGA-06-0241 TCGA-06-0410 TCGA-06-0646 TCGA-06-0649 TCGA-06-0743 TCGA-06-0749 
       48.69         4.70         5.75         2.10        26.40         2.70 
TCGA-06-0750 TCGA-06-1802 TCGA-06-2561 TCGA-06-2567 TCGA-06-5411 TCGA-08-0244 
        0.92        15.32        17.65         4.37         8.35        22.68 
TCGA-08-0344 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 TCGA-08-0529 TCGA-12-0654 
      115.86        13.97         0.72         4.27        18.41         7.59 
TCGA-12-0773 TCGA-12-0776 TCGA-12-1092 TCGA-12-3649 TCGA-14-0813 TCGA-14-1452 
       43.23         9.73        21.73        15.22         1.35         7.10 
TCGA-14-1455 TCGA-14-1458 TCGA-14-1795 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 
        0.92         6.67         1.97        29.03         5.95        25.38 
TCGA-19-2619 TCGA-19-2629 TCGA-19-5958 TCGA-26-1440 TCGA-26-1799 TCGA-26-5134 
        9.67        24.23        14.07         9.73         9.37         5.49 
TCGA-27-2521 TCGA-27-2527 TCGA-28-2514 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       10.39        14.40         5.26        31.27        11.01        13.64 
TCGA-28-5220 TCGA-41-4097 TCGA-74-6575 TCGA-76-4931 TCGA-76-6282 TCGA-OX-A56R 
       10.49         0.20        20.91         9.17        17.06         5.92 

$`DEL PEAK  3(1P32.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        24.59        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       65.00        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 
       48.95        16.54        16.93        17.72        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        47.11        11.34        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       16.80        12.92        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.11        12.62         5.75         9.80        23.57        14.20 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
       46.88         7.86         2.70        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        6.84         4.04        26.79        11.84        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        3.55         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 
        3.12         2.56        14.60        17.72        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       15.35        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 
       19.33        10.75         4.80         7.27        15.98         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 
       15.35        14.73        12.99        34.92        10.45        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 
       20.38        28.41        15.06        53.85         7.63        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        44.02        26.93        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 
        1.12         3.75        32.05        58.78        23.11         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 
       30.18        40.96        12.43         0.99        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1047 
        3.91        17.59        26.07        16.37         4.31         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07        12.95         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
       12.66         3.25         0.13         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5135 
       13.87        31.33         7.13         9.40        14.86         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
        2.86        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         4.77         7.30        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       17.88         2.53        11.77        23.44         5.16        22.68 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 
        7.50         4.80         4.54         3.09         3.65         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 
       36.85        16.70         3.29         2.70        11.38         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       36.20         1.61        17.72        26.30         6.28        20.55 

  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                          0.2                           0.1 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                       115.86                        127.59 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                         9.96                         12.36 
[1] "0.2 - 115.9 (10.0)" "0.1 - 127.6 (12.4)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED    18  42
  DEL PEAK  3(1P32.3) WILD-TYPE 206 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     18   42
  DEL PEAK  3(1P32.3) WILD-TYPE  206  305
        clus
vv       DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  FEMALE                          18                           206
  MALE                            42                           305
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED    10  49
  DEL PEAK  3(1P32.3) WILD-TYPE  64 425
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     10   49
  DEL PEAK  3(1P32.3) WILD-TYPE   64  425
     clus
vv    DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  NO                           10                            64
  YES                          49                           425
[1] 2 2
[1] FALSE
D28V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  3(1P32.3) MUTATED                               1
  DEL PEAK  3(1P32.3) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK  3(1P32.3) MUTATED                     2
  DEL PEAK  3(1P32.3) WILD-TYPE                  16
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  3(1P32.3) MUTATED                                57
  DEL PEAK  3(1P32.3) WILD-TYPE                             468
D28V6, multiclass
                                 clus
vv                                DEL PEAK  3(1P32.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          57
                                 clus
vv                                DEL PEAK  3(1P32.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P32.3) MUTATED       3                         4    51
  DEL PEAK  3(1P32.3) WILD-TYPE    10                        46   434
D28V7, multiclass
                           clus
vv                          DEL PEAK  3(1P32.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              51
                           clus
vv                          DEL PEAK  3(1P32.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               434
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED     1  48
  DEL PEAK  3(1P32.3) WILD-TYPE  11 425
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED      1   48
  DEL PEAK  3(1P32.3) WILD-TYPE   11  425
                        clus
vv                       DEL PEAK  3(1P32.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          48
                        clus
vv                       DEL PEAK  3(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           425
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  4(1P22.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(1P22.1) MUTATED     7  40
  DEL PEAK  4(1P22.1) WILD-TYPE  93 430
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           523 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           40                           430 
$`DEL PEAK  4(1P22.1) MUTATED`
TCGA-02-0015 TCGA-02-0024 TCGA-02-0027 TCGA-02-0028 TCGA-02-0038 TCGA-02-0043 
       20.61        53.10        12.16        90.58        10.72        18.31 
TCGA-02-0083 TCGA-02-0451 TCGA-06-0122 TCGA-06-0133 TCGA-06-0169 TCGA-06-0175 
       22.72        16.21         6.15        14.30         3.29         4.04 
TCGA-06-1802 TCGA-06-2565 TCGA-06-5411 TCGA-06-A5U1 TCGA-08-0244 TCGA-08-0344 
       15.32        16.64         8.35         1.87        22.68       115.86 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0392 TCGA-08-0510 TCGA-12-0615 TCGA-12-0691 
       25.71        12.16         0.72         4.27        15.35        12.13 
TCGA-12-0819 TCGA-12-0827 TCGA-12-3652 TCGA-14-1452 TCGA-16-1047 TCGA-16-1055 
       24.79        38.76        34.92         7.10         4.57        10.29 
TCGA-16-1062 TCGA-19-0964 TCGA-19-1387 TCGA-19-1390 TCGA-19-2619 TCGA-19-2629 
       21.24         3.39         5.95        25.38         9.67        24.23 
TCGA-19-5953 TCGA-19-5959 TCGA-26-1440 TCGA-27-1837 TCGA-28-2502 TCGA-28-5208 
        4.73        16.80         9.73        14.04         0.66        17.88 
TCGA-28-5213 TCGA-32-4719 TCGA-41-5651 TCGA-74-6575 TCGA-76-6285 
       31.27        10.85        15.12        20.91         8.35 

$`DEL PEAK  4(1P22.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       20.71        82.59        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0039 TCGA-02-0046 
       24.59         2.83        14.14         3.62        10.52         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       89.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 
       14.50        10.55        47.11        11.34         9.27         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 
       56.91        10.65         5.85        19.66        13.12         4.47 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.22        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
       23.93         6.84         4.04        26.79        11.84        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       12.56        30.64         5.95         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 
       26.79         3.12         2.56        14.60        17.72        37.84 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.18         1.74         8.42         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       13.97        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       94.78         0.10        38.17        25.97        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 
        9.73        14.93        14.86        91.76        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        27.78         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1056 
       17.59        26.07        16.37         4.31        29.03        14.01 
TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
        9.14        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 
        0.66        14.27        10.75         9.07        12.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        3.65         7.17        12.66         3.25         0.13         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19         8.02        18.90        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       22.49        14.07        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       40.54        21.30        30.05        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         2.83         0.13         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        11.28         2.53        11.77 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84         0.20        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                         0.66                          0.10 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                       115.86                        127.59 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                        14.30                         11.97 
[1] "0.7 - 115.9 (14.3)" "0.1 - 127.6 (12.0)"
[1] "hr=" "1.1"
D29V2, continuous
D29V3, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED    18  29
  DEL PEAK  4(1P22.1) WILD-TYPE 206 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED     18   29
  DEL PEAK  4(1P22.1) WILD-TYPE  206  318
        clus
vv       DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  FEMALE                          18                           206
  MALE                            29                           318
[1] 2 2
[1] FALSE
D29V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED     6  39
  DEL PEAK  4(1P22.1) WILD-TYPE  68 435
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED      6   39
  DEL PEAK  4(1P22.1) WILD-TYPE   68  435
     clus
vv    DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  NO                            6                            68
  YES                          39                           435
[1] 2 2
[1] FALSE
D29V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  4(1P22.1) MUTATED                               1
  DEL PEAK  4(1P22.1) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK  4(1P22.1) MUTATED                     4
  DEL PEAK  4(1P22.1) WILD-TYPE                  14
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  4(1P22.1) MUTATED                                42
  DEL PEAK  4(1P22.1) WILD-TYPE                             483
D29V6, multiclass
                                 clus
vv                                DEL PEAK  4(1P22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       4
  UNTREATED PRIMARY (DE NOVO) GBM                          42
                                 clus
vv                                DEL PEAK  4(1P22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        14
  UNTREATED PRIMARY (DE NOVO) GBM                           483
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1P22.1) MUTATED       1                         4    39
  DEL PEAK  4(1P22.1) WILD-TYPE    12                        46   446
D29V7, multiclass
                           clus
vv                          DEL PEAK  4(1P22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              39
                           clus
vv                          DEL PEAK  4(1P22.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED     1  40
  DEL PEAK  4(1P22.1) WILD-TYPE  11 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED      1   40
  DEL PEAK  4(1P22.1) WILD-TYPE   11  433
                        clus
vv                       DEL PEAK  4(1P22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       DEL PEAK  4(1P22.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           433
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  5(1Q42.11) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(1Q42.11) MUTATED     9  40
  DEL PEAK  5(1Q42.11) WILD-TYPE  91 430
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            49                            521 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            40                            430 
$`DEL PEAK  5(1Q42.11) MUTATED`
TCGA-02-0084 TCGA-02-0099 TCGA-02-0106 TCGA-02-0281 TCGA-02-0333 TCGA-02-0446 
       12.62         3.48        11.67         3.98         4.37         9.27 
TCGA-02-2466 TCGA-06-0126 TCGA-06-0190 TCGA-06-0238 TCGA-06-0402 TCGA-06-1084 
       16.80         6.94        10.42        13.32         0.26        23.93 
TCGA-06-1802 TCGA-06-1806 TCGA-06-2558 TCGA-06-5411 TCGA-06-6390 TCGA-08-0246 
       15.32        15.32        12.49         8.35         5.39         4.18 
TCGA-08-0392 TCGA-08-0510 TCGA-12-0620 TCGA-12-0656 TCGA-12-0776 TCGA-12-1599 
        0.72         4.27        10.45        94.78         9.73        25.68 
TCGA-14-0740 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-1034 TCGA-14-1395 
       11.97        13.78         3.25         5.39        15.95         1.38 
TCGA-14-1450 TCGA-19-0957 TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 
       58.78        21.90         0.66         5.95        12.95        25.38 
TCGA-19-2619 TCGA-19-2629 TCGA-19-A6J5 TCGA-26-5133 TCGA-27-2524 TCGA-28-2502 
        9.67        24.23        28.54        14.86         7.59         0.66 
TCGA-32-1977 TCGA-32-1986 TCGA-32-1987 TCGA-74-6575 TCGA-74-6577 TCGA-76-6193 
        0.10        12.69        14.86        20.91         4.34         2.70 
TCGA-RR-A6KA 
        6.28 

$`DEL PEAK  5(1Q42.11) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        51.32         8.81        57.76        16.96 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        65.00        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 
        7.73        10.62         7.33        15.91        25.71        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 
        2.70         6.15        20.38        47.61         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        44.58        15.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       13.64        20.42        48.69        10.82         9.01        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
       26.76         6.84         4.04        26.79        11.84        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.74         3.55         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        7.79         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
       34.92         7.59         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        4.14        15.65        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        15.12         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
       23.05         2.24        11.24         1.35         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1396 
       26.33         2.04        28.93        19.30         0.79         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
        3.75        32.05        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42        13.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19        13.28         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0963 
       21.24        13.97         6.41        11.77         8.61        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
        3.39        10.75         9.07         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
       12.66         3.25         0.13         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 
       14.07        16.80        14.96        17.79         3.98        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        1.55         2.83         0.13         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 
       10.49         5.42        15.39        21.07         0.49        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
       19.50         1.18         4.67        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
       11.84         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       25.58         3.45        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92        20.55 

  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                         94.78                         127.59 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                         10.42                          12.23 
[1] "0.1 - 94.8 (10.4)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED    19  30
  DEL PEAK  5(1Q42.11) WILD-TYPE 205 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED     19   30
  DEL PEAK  5(1Q42.11) WILD-TYPE  205  317
        clus
vv       DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  FEMALE                           19                            205
  MALE                             30                            317
[1] 2 2
[1] FALSE
D30V4, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED     8  38
  DEL PEAK  5(1Q42.11) WILD-TYPE  66 436
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED      8   38
  DEL PEAK  5(1Q42.11) WILD-TYPE   66  436
     clus
vv    DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  NO                             8                             66
  YES                           38                            436
[1] 2 2
[1] FALSE
D30V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  5(1Q42.11) MUTATED                               3
  DEL PEAK  5(1Q42.11) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK  5(1Q42.11) MUTATED                     1
  DEL PEAK  5(1Q42.11) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  5(1Q42.11) MUTATED                                45
  DEL PEAK  5(1Q42.11) WILD-TYPE                             480
D30V6, multiclass
                                 clus
vv                                DEL PEAK  5(1Q42.11) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           45
                                 clus
vv                                DEL PEAK  5(1Q42.11) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            480
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(1Q42.11) MUTATED       0                         6    39
  DEL PEAK  5(1Q42.11) WILD-TYPE    13                        44   446
D30V7, multiclass
                           clus
vv                          DEL PEAK  5(1Q42.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               39
                           clus
vv                          DEL PEAK  5(1Q42.11) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             44
  WHITE                                                446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED     2  37
  DEL PEAK  5(1Q42.11) WILD-TYPE  10 436
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED      2   37
  DEL PEAK  5(1Q42.11) WILD-TYPE   10  436
                        clus
vv                       DEL PEAK  5(1Q42.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK  5(1Q42.11) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            436
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  6(1Q44) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  6(1Q44) MUTATED     8  26
  DEL PEAK  6(1Q44) WILD-TYPE  92 444
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         536 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         26                         444 
$`DEL PEAK  6(1Q44) MUTATED`
TCGA-02-0026 TCGA-02-0084 TCGA-02-0333 TCGA-02-2466 TCGA-02-2485 TCGA-06-0145 
       24.59        12.62         4.37        16.80        15.45         2.33 
TCGA-06-0149 TCGA-06-1806 TCGA-06-2558 TCGA-06-5411 TCGA-08-0386 TCGA-08-0392 
        8.61        15.32        12.49         8.35        18.02         0.72 
TCGA-08-0510 TCGA-12-0776 TCGA-12-0780 TCGA-12-3648 TCGA-14-0740 TCGA-14-0812 
        4.27         9.73        14.86        26.93        11.97         3.25 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1456 TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 
       15.95         1.38        40.96         0.66         5.95        12.95 
TCGA-19-1390 TCGA-19-2619 TCGA-19-A6J5 TCGA-26-5133 TCGA-28-5215 TCGA-32-1986 
       25.38         9.67        28.54        14.86        11.01        12.69 
TCGA-74-6575 TCGA-74-6577 TCGA-76-4925 TCGA-76-6193 
       20.91         4.34         4.80         2.70 

$`DEL PEAK  6(1Q44) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
       25.71        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 
       47.11        11.34         9.27        16.21         3.35        12.92 
TCGA-02-2483 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.32        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 
        2.20        11.74        20.09        17.79        10.09        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.74         3.55         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56        14.60        17.72        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 
       12.23        14.93        15.35        13.97        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        15.06        53.85        43.23         7.63        14.93 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        44.02        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       28.93        19.30         0.79         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         8.61        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       10.75         9.07         4.64         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         0.13         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 
       14.07        16.80        14.96        17.79         3.98        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        2.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 
        0.10        15.85        19.50         1.18         4.67        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6578 
       12.46         4.08         1.45        25.58         3.45        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        2.53        36.85        16.70         3.29        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                       0.66                        0.10 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                      40.96                      127.59 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                     12.230                      12.195 
[1] "0.7 - 41.0 (12.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED    13  21
  DEL PEAK  6(1Q44) WILD-TYPE 211 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED     13   21
  DEL PEAK  6(1Q44) WILD-TYPE  211  326
        clus
vv       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  FEMALE                        13                         211
  MALE                          21                         326
[1] 2 2
[1] FALSE
D31V4, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED     6  27
  DEL PEAK  6(1Q44) WILD-TYPE  68 447
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED      6   27
  DEL PEAK  6(1Q44) WILD-TYPE   68  447
     clus
vv    DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  NO                          6                          68
  YES                        27                         447
[1] 2 2
[1] FALSE
D31V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK  6(1Q44) MUTATED                               2                   1
  DEL PEAK  6(1Q44) WILD-TYPE                            26                  17
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  6(1Q44) MUTATED                                31
  DEL PEAK  6(1Q44) WILD-TYPE                             494
D31V6, multiclass
                                 clus
vv                                DEL PEAK  6(1Q44) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           2
  TREATED PRIMARY GBM                                     1
  UNTREATED PRIMARY (DE NOVO) GBM                        31
                                 clus
vv                                DEL PEAK  6(1Q44) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            26
  TREATED PRIMARY GBM                                      17
  UNTREATED PRIMARY (DE NOVO) GBM                         494
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(1Q44) MUTATED       0                         3    27
  DEL PEAK  6(1Q44) WILD-TYPE    13                        47   458
D31V7, multiclass
                           clus
vv                          DEL PEAK  6(1Q44) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            27
                           clus
vv                          DEL PEAK  6(1Q44) WILD-TYPE
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                          47
  WHITE                                             458
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED     1  24
  DEL PEAK  6(1Q44) WILD-TYPE  11 449
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED      1   24
  DEL PEAK  6(1Q44) WILD-TYPE   11  449
                        clus
vv                       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        24                         449
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  7(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q22.1) MUTATED     5  42
  DEL PEAK  7(2Q22.1) WILD-TYPE  95 428
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           523 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           42                           428 
$`DEL PEAK  7(2Q22.1) MUTATED`
TCGA-02-0024 TCGA-02-0059 TCGA-02-0074 TCGA-02-0075 TCGA-02-0289 TCGA-02-0338 
       53.10         9.57        10.19        20.84        14.20        10.59 
TCGA-02-2466 TCGA-06-0152 TCGA-06-0182 TCGA-06-0188 TCGA-06-0414 TCGA-06-0649 
       16.80        12.33         3.65        44.58        35.11         2.10 
TCGA-06-0749 TCGA-06-1087 TCGA-06-5416 TCGA-06-5856 TCGA-06-6390 TCGA-06-6694 
        2.70         4.04         6.71         3.75         5.39         7.36 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-12-0615 TCGA-12-0821 TCGA-12-0826 TCGA-12-1099 
        1.87         3.12        15.35        10.62        27.78         4.14 
TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 TCGA-14-0812 
       15.65        14.73        44.02        15.12         6.21         3.25 
TCGA-14-0867 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 TCGA-19-1390 
        2.04        50.53        53.19        16.37        12.95        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-26-A7UX TCGA-28-2509 TCGA-28-5215 
        3.65         4.08        22.49        19.33         4.77        11.01 
TCGA-32-1978 TCGA-32-2615 TCGA-4W-AA9R TCGA-76-4934 TCGA-76-6191 
       15.85        15.95         4.08         2.53        16.70 

$`DEL PEAK  7(2Q22.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
        3.98        13.87        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        4.18        88.14        20.25        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        7.79         1.48       120.56         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-06-A7TK 
        1.55         4.77         4.96        26.79         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       17.72        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       91.76        24.79        18.48        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68         6.77        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        1.35         5.39         2.89        16.50        26.33        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
        7.96         3.78         3.42        13.78        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91        17.59        26.07         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 
       10.75         9.07         5.95         4.64         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        23.44        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       36.85         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                         1.87                          0.10 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                        53.19                        127.59 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                        11.01                         12.23 
[1] "1.9 - 53.2 (11.0)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    21  26
  DEL PEAK  7(2Q22.1) WILD-TYPE 203 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     21   26
  DEL PEAK  7(2Q22.1) WILD-TYPE  203  321
        clus
vv       DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  FEMALE                          21                           203
  MALE                            26                           321
[1] 2 2
[1] FALSE
D32V4, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    10  35
  DEL PEAK  7(2Q22.1) WILD-TYPE  64 439
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     10   35
  DEL PEAK  7(2Q22.1) WILD-TYPE   64  439
     clus
vv    DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  NO                           10                            64
  YES                          35                           439
[1] 2 2
[1] FALSE
D32V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  7(2Q22.1) MUTATED                               5
  DEL PEAK  7(2Q22.1) WILD-TYPE                            23
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK  7(2Q22.1) MUTATED                     2
  DEL PEAK  7(2Q22.1) WILD-TYPE                  16
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  7(2Q22.1) MUTATED                                40
  DEL PEAK  7(2Q22.1) WILD-TYPE                             485
D32V6, multiclass
                                 clus
vv                                DEL PEAK  7(2Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             5
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          40
                                 clus
vv                                DEL PEAK  7(2Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              23
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           485
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(2Q22.1) MUTATED       0                         7    40
  DEL PEAK  7(2Q22.1) WILD-TYPE    13                        43   445
D32V7, multiclass
                           clus
vv                          DEL PEAK  7(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              40
                           clus
vv                          DEL PEAK  7(2Q22.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            43
  WHITE                                               445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED     0  39
  DEL PEAK  7(2Q22.1) WILD-TYPE  12 434
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED      0   39
  DEL PEAK  7(2Q22.1) WILD-TYPE   12  434
                        clus
vv                       DEL PEAK  7(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       DEL PEAK  7(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           434
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  8(2Q37.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(2Q37.1) MUTATED     7  48
  DEL PEAK  8(2Q37.1) WILD-TYPE  93 422
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           515 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           48                           422 
$`DEL PEAK  8(2Q37.1) MUTATED`
TCGA-02-0025 TCGA-02-0059 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0084 
       42.74         9.57        10.19        20.84        89.72        12.62 
TCGA-02-0104 TCGA-02-0338 TCGA-06-0152 TCGA-06-0182 TCGA-06-0188 TCGA-06-0221 
       65.00        10.59        12.33         3.65        44.58        19.82 
TCGA-06-0414 TCGA-06-0649 TCGA-06-2562 TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 
       35.11         2.10        12.56         6.71         3.75         7.36 
TCGA-06-A6S0 TCGA-08-0351 TCGA-08-0355 TCGA-08-0512 TCGA-12-0703 TCGA-12-0826 
        3.12        65.33        24.56        42.15        20.38        27.78 
TCGA-12-1099 TCGA-12-1600 TCGA-12-3646 TCGA-12-5301 TCGA-14-0783 TCGA-14-0812 
        4.14        14.73        44.02         2.04         6.21         3.25 
TCGA-14-0867 TCGA-14-1821 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 
        2.04        17.79         3.42        50.53        53.19        16.37 
TCGA-16-1047 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 
        4.57        12.95        25.38         3.65         4.08        22.49 
TCGA-27-2521 TCGA-28-1750 TCGA-28-2509 TCGA-28-5215 TCGA-32-1978 TCGA-32-2495 
       10.39         8.35         4.77        11.01        15.85        15.02 
TCGA-32-2615 TCGA-41-3393 TCGA-41-6646 TCGA-4W-AA9R TCGA-76-4934 TCGA-76-6280 
       15.95         4.44        12.46         4.08         2.53        11.38 
TCGA-76-6657 
        5.03 

$`DEL PEAK  8(2Q37.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
        5.49        27.25        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0339 TCGA-02-0422 
       15.91        25.71         4.37        25.12        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       88.14        20.25        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 
       15.32         1.08        12.49         4.93        17.65        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        8.55         2.73         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48       120.56         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 
        1.55         4.77         4.96        26.79         1.87         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
       14.60        17.72        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28         8.42        17.95        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56         4.27        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
       12.13         3.65        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       12.23        15.85         9.11        14.53         3.98        15.65 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68         6.77        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 
       12.69        34.92        14.53        14.93         3.22        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        1.35         5.39         2.89        16.50        26.33        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
        3.78        13.78        19.10        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07         4.31        29.03        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        4.64         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         7.53         0.16        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
       12.10         1.78        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       17.88         2.53        11.77        31.27        23.44        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 
       14.86        16.93        12.23        20.78         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9S TCGA-4W-AA9T 
        0.99        11.84         0.20        15.12         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        4.83        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                         2.04                          0.10 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                        89.72                        127.59 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                        12.33                         12.16 
[1] "2.0 - 89.7 (12.3)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    26  29
  DEL PEAK  8(2Q37.1) WILD-TYPE 198 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     26   29
  DEL PEAK  8(2Q37.1) WILD-TYPE  198  318
        clus
vv       DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  FEMALE                          26                           198
  MALE                            29                           318
[1] 2 2
[1] FALSE
D33V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    10  42
  DEL PEAK  8(2Q37.1) WILD-TYPE  64 432
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     10   42
  DEL PEAK  8(2Q37.1) WILD-TYPE   64  432
     clus
vv    DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  NO                           10                            64
  YES                          42                           432
[1] 2 2
[1] FALSE
D33V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  8(2Q37.1) MUTATED                               3
  DEL PEAK  8(2Q37.1) WILD-TYPE                            25
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK  8(2Q37.1) MUTATED                     1
  DEL PEAK  8(2Q37.1) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  8(2Q37.1) MUTATED                                51
  DEL PEAK  8(2Q37.1) WILD-TYPE                             474
D33V6, multiclass
                                 clus
vv                                DEL PEAK  8(2Q37.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          51
                                 clus
vv                                DEL PEAK  8(2Q37.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              25
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           474
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(2Q37.1) MUTATED       0                         4    50
  DEL PEAK  8(2Q37.1) WILD-TYPE    13                        46   435
D33V7, multiclass
                           clus
vv                          DEL PEAK  8(2Q37.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              50
                           clus
vv                          DEL PEAK  8(2Q37.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED     1  46
  DEL PEAK  8(2Q37.1) WILD-TYPE  11 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED      1   46
  DEL PEAK  8(2Q37.1) WILD-TYPE   11  427
                        clus
vv                       DEL PEAK  8(2Q37.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  8(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           427
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  9(3P21.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P21.1) MUTATED    12  41
  DEL PEAK  9(3P21.1) WILD-TYPE  88 429
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           53                           517 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           41                           429 
$`DEL PEAK  9(3P21.1) MUTATED`
TCGA-02-0014 TCGA-02-0015 TCGA-02-0055 TCGA-02-0083 TCGA-02-0084 TCGA-02-0104 
       82.59        20.61         2.50        22.72        12.62        65.00 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0114 TCGA-02-0266 TCGA-02-0330 TCGA-02-0432 
       11.67        92.65        99.98        17.72        15.91        47.11 
TCGA-02-2486 TCGA-06-0128 TCGA-06-0152 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 
       20.32        22.72        12.33        15.02        24.16        19.82 
TCGA-06-0409 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-5416 TCGA-06-5859 
       72.36         7.86         7.17         4.04         6.71         4.57 
TCGA-06-6390 TCGA-06-A7TL TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 
        5.39        17.72        37.84         4.18        18.02        13.97 
TCGA-08-0516 TCGA-08-0517 TCGA-12-0776 TCGA-12-0826 TCGA-12-3653 TCGA-14-0862 
       19.59        58.68         9.73        27.78        14.53         2.89 
TCGA-14-1458 TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
        6.67        17.85         3.78        53.19        13.28        26.07 
TCGA-16-1047 TCGA-19-0964 TCGA-19-1388 TCGA-19-2625 TCGA-26-1439 TCGA-26-1440 
        4.57         3.39        12.95         4.08        13.87         9.73 
TCGA-28-1752 TCGA-28-1756 TCGA-32-1991 TCGA-32-2615 TCGA-76-4929 
        8.48         2.83        16.93        15.95         3.65 

$`DEL PEAK  9(3P21.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.71        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0085 TCGA-02-0086 
       10.19        20.84        27.25        89.72        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 
       57.76        16.96         3.48        27.02        17.65        23.18 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.54        16.93        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       10.59        12.39        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        2.10        23.57        14.20        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.70         0.92        43.46        46.19         5.65        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
       16.57        20.78        26.76        23.93         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 
        2.73         3.75         6.15         5.23         7.79         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       14.60        22.68       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       12.23        14.93        15.35         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       42.15        11.08        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85        43.23         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
       91.76        24.79        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         5.39        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92        40.96        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 
        3.42        13.78        50.53        19.10         3.91        17.59 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       16.37         4.31        29.03        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
        0.66        14.27        10.75         9.07         5.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 
        9.67         4.87         1.08         7.53         0.16        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 
       14.96        17.79         3.98        28.54        10.03        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        9.21         8.35         7.63         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        14.86        12.23        20.78 
TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.09         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                          2.5                           0.1 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                        99.98                        127.59 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                        14.53                         11.84 
[1] "2.5 - 100.0 (14.5)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.4"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED    22  31
  DEL PEAK  9(3P21.1) WILD-TYPE 202 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED     22   31
  DEL PEAK  9(3P21.1) WILD-TYPE  202  316
        clus
vv       DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  FEMALE                          22                           202
  MALE                            31                           316
[1] 2 2
[1] FALSE
D34V4, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED     4  47
  DEL PEAK  9(3P21.1) WILD-TYPE  70 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED      4   47
  DEL PEAK  9(3P21.1) WILD-TYPE   70  427
     clus
vv    DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  NO                            4                            70
  YES                          47                           427
[1] 2 2
[1] FALSE
D34V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  9(3P21.1) MUTATED                               1
  DEL PEAK  9(3P21.1) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK  9(3P21.1) MUTATED                     3
  DEL PEAK  9(3P21.1) WILD-TYPE                  15
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  9(3P21.1) MUTATED                                49
  DEL PEAK  9(3P21.1) WILD-TYPE                             476
D34V6, multiclass
                                 clus
vv                                DEL PEAK  9(3P21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          49
                                 clus
vv                                DEL PEAK  9(3P21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        15
  UNTREATED PRIMARY (DE NOVO) GBM                           476
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P21.1) MUTATED       0                         6    45
  DEL PEAK  9(3P21.1) WILD-TYPE    13                        44   440
D34V7, multiclass
                           clus
vv                          DEL PEAK  9(3P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              45
                           clus
vv                          DEL PEAK  9(3P21.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED     2  46
  DEL PEAK  9(3P21.1) WILD-TYPE  10 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED      2   46
  DEL PEAK  9(3P21.1) WILD-TYPE   10  427
                        clus
vv                       DEL PEAK  9(3P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  9(3P21.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           427
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 10(3Q13.31) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(3Q13.31) MUTATED     9  47
  DEL PEAK 10(3Q13.31) WILD-TYPE  91 423
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            514 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            47                            423 
$`DEL PEAK 10(3Q13.31) MUTATED`
TCGA-02-0001 TCGA-02-0021 TCGA-02-0054 TCGA-02-0055 TCGA-02-0060 TCGA-02-0069 
       11.77        77.65         6.54         2.50         6.02        28.70 
TCGA-02-0084 TCGA-02-0113 TCGA-02-0330 TCGA-02-0332 TCGA-02-2466 TCGA-06-0128 
       12.62        92.65        15.91        25.71        16.80        22.72 
TCGA-06-0152 TCGA-06-0182 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       12.33         3.65        15.02        24.16         0.72        19.82 
TCGA-06-0409 TCGA-06-1806 TCGA-06-2569 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 
       72.36        15.32         0.43         4.57         7.79         5.39 
TCGA-06-A5U1 TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 
        1.87        37.84         4.18        18.02        13.97        19.59 
TCGA-12-0691 TCGA-12-0773 TCGA-12-0776 TCGA-12-0826 TCGA-12-1089 TCGA-12-1093 
       12.13        43.23         9.73        27.78         5.82        15.98 
TCGA-12-1600 TCGA-12-3651 TCGA-12-3653 TCGA-14-0812 TCGA-14-0871 TCGA-14-1458 
       14.73        12.69        14.53         3.25        28.93         6.67 
TCGA-14-1823 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-19-2621 TCGA-19-A6J4 
       17.85        53.19        13.28        12.95         1.08         3.98 
TCGA-26-1439 TCGA-28-1752 TCGA-28-1757 TCGA-28-5220 TCGA-32-1973 TCGA-32-2615 
       13.87         8.48         0.13        10.49        21.07        15.95 
TCGA-76-4929 TCGA-76-6280 
        3.65        11.38 

$`DEL PEAK 10(3Q13.31) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       82.59        20.61        87.06        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 
       15.09        12.59        19.86         8.35         9.57        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       26.43        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0333 
       12.23         9.90         7.73        10.62         7.33         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27        16.21         3.35        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 
       91.00         4.18        88.14        20.25        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        7.40        11.84         0.53        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.55         6.71         2.73         3.75         6.15         5.23 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96        26.79         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       14.60        17.72        22.68       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
        3.39        12.23        14.93        15.35         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        4.27        42.15        11.08        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       28.41        15.06        53.85         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
       91.76        24.79        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94        20.58       127.59         7.59        33.21        21.73 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       15.22        10.95        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       11.24        13.78         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18         0.92        40.96        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42        13.78        50.53        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07         5.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       17.79        28.54        10.03         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 
        8.35         7.63         1.22         1.55         2.83         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
       13.64         5.16        22.68         5.42        15.39         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 
       14.86        16.93        12.23        20.78        15.02         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                        13.115                         11.935 
[1] "0.1 - 92.7 (13.1)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D35V2, continuous
D35V3, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED    24  32
  DEL PEAK 10(3Q13.31) WILD-TYPE 200 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED     24   32
  DEL PEAK 10(3Q13.31) WILD-TYPE  200  315
        clus
vv       DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  FEMALE                           24                            200
  MALE                             32                            315
[1] 2 2
[1] FALSE
D35V4, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED     6  45
  DEL PEAK 10(3Q13.31) WILD-TYPE  68 429
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED      6   45
  DEL PEAK 10(3Q13.31) WILD-TYPE   68  429
     clus
vv    DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  NO                             6                             68
  YES                           45                            429
[1] 2 2
[1] FALSE
D35V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 10(3Q13.31) MUTATED                               3
  DEL PEAK 10(3Q13.31) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 10(3Q13.31) MUTATED                     2
  DEL PEAK 10(3Q13.31) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 10(3Q13.31) MUTATED                                51
  DEL PEAK 10(3Q13.31) WILD-TYPE                             474
D35V6, multiclass
                                 clus
vv                                DEL PEAK 10(3Q13.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           51
                                 clus
vv                                DEL PEAK 10(3Q13.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            474
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q13.31) MUTATED       2                         6    48
  DEL PEAK 10(3Q13.31) WILD-TYPE    11                        44   437
D35V7, multiclass
                           clus
vv                          DEL PEAK 10(3Q13.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               48
                           clus
vv                          DEL PEAK 10(3Q13.31) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             44
  WHITE                                                437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED     2  47
  DEL PEAK 10(3Q13.31) WILD-TYPE  10 426
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED      2   47
  DEL PEAK 10(3Q13.31) WILD-TYPE   10  426
                        clus
vv                       DEL PEAK 10(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 10(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            426
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 11(3Q22.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(3Q22.1) MUTATED     9  49
  DEL PEAK 11(3Q22.1) WILD-TYPE  91 421
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           512 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           49                           421 
$`DEL PEAK 11(3Q22.1) MUTATED`
TCGA-02-0001 TCGA-02-0026 TCGA-02-0039 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 
       11.77        24.59        10.52         6.54         2.50         9.57 
TCGA-02-0060 TCGA-02-0069 TCGA-02-0084 TCGA-02-0104 TCGA-02-0113 TCGA-02-0115 
        6.02        28.70        12.62        65.00        92.65        15.65 
TCGA-02-0289 TCGA-02-0330 TCGA-06-0128 TCGA-06-0137 TCGA-06-0152 TCGA-06-0182 
       14.20        15.91        22.72        26.70        12.33         3.65 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0409 TCGA-06-1806 TCGA-06-2569 
       15.02        24.16        19.82        72.36        15.32         0.43 
TCGA-06-5415 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-A5U1 TCGA-08-0244 
        8.55         4.57         7.79         5.39         1.87        22.68 
TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 TCGA-12-0691 TCGA-12-0773 
        4.18        18.02        13.97        19.59        12.13        43.23 
TCGA-12-0776 TCGA-12-0826 TCGA-12-1089 TCGA-12-1600 TCGA-12-3651 TCGA-12-3653 
        9.73        27.78         5.82        14.73        12.69        14.53 
TCGA-14-0812 TCGA-14-0871 TCGA-14-1453 TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 
        3.25        28.93         1.15         6.67        17.85        53.19 
TCGA-15-1449 TCGA-19-1388 TCGA-19-2621 TCGA-19-A6J4 TCGA-26-1439 TCGA-28-1752 
       13.28        12.95         1.08         3.98        13.87         8.48 
TCGA-28-1757 TCGA-32-1973 TCGA-32-2615 TCGA-76-4929 
        0.13        21.07        15.95         3.65 

$`DEL PEAK 11(3Q22.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.72        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0057 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
       12.59        19.86         8.35        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 
       11.67        17.65        23.18        99.98        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
        6.15        20.38        47.61         6.94         3.98        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        14.30        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 
        8.42         7.63         7.40        11.84         0.53         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        6.15         5.23         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 TCGA-08-0344 
        3.12         2.56        14.60        17.72        37.84       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
        0.72        12.56         4.27        42.15        11.08        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 
       23.51        38.76         8.94        20.58       127.59         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       14.53         3.98         4.14        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.77        44.02        26.93        15.22        10.95        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        6.21        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        5.39         2.89        16.50        26.33         2.04        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         9.67         4.87         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       16.80        14.96        17.79        28.54        10.03         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
        2.53         9.21         8.35         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        2.83         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
       11.84         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 
        7.50         4.80         4.54         3.09         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                        92.65                        127.59 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                       13.115                        11.935 
[1] "0.1 - 92.7 (13.1)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q22.1) MUTATED    23  35
  DEL PEAK 11(3Q22.1) WILD-TYPE 201 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED     23   35
  DEL PEAK 11(3Q22.1) WILD-TYPE  201  312
        clus
vv       DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE
  FEMALE                          23                           201
  MALE                            35                           312
[1] 2 2
[1] FALSE
D36V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q22.1) MUTATED     6  47
  DEL PEAK 11(3Q22.1) WILD-TYPE  68 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED      6   47
  DEL PEAK 11(3Q22.1) WILD-TYPE   68  427
     clus
vv    DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE
  NO                            6                            68
  YES                          47                           427
[1] 2 2
[1] FALSE
D36V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 11(3Q22.1) MUTATED                               3
  DEL PEAK 11(3Q22.1) WILD-TYPE                            25
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 11(3Q22.1) MUTATED                     2
  DEL PEAK 11(3Q22.1) WILD-TYPE                  16
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 11(3Q22.1) MUTATED                                53
  DEL PEAK 11(3Q22.1) WILD-TYPE                             472
D36V6, multiclass
                                 clus
vv                                DEL PEAK 11(3Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          53
                                 clus
vv                                DEL PEAK 11(3Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              25
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           472
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(3Q22.1) MUTATED       3                         5    50
  DEL PEAK 11(3Q22.1) WILD-TYPE    10                        45   435
D36V7, multiclass
                           clus
vv                          DEL PEAK 11(3Q22.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              50
                           clus
vv                          DEL PEAK 11(3Q22.1) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            45
  WHITE                                               435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q22.1) MUTATED     2  49
  DEL PEAK 11(3Q22.1) WILD-TYPE  10 424
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED      2   49
  DEL PEAK 11(3Q22.1) WILD-TYPE   10  424
                        clus
vv                       DEL PEAK 11(3Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          49
                        clus
vv                       DEL PEAK 11(3Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           424
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 12(3Q29) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(3Q29) MUTATED    10  55
  DEL PEAK 12(3Q29) WILD-TYPE  90 415
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         505 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         55                         415 
$`DEL PEAK 12(3Q29) MUTATED`
TCGA-02-0010 TCGA-02-0021 TCGA-02-0026 TCGA-02-0055 TCGA-02-0084 TCGA-02-0113 
       35.41        77.65        24.59         2.50        12.62        92.65 
TCGA-02-0330 TCGA-02-0332 TCGA-06-0128 TCGA-06-0145 TCGA-06-0152 TCGA-06-0158 
       15.91        25.71        22.72         2.33        12.33        10.82 
TCGA-06-0159 TCGA-06-0175 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        9.44         4.04        15.02        24.16         0.72        19.82 
TCGA-06-0409 TCGA-06-0745 TCGA-06-1806 TCGA-06-2563 TCGA-06-2565 TCGA-06-5415 
       72.36         7.86        15.32        30.64        16.64         8.55 
TCGA-06-5859 TCGA-06-6390 TCGA-06-6693 TCGA-08-0246 TCGA-08-0351 TCGA-08-0386 
        4.57         5.39       120.56         4.18        65.33        18.02 
TCGA-08-0392 TCGA-08-0516 TCGA-08-0531 TCGA-12-0662 TCGA-12-0776 TCGA-12-0826 
        0.72        19.59         7.56        38.17         9.73        27.78 
TCGA-12-0829 TCGA-12-1091 TCGA-12-1098 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       20.58        33.21         3.98        34.92        14.53        14.93 
TCGA-14-0812 TCGA-14-0871 TCGA-14-1821 TCGA-14-1823 TCGA-14-4157 TCGA-15-1447 
        3.25        28.93        17.79        17.85         3.42        53.19 
TCGA-15-1449 TCGA-19-1388 TCGA-19-1390 TCGA-19-2631 TCGA-19-5956 TCGA-19-A6J4 
       13.28        12.95        25.38         7.00        22.49         3.98 
TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-27-2523 TCGA-27-2528 TCGA-28-5220 
       13.87         5.06        10.39        16.08        15.78        10.49 
TCGA-32-2615 TCGA-41-2575 TCGA-74-6581 TCGA-74-6584 TCGA-76-4929 
       15.95         9.53         8.22         7.50         3.65 

$`DEL PEAK 12(3Q29) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       82.59        20.61        87.06        20.12        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         6.54        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 
       20.84        27.25        89.72        22.72        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
        7.33         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
        6.15        20.38        47.61         6.94         3.98        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 
        0.20        10.29         2.20        11.74        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       19.66         3.29        13.12         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        7.40        11.84         0.53        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        2.10        23.57        14.20        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 
        1.08        12.49         4.93        17.65        12.56         5.95 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 
        8.35         4.54         8.81         8.98         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6694 
        3.75         6.15         5.23         7.79         1.48         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       12.16         9.80        29.23         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       14.93        15.35        13.97        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       10.45         7.59        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 
       18.48        10.62        23.51        38.76         8.94       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       12.69         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        6.21        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        5.39         2.89        16.50        26.33         2.04        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 
       40.96         6.67        12.43         0.99         1.97         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.78        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       17.79        28.54        10.03         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33        19.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 
       24.76        18.08         7.59         2.86        14.40         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       22.68         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 
       10.85        19.23         0.85        13.35         8.94         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.09         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                       0.72                        0.10 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                     120.56                      127.59 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                      14.93                       11.84 
[1] "0.7 - 120.6 (14.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                             cls
clus                            0   1
  DEL PEAK 12(3Q29) MUTATED    25  40
  DEL PEAK 12(3Q29) WILD-TYPE 199 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED     25   40
  DEL PEAK 12(3Q29) WILD-TYPE  199  307
        clus
vv       DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  FEMALE                        25                         199
  MALE                          40                         307
[1] 2 2
[1] FALSE
D37V4, binary
                             cls
clus                            0   1
  DEL PEAK 12(3Q29) MUTATED     8  53
  DEL PEAK 12(3Q29) WILD-TYPE  66 421
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED      8   53
  DEL PEAK 12(3Q29) WILD-TYPE   66  421
     clus
vv    DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  NO                          8                          66
  YES                        53                         421
[1] 2 2
[1] FALSE
D37V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 12(3Q29) MUTATED                               3                   2
  DEL PEAK 12(3Q29) WILD-TYPE                            25                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 12(3Q29) MUTATED                                60
  DEL PEAK 12(3Q29) WILD-TYPE                             465
D37V6, multiclass
                                 clus
vv                                DEL PEAK 12(3Q29) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           3
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                        60
                                 clus
vv                                DEL PEAK 12(3Q29) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            25
  TREATED PRIMARY GBM                                      16
  UNTREATED PRIMARY (DE NOVO) GBM                         465
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(3Q29) MUTATED       1                         5    57
  DEL PEAK 12(3Q29) WILD-TYPE    12                        45   428
D37V7, multiclass
                           clus
vv                          DEL PEAK 12(3Q29) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            57
                           clus
vv                          DEL PEAK 12(3Q29) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          45
  WHITE                                             428
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(3Q29) MUTATED     1  54
  DEL PEAK 12(3Q29) WILD-TYPE  11 419
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED      1   54
  DEL PEAK 12(3Q29) WILD-TYPE   11  419
                        clus
vv                       DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        54                         419
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 13(4P16.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4P16.3) MUTATED    10  67
  DEL PEAK 13(4P16.3) WILD-TYPE  90 403
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           77                           493 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           67                           403 
$`DEL PEAK 13(4P16.3) MUTATED`
TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0025 TCGA-02-0051 
       35.41        82.59        20.61        87.06        42.74        15.09 
TCGA-02-0054 TCGA-02-0069 TCGA-02-0079 TCGA-02-0266 TCGA-02-2483 TCGA-02-2485 
        6.54        28.70        27.25        17.72        15.32        15.45 
TCGA-06-0138 TCGA-06-0152 TCGA-06-0166 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       24.23        12.33         5.85         4.47         3.22         4.04 
TCGA-06-0177 TCGA-06-0192 TCGA-06-0216 TCGA-06-0414 TCGA-06-0645 TCGA-06-0744 
        4.18        38.96        24.16        35.11         5.75        46.88 
TCGA-06-1087 TCGA-06-1800 TCGA-06-2557 TCGA-06-5416 TCGA-06-6693 TCGA-06-A6S0 
        4.04        26.79         1.08         6.71       120.56         3.12 
TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 
       37.84         1.74         8.42        12.16        29.23        65.33 
TCGA-08-0355 TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0516 TCGA-08-0525 
       24.56         3.39        14.93        18.02        19.59        15.98 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0662 TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 
       34.92        10.45        38.17        38.76        15.65        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3653 TCGA-14-0867 TCGA-14-1454 TCGA-14-1458 
       44.02        26.93        14.53         2.04        30.18         6.67 
TCGA-14-1821 TCGA-14-1823 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-19-1388 
       17.79        17.85        13.28        17.59        26.07        12.95 
TCGA-19-2629 TCGA-19-4065 TCGA-27-1830 TCGA-27-1837 TCGA-27-1838 TCGA-28-2509 
       24.23         7.04         5.06        14.04        11.51         4.77 
TCGA-28-2514 TCGA-28-5207 TCGA-28-5211 TCGA-28-5214 TCGA-32-1978 TCGA-32-2632 
        5.26        11.28        11.77        23.44        15.85         8.84 
TCGA-32-4210 TCGA-4W-AA9R TCGA-76-4925 TCGA-76-4928 TCGA-76-4934 
        3.72         4.08         4.80         3.09         2.53 

$`DEL PEAK 13(4P16.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       77.65        20.12        53.10        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 
        6.87        14.73         3.22        12.59         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        10.19        20.84        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       65.00        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.54        16.93        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       26.70        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       13.12        91.00        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        27.22        44.58        15.42        10.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        72.36         4.70         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       23.93         6.84        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        2.56        14.60        17.72        22.68         4.18       115.86 
TCGA-08-0347 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 
       25.71         9.80         1.28         8.42        17.95        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       37.58        22.29        12.23        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        42.15        11.08        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         7.27        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 
       14.73        12.99         7.59        94.78         0.10        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3649 
        3.98         4.14        25.68        14.73         6.77        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 
        7.10         1.15         0.92        40.96        12.43         0.99 
TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
        1.97         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07         5.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        7.53         0.16         4.08         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33        19.33        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       40.54        21.30        30.05        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.55         2.83         0.13         0.66         6.74         7.30 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       14.93        17.88         2.53        31.27        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        7.36        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        8.22         7.50         4.54         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                         1.08                          0.10 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                       120.56                        127.59 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                        15.32                         11.84 
[1] "1.1 - 120.6 (15.3)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED    25  52
  DEL PEAK 13(4P16.3) WILD-TYPE 199 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED     25   52
  DEL PEAK 13(4P16.3) WILD-TYPE  199  295
        clus
vv       DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  FEMALE                          25                           199
  MALE                            52                           295
[1] 2 2
[1] FALSE
D38V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED     9  65
  DEL PEAK 13(4P16.3) WILD-TYPE  65 409
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      9   65
  DEL PEAK 13(4P16.3) WILD-TYPE   65  409
     clus
vv    DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  NO                            9                            65
  YES                          65                           409
[1] 2 2
[1] FALSE
D38V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 13(4P16.3) MUTATED                               2
  DEL PEAK 13(4P16.3) WILD-TYPE                            26
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 13(4P16.3) MUTATED                     1
  DEL PEAK 13(4P16.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 13(4P16.3) MUTATED                                74
  DEL PEAK 13(4P16.3) WILD-TYPE                             451
D38V6, multiclass
                                 clus
vv                                DEL PEAK 13(4P16.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          74
                                 clus
vv                                DEL PEAK 13(4P16.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              26
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           451
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4P16.3) MUTATED       3                         6    63
  DEL PEAK 13(4P16.3) WILD-TYPE    10                        44   422
D38V7, multiclass
                           clus
vv                          DEL PEAK 13(4P16.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              63
                           clus
vv                          DEL PEAK 13(4P16.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               422
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED     2  61
  DEL PEAK 13(4P16.3) WILD-TYPE  10 412
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      2   61
  DEL PEAK 13(4P16.3) WILD-TYPE   10  412
                        clus
vv                       DEL PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           412
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 14(4Q34.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4Q34.3) MUTATED    21  71
  DEL PEAK 14(4Q34.3) WILD-TYPE  79 399
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           92                           478 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           71                           399 
$`DEL PEAK 14(4Q34.3) MUTATED`
TCGA-02-0024 TCGA-02-0026 TCGA-02-0054 TCGA-02-0064 TCGA-02-0079 TCGA-02-0432 
       53.10        24.59         6.54        19.73        27.25        47.11 
TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0129 TCGA-06-0138 TCGA-06-0152 
       16.80        15.32        15.45        33.67        24.23        12.33 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0192 TCGA-06-0216 
        5.85         3.22         4.04         4.18        38.96        24.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 
       35.11        12.62         5.75        46.88         4.04        26.79 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2569 TCGA-06-5416 TCGA-06-5856 
       13.61        33.90         1.08         0.43         6.71         3.75 
TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-A5U0 TCGA-08-0246 TCGA-08-0350 
        4.57         7.79         5.39        26.79         4.18        29.23 
TCGA-08-0351 TCGA-08-0354 TCGA-08-0356 TCGA-08-0358 TCGA-08-0386 TCGA-12-0619 
       65.33        17.95        31.10        22.29        18.02        34.92 
TCGA-12-0691 TCGA-12-0769 TCGA-12-0827 TCGA-12-1098 TCGA-12-1598 TCGA-12-3644 
       12.13        15.06        38.76         3.98        15.65        59.77 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-0787 TCGA-14-0813 
       44.02        14.53        15.12        11.97         2.24         1.35 
TCGA-14-0862 TCGA-14-0867 TCGA-14-1453 TCGA-14-1454 TCGA-14-1458 TCGA-14-1821 
        2.89         2.04         1.15        30.18         6.67        17.79 
TCGA-14-1823 TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 
       17.85        13.78        53.19        13.28        17.59        29.03 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 
        5.95        12.95        25.38        24.23         7.04        28.54 
TCGA-26-1442 TCGA-26-A7UX TCGA-27-1838 TCGA-27-2518 TCGA-28-1749 TCGA-28-1756 
       31.33        19.33        11.51        24.76         9.21         2.83 
TCGA-28-2514 TCGA-28-5214 TCGA-28-5220 TCGA-32-1973 TCGA-32-2491 TCGA-32-2632 
        5.26        23.44        10.49        21.07        12.23         8.84 
TCGA-32-2634 TCGA-32-4208 TCGA-41-5651 TCGA-4W-AA9R TCGA-76-4934 TCGA-76-6285 
       22.78        21.14        15.12         4.08         2.53         8.35 
TCGA-76-6286 TCGA-OX-A56R 
       20.98         5.92 

$`DEL PEAK 14(4Q34.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
        6.02        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       20.84        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       17.65        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       10.59        12.39        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.21         3.35        12.92        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
       20.38        47.61         6.94         3.98        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        14.30        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        46.59        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0176 TCGA-06-0178 
       19.66         3.29        13.12         4.47        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        9.57         3.16         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93         6.84        11.84        15.32 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         4.37        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        2.73         6.15         5.23         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56        14.60        17.72        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0357 TCGA-08-0359 
        9.80         1.28         8.42        24.56        37.58         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       15.35        14.73        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       27.78         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 
       14.53         4.14        25.68        14.73         6.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 
        2.04         0.95         6.21        23.05        11.24        13.78 
TCGA-14-0812 TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 
        3.25         5.39        16.50        26.33        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
       58.78        23.11         7.10         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        0.99         1.97         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 
        7.96         3.78         3.42        50.53        19.10         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07        16.37         4.31         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       17.79         3.98        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2519 
       24.23        40.54        21.30        30.05        14.04        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        1.55         0.13         0.66         6.74         4.77         7.30 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 
       11.01        13.64         5.16        22.68         5.42        15.39 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        16.93        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        7.36        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        11.84         0.20        12.46         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 
       16.70         3.29         2.70        11.38        17.06         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         6.28        20.55 

  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                        65.33                        127.59 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                        15.12                         11.77 
[1] "0.4 - 65.3 (15.1)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q34.3) MUTATED    27  65
  DEL PEAK 14(4Q34.3) WILD-TYPE 197 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED     27   65
  DEL PEAK 14(4Q34.3) WILD-TYPE  197  282
        clus
vv       DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE
  FEMALE                          27                           197
  MALE                            65                           282
[1] 2 2
[1] FALSE
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q34.3) MUTATED    16  73
  DEL PEAK 14(4Q34.3) WILD-TYPE  58 401
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED     16   73
  DEL PEAK 14(4Q34.3) WILD-TYPE   58  401
     clus
vv    DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE
  NO                           16                            58
  YES                          73                           401
[1] 2 2
[1] FALSE
D39V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 14(4Q34.3) MUTATED                               5
  DEL PEAK 14(4Q34.3) WILD-TYPE                            23
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 14(4Q34.3) MUTATED                     2
  DEL PEAK 14(4Q34.3) WILD-TYPE                  16
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 14(4Q34.3) MUTATED                                85
  DEL PEAK 14(4Q34.3) WILD-TYPE                             440
D39V6, multiclass
                                 clus
vv                                DEL PEAK 14(4Q34.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             5
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          85
                                 clus
vv                                DEL PEAK 14(4Q34.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              23
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q34.3) MUTATED       4                        11    77
  DEL PEAK 14(4Q34.3) WILD-TYPE     9                        39   408
D39V7, multiclass
                           clus
vv                          DEL PEAK 14(4Q34.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              77
                           clus
vv                          DEL PEAK 14(4Q34.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            39
  WHITE                                               408
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q34.3) MUTATED     2  74
  DEL PEAK 14(4Q34.3) WILD-TYPE  10 399
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED      2   74
  DEL PEAK 14(4Q34.3) WILD-TYPE   10  399
                        clus
vv                       DEL PEAK 14(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          74
                        clus
vv                       DEL PEAK 14(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           399
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 15(5Q34) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(5Q34) MUTATED    17  52
  DEL PEAK 15(5Q34) WILD-TYPE  83 418
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                         69                         501 
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                         52                         418 
$`DEL PEAK 15(5Q34) MUTATED`
TCGA-02-0010 TCGA-02-0011 TCGA-02-0026 TCGA-02-0052 TCGA-02-0069 TCGA-02-0084 
       35.41        20.71        24.59        12.59        28.70        12.62 
TCGA-02-0104 TCGA-02-0333 TCGA-02-2483 TCGA-06-0128 TCGA-06-0148 TCGA-06-0175 
       65.00         4.37        15.32        22.72        10.09         4.04 
TCGA-06-0188 TCGA-06-0211 TCGA-06-0237 TCGA-06-0414 TCGA-06-0644 TCGA-06-0649 
       44.58        11.84        13.64        35.11        12.62         2.10 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0877 TCGA-06-1087 TCGA-06-2569 TCGA-06-6389 
       14.20        46.88         5.65         4.04         0.43         7.79 
TCGA-06-A5U0 TCGA-06-A7TL TCGA-08-0344 TCGA-08-0350 TCGA-08-0386 TCGA-08-0516 
       26.79        17.72       115.86        29.23        18.02        19.59 
TCGA-08-0517 TCGA-08-0524 TCGA-12-0818 TCGA-12-1600 TCGA-12-3653 TCGA-14-0740 
       58.68         7.27        91.76        14.73        14.53        11.97 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1821 
        5.39        16.50         2.04        28.93         1.15        17.79 
TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-16-1045 TCGA-19-0960 
        3.78        50.53        53.19        16.37        29.03         8.61 
TCGA-19-1387 TCGA-19-1786 TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-5133 
        5.95         7.17        24.23         7.04        28.54        14.86 
TCGA-26-5135 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2521 TCGA-28-1756 
        8.88        40.54        21.30        30.05        10.39         2.83 
TCGA-28-5215 TCGA-41-2572 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9R TCGA-76-4925 
       11.01        13.35         0.20        15.12         4.08         4.80 
TCGA-76-4929 TCGA-76-4934 TCGA-RR-A6KC 
        3.65         2.53        20.55 

$`DEL PEAK 15(5Q34) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0014 
       11.77         4.73        18.35        23.18        10.59        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        6.54         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        89.72        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91        25.71        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.22        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       69.90        73.84        27.22        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.63         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 
        0.26        72.36         4.70         9.57         3.16         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        5.75         9.80        23.57        26.40         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
       16.57        20.78        26.76        23.93         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
       16.64         5.98         4.37        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        2.73         3.75         6.15         4.57         5.23         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
       14.60        22.68        37.84         4.18         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       25.71        12.16         9.80        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        4.27        42.15        11.08        19.33        10.75         4.80 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.86        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       14.53         3.98         4.14        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       34.92        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
       17.49         7.96         3.42        13.78        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 
        3.91        17.59        26.07         4.31         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         3.65        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79         3.98        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5136 
       31.33         7.13         9.37         9.40         5.49        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
        9.86        24.23        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        1.55         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23         0.85         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        4.44        11.84        12.46         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.09         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       26.30         5.92         6.28 

  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                        0.2                         0.1 
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                     115.86                      127.59 
  DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE 
                      14.53                       11.84 
[1] "0.2 - 115.9 (14.5)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                             cls
clus                            0   1
  DEL PEAK 15(5Q34) MUTATED    32  37
  DEL PEAK 15(5Q34) WILD-TYPE 192 310
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(5Q34) MUTATED     32   37
  DEL PEAK 15(5Q34) WILD-TYPE  192  310
        clus
vv       DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE
  FEMALE                        32                         192
  MALE                          37                         310
[1] 2 2
[1] FALSE
D40V4, binary
                             cls
clus                            0   1
  DEL PEAK 15(5Q34) MUTATED     7  58
  DEL PEAK 15(5Q34) WILD-TYPE  67 416
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(5Q34) MUTATED      7   58
  DEL PEAK 15(5Q34) WILD-TYPE   67  416
     clus
vv    DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE
  NO                          7                          67
  YES                        58                         416
[1] 2 2
[1] FALSE
D40V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 15(5Q34) MUTATED                               6                   1
  DEL PEAK 15(5Q34) WILD-TYPE                            22                  17
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 15(5Q34) MUTATED                                62
  DEL PEAK 15(5Q34) WILD-TYPE                             463
D40V6, multiclass
                                 clus
vv                                DEL PEAK 15(5Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           6
  TREATED PRIMARY GBM                                     1
  UNTREATED PRIMARY (DE NOVO) GBM                        62
                                 clus
vv                                DEL PEAK 15(5Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            22
  TREATED PRIMARY GBM                                      17
  UNTREATED PRIMARY (DE NOVO) GBM                         463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q34) MUTATED       3                        11    55
  DEL PEAK 15(5Q34) WILD-TYPE    10                        39   430
D40V7, multiclass
                           clus
vv                          DEL PEAK 15(5Q34) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                            55
                           clus
vv                          DEL PEAK 15(5Q34) WILD-TYPE
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          39
  WHITE                                             430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                             cls
clus                            0   1
  DEL PEAK 15(5Q34) MUTATED     3  56
  DEL PEAK 15(5Q34) WILD-TYPE   9 417
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(5Q34) MUTATED      3   56
  DEL PEAK 15(5Q34) WILD-TYPE    9  417
                        clus
vv                       DEL PEAK 15(5Q34) MUTATED DEL PEAK 15(5Q34) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        56                         417
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 16(6Q22.31) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(6Q22.31) MUTATED    24 133
  DEL PEAK 16(6Q22.31) WILD-TYPE  76 337
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           157                            413 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           133                            337 
$`DEL PEAK 16(6Q22.31) MUTATED`
TCGA-02-0003 TCGA-02-0007 TCGA-02-0014 TCGA-02-0023 TCGA-02-0026 TCGA-02-0038 
        4.73        23.18        82.59        20.12        24.59        10.72 
TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 TCGA-02-0058 TCGA-02-0060 TCGA-02-0074 
       10.52         3.22        15.09         8.35         6.02        10.19 
TCGA-02-0080 TCGA-02-0086 TCGA-02-0099 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 
       89.72         8.81         3.48        11.67        92.65        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0281 TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 
       48.95        16.54         3.98        12.23         7.73        10.62 
TCGA-02-0330 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-2466 TCGA-02-2483 
       15.91        14.50        10.55        47.11        16.80        15.32 
TCGA-06-0122 TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0154 TCGA-06-0162 
        6.15        12.95        24.23        10.29        13.94         3.42 
TCGA-06-0166 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0192 TCGA-06-0201 
        5.85        69.90        73.84        27.22        38.96         0.39 
TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0402 TCGA-06-0644 
        7.63        15.02        24.16         0.72         0.26        12.62 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
        5.75         2.10         0.92        15.32         1.08        17.65 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
       11.74         3.55         8.81         8.55         6.71         3.75 
TCGA-06-6390 TCGA-06-6694 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0246 
        5.39         7.36         1.55         1.87         2.56         4.18 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0392 
        8.42        24.56        22.29        12.23        14.93         0.72 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 
        4.27        42.15        58.68        15.98        15.35        14.73 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0691 TCGA-12-0692 TCGA-12-0772 TCGA-12-0780 
        7.59        94.78        12.13         3.65        53.85        14.86 
TCGA-12-0822 TCGA-12-1093 TCGA-12-1095 TCGA-12-1098 TCGA-12-1099 TCGA-12-1602 
       23.51        15.98        15.85         3.98         4.14         6.77 
TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0787 TCGA-14-0817 
       44.02        14.53         3.22        15.12         2.24         5.39 
TCGA-14-0865 TCGA-14-1037 TCGA-14-1396 TCGA-14-1453 TCGA-14-1823 TCGA-14-4157 
       16.50        19.30         1.12         1.15        17.85         3.42 
TCGA-15-0742 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-16-1060 TCGA-16-1063 
       13.78         3.91         4.31        29.03         9.14        13.97 
TCGA-19-0962 TCGA-19-1392 TCGA-19-2619 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 
        0.66         3.65         9.67        24.23         7.04         6.64 
TCGA-19-5952 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1443 
       18.90        14.96         3.98        10.03        13.87         7.13 
TCGA-27-1832 TCGA-27-1833 TCGA-27-2524 TCGA-27-2526 TCGA-28-1750 TCGA-28-2506 
        9.86        24.23         7.59         2.86         8.35         6.74 
TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5213 
        4.77         5.26        14.93        11.28         2.53        31.27 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1980 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       10.49         5.42         1.18        15.02        15.95        22.78 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
       21.14         3.72        12.59        10.85         0.85        13.35 
TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        0.99         0.20        15.12        25.58         3.45        20.91 
TCGA-76-4925 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-6282 TCGA-76-6285 
        4.80         3.09         3.65         9.17        17.06         8.35 
TCGA-OX-A56R 
        5.92 

$`DEL PEAK 16(6Q22.31) WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 
       11.77        18.35        10.59        35.41        20.71        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 
       87.06        77.65        53.10        42.74        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        2.83        14.14         3.62        18.31         6.87        14.73 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 
       12.59         6.54         2.50        19.86         9.57        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       26.43        28.70        25.05         5.49        20.84        27.25 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 
       22.72        12.62        51.32        57.76        16.96        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0260 TCGA-02-0266 
       65.00        17.65        23.18        99.98        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0321 
       10.75        14.47        13.87        14.20        15.95         9.90 
TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 
       11.34         9.27        16.21         3.35        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
       20.32         2.70        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        25.35        14.30        26.70        11.90 
TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        0.20         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
       10.09         8.61        19.46        46.59        12.33        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82         9.44        11.80        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0188 
       91.00         4.18        88.14        20.25         3.65        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 
       15.42        10.42         4.67         7.40         5.56         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0221 TCGA-06-0237 
        8.42         7.40        11.84         0.53        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       13.32        20.42        48.69        10.82         9.01        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 
        4.70         9.57         3.16        35.11         5.75         9.80 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79        11.84        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 
        4.37         0.43        31.50         8.35         4.54         8.98 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 
        2.73         6.15         4.57         5.23         7.79         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
      120.56         8.32        12.85         4.77         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
       26.79         3.12        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 
       29.23        65.33         1.28        17.95        31.10        37.58 
TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 
        3.39        18.02        15.35        13.97        12.56        11.08 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       19.59        19.33        10.75         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0657 TCGA-12-0662 
        7.56        12.99        34.92        10.45         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
       25.97        26.66        20.38        28.41        15.06        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1094 TCGA-12-1096 
        5.82         7.59        33.21        21.73        12.23         9.11 
TCGA-12-1097 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
       14.53        15.65        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 
       15.22        10.95        12.69        34.92        14.93         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95         6.21        23.05        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        3.25         1.35         2.89        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-15-1444 TCGA-15-1446 
        7.17        17.49         7.96         3.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 
       53.19        13.28        17.59        26.07        16.37         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
       10.29        14.01        21.24         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        8.61        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        7.00        17.19         8.02         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1440 
       22.49        14.07        16.80        17.79        28.54         9.73 
TCGA-26-1442 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       31.33         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       16.60        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-27-2528 
       24.76        18.08        10.39        16.08        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-5208 
        1.55         2.83         0.13         0.66         7.30        17.88 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        23.44        11.01        13.64         5.16        22.68 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2573 
        7.36         8.84        25.18        19.86        19.23         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        9.53         4.44        11.84        12.46         4.08         1.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4934 
        4.34        14.33         8.22         7.50         4.54         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6286 
       36.85        16.70         3.29         2.70        11.38        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         6.28        20.55 

  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           0.2                            0.1 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                         94.78                         127.59 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                         10.49                          12.59 
[1] "0.2 - 94.8 (10.5)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.3"
D41V2, continuous
D41V3, binary
                                cls
clus                               0   1
  DEL PEAK 16(6Q22.31) MUTATED    71  86
  DEL PEAK 16(6Q22.31) WILD-TYPE 153 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED     71   86
  DEL PEAK 16(6Q22.31) WILD-TYPE  153  261
        clus
vv       DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE
  FEMALE                           71                            153
  MALE                             86                            261
[1] 2 2
[1] FALSE
D41V4, binary
                                cls
clus                               0   1
  DEL PEAK 16(6Q22.31) MUTATED    27 124
  DEL PEAK 16(6Q22.31) WILD-TYPE  47 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED     27  124
  DEL PEAK 16(6Q22.31) WILD-TYPE   47  350
     clus
vv    DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE
  NO                            27                             47
  YES                          124                            350
[1] 2 2
[1] FALSE
D41V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 16(6Q22.31) MUTATED                               6
  DEL PEAK 16(6Q22.31) WILD-TYPE                            22
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 16(6Q22.31) MUTATED                     7
  DEL PEAK 16(6Q22.31) WILD-TYPE                  11
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 16(6Q22.31) MUTATED                               144
  DEL PEAK 16(6Q22.31) WILD-TYPE                             381
D41V6, multiclass
                                 clus
vv                                DEL PEAK 16(6Q22.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                          144
                                 clus
vv                                DEL PEAK 16(6Q22.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               22
  TREATED PRIMARY GBM                                         11
  UNTREATED PRIMARY (DE NOVO) GBM                            381
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q22.31) MUTATED       5                        15   130
  DEL PEAK 16(6Q22.31) WILD-TYPE     8                        35   355
D41V7, multiclass
                           clus
vv                          DEL PEAK 16(6Q22.31) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              130
                           clus
vv                          DEL PEAK 16(6Q22.31) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             35
  WHITE                                                355
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                                cls
clus                               0   1
  DEL PEAK 16(6Q22.31) MUTATED     1 133
  DEL PEAK 16(6Q22.31) WILD-TYPE  11 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED      1  133
  DEL PEAK 16(6Q22.31) WILD-TYPE   11  340
                        clus
vv                       DEL PEAK 16(6Q22.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 16(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            340
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    28 150
  DEL PEAK 17(6Q26) WILD-TYPE  72 320
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        178                         392 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        150                         320 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-02-0003 TCGA-02-0007 TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 
        4.73        23.18        20.61        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 TCGA-02-0057 TCGA-02-0058 
       12.16        10.52         3.22        15.09        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0074 TCGA-02-0080 TCGA-02-0086 TCGA-02-0089 
        9.57         6.02        10.19        89.72         8.81        16.96 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0281 
       11.67        92.65        15.65        48.95        16.54         3.98 
TCGA-02-0289 TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0422 
       14.20        12.23         7.73        10.62        15.91        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-2466 TCGA-02-2483 TCGA-06-0124 TCGA-06-0125 
       10.55        47.11        16.80        15.32        20.38        47.61 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0142 TCGA-06-0155 TCGA-06-0162 
       12.95        24.23        10.29         2.20        10.45         3.42 
TCGA-06-0166 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0209 TCGA-06-0214 
        5.85        69.90        73.84        27.22         7.63        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 
       24.16         0.72        12.62         5.75         2.10         0.92 
TCGA-06-0878 TCGA-06-0882 TCGA-06-1084 TCGA-06-1087 TCGA-06-1806 TCGA-06-2557 
        7.17        20.78        23.93         4.04        15.32         1.08 
TCGA-06-2561 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 TCGA-06-5416 
       17.65        11.74         3.55         8.81         8.55         6.71 
TCGA-06-5856 TCGA-06-5859 TCGA-06-6390 TCGA-06-6694 TCGA-06-6699 TCGA-06-A5U1 
        3.75         4.57         5.39         7.36         1.55         1.87 
TCGA-06-A6S1 TCGA-08-0246 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 
        2.56         4.18         8.42        24.56        31.10        22.29 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 
       12.23        14.93         0.72         4.27        42.15        58.68 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       15.98        15.35        14.73         7.59        94.78         0.10 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0780 
       12.13         3.65        28.41        15.06        53.85        14.86 
TCGA-12-0822 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1095 TCGA-12-1099 
       23.51         5.82        33.21        15.98        15.85         4.14 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0817 
        6.77        44.02        14.53         3.22        15.12         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1037 TCGA-14-1395 TCGA-14-1402 TCGA-14-1453 
        2.89        16.50        19.30         1.38        32.05         1.15 
TCGA-14-1823 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-16-0846 TCGA-16-0861 
       17.85         3.42        13.78        19.10         3.91         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 TCGA-19-0962 TCGA-19-1386 
       29.03         4.57         9.14        13.97         0.66         9.07 
TCGA-19-1392 TCGA-19-1789 TCGA-19-2619 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        3.65         3.25         9.67        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 
        6.64        18.90        22.49        14.96         3.98        13.87 
TCGA-26-1443 TCGA-26-6173 TCGA-27-1832 TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 
        7.13         7.92         9.86        24.23        24.76        10.39 
TCGA-27-2524 TCGA-28-1747 TCGA-28-1750 TCGA-28-1753 TCGA-28-2506 TCGA-28-2509 
        7.59         2.53         8.35         1.22         6.74         4.77 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5213 TCGA-28-5220 
        5.26        14.93        11.28         2.53        31.27        10.49 
TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-2495 TCGA-32-2615 TCGA-32-4208 
       15.85         1.18         4.67        15.02        15.95        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2572 TCGA-41-3392 TCGA-41-4097 
        3.72        12.59        10.85        13.35         0.99         0.20 
TCGA-41-5651 TCGA-4W-AA9T TCGA-74-6573 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
       15.12        25.58         3.45         3.09         3.65         9.17 
TCGA-76-6282 TCGA-76-6285 TCGA-81-5911 TCGA-OX-A56R 
       17.06         8.35        17.72         5.92 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       11.77        18.35        10.59        35.41        20.71        82.59 
TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       87.06        53.10        42.74        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0052 
        3.62        10.72        18.31         6.87        14.73        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        6.54         2.50        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        20.84        27.25        22.72        12.62        51.32 
TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 
       57.76         3.48        27.02        65.00        17.65        23.18 
TCGA-02-0114 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       99.98        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0290 TCGA-02-0321 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       15.95         9.90         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.59        12.39        11.34         9.27        16.21         3.35 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0126 
       12.92        15.45        20.32         2.70         6.15         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        33.67        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       11.90         0.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82         9.44        11.80        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0188 
       91.00         4.18        88.14        20.25         3.65        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
       35.11         5.75         9.80        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 
       46.88         7.86         2.70         2.70        43.46        46.19 
TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 
        5.65        40.41        16.57        26.76         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5418 
        0.43        31.50         8.35         4.54         8.98         2.73 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        6.15         5.23         7.79         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 
       12.85         4.77         4.77         4.96        26.79         3.12 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
       14.60        17.72        22.68        37.84       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 
        1.28        17.95        37.58         3.39        18.02        15.35 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 
       13.97        12.56        11.08        19.59        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 
        4.80         7.27        18.41         7.56        12.99        34.92 
TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0773 
       10.45        38.17        25.97        26.66        20.38        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1090 TCGA-12-1092 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
        7.59        21.73        12.23         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 TCGA-14-0740 
       10.95        12.69        34.92        14.93         2.04        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        3.25         1.35        26.33         2.04        28.93        15.95 
TCGA-14-1043 TCGA-14-1396 TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        0.79         1.12         3.75        58.78        23.11         7.10 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
        7.96         3.78        50.53        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1460 
       26.07        16.37        10.29        14.01        21.24         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         8.61        14.27         3.39        10.75 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        5.95        12.95         4.64        25.38         7.17        12.66 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         4.87         1.08         7.53         0.16         4.08 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       17.19         8.02         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       16.80        17.79        28.54        10.03         9.73        31.33 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 
        1.58         2.33        19.33         5.06        16.60        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2523 
       21.30        30.05        14.04        11.51        18.08        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 TCGA-28-1751 
        2.86        14.40        15.78         0.20         9.21         7.63 
TCGA-28-1752 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        8.48         1.55         2.83         0.13         0.66         7.30 
TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       17.88        11.77        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       22.68         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1979 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
       19.50        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 
        7.36         8.84        22.78        25.18        19.86        19.23 
TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 
        0.85         8.94         9.53         4.44        11.84        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        4.08         1.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        7.50         4.80         4.54         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        3.29         2.70        11.38        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
       23.90        34.45        18.64        36.20         1.61        26.30 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        0.1                         0.1 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      94.78                      127.59 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     10.735                      12.475 
[1] "0.1 - 94.8 (10.7)"  "0.1 - 127.6 (12.5)"
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    77 101
  DEL PEAK 17(6Q26) WILD-TYPE 147 246
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     77  101
  DEL PEAK 17(6Q26) WILD-TYPE  147  246
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        77                         147
  MALE                         101                         246
[1] 2 2
[1] FALSE
D42V4, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    25 145
  DEL PEAK 17(6Q26) WILD-TYPE  49 329
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     25  145
  DEL PEAK 17(6Q26) WILD-TYPE   49  329
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                         25                          49
  YES                       145                         329
[1] 2 2
[1] FALSE
D42V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 17(6Q26) MUTATED                               7                   9
  DEL PEAK 17(6Q26) WILD-TYPE                            21                   9
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 17(6Q26) MUTATED                               162
  DEL PEAK 17(6Q26) WILD-TYPE                             363
D42V6, multiclass
                                 clus
vv                                DEL PEAK 17(6Q26) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           7
  TREATED PRIMARY GBM                                     9
  UNTREATED PRIMARY (DE NOVO) GBM                       162
                                 clus
vv                                DEL PEAK 17(6Q26) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            21
  TREATED PRIMARY GBM                                       9
  UNTREATED PRIMARY (DE NOVO) GBM                         363
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED       4                        16   151
  DEL PEAK 17(6Q26) WILD-TYPE     9                        34   334
D42V7, multiclass
                           clus
vv                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        16
  WHITE                                           151
                           clus
vv                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          34
  WHITE                                             334
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     2 151
  DEL PEAK 17(6Q26) WILD-TYPE  10 322
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      2  151
  DEL PEAK 17(6Q26) WILD-TYPE   10  322
                        clus
vv                       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                       151                         322
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED    13  53
  DEL PEAK 18(8P23.2) WILD-TYPE  87 417
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           66                           504 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           53                           417 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-02-0001 TCGA-02-0009 TCGA-02-0025 TCGA-02-0051 TCGA-02-0059 TCGA-02-0060 
       11.77        10.59        42.74        15.09         9.57         6.02 
TCGA-02-0086 TCGA-02-0106 TCGA-02-0111 TCGA-02-0115 TCGA-02-0281 TCGA-02-0324 
        8.81        11.67        23.18        15.65         3.98         7.73 
TCGA-02-0430 TCGA-02-2486 TCGA-06-0159 TCGA-06-0169 TCGA-06-0171 TCGA-06-0195 
       10.55        20.32         9.44         3.29        13.12         7.40 
TCGA-06-0216 TCGA-06-0410 TCGA-06-0743 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 
       24.16         4.70        26.40        11.74         8.35         8.81 
TCGA-06-6693 TCGA-06-A5U1 TCGA-08-0246 TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 
      120.56         1.87         4.18         0.72         4.27        15.98 
TCGA-12-0691 TCGA-12-0776 TCGA-12-0826 TCGA-12-0827 TCGA-12-1093 TCGA-12-1098 
       12.13         9.73        27.78        38.76        15.98         3.98 
TCGA-12-1598 TCGA-12-3651 TCGA-14-0736 TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 
       15.65        12.69        15.12         2.89        15.95        58.78 
TCGA-14-1794 TCGA-14-1823 TCGA-15-1447 TCGA-16-0846 TCGA-16-1056 TCGA-16-1063 
        0.99        17.85        53.19         3.91        14.01        13.97 
TCGA-19-0960 TCGA-19-1385 TCGA-19-1786 TCGA-26-1439 TCGA-26-5136 TCGA-27-2521 
        8.61        10.75         7.17        13.87        18.97        10.39 
TCGA-27-2524 TCGA-28-1750 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2514 
        7.59         8.35         0.13         0.66         4.77         5.26 
TCGA-28-5204 TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-4W-AA9T TCGA-76-4934 
       14.93        21.14         3.72        10.85        25.58         2.53 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        4.73        18.35        23.18        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 
       20.61        87.06        77.65        20.12        53.10        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       10.52        18.31         6.87        14.73         3.22        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 
        6.54         2.50        19.86         8.35        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0113 TCGA-02-0114 
        3.48        27.02        65.00        17.65        92.65        99.98 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 
       13.87        14.20        15.95        12.23         9.90        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       12.39        14.50        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 
        3.35        16.80        12.92        15.32        15.45         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       12.33        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 
        3.42        56.91        10.65         5.85        19.66         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         4.67         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       23.57        14.20        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        3.55         4.54         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96        26.79         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       17.72        22.68        37.84       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         7.27        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        15.06        53.85        43.23         7.63        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       21.73        12.23        15.85         9.11        14.53         4.14 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
       11.24        13.78         3.25         1.35         5.39        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        28.93        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        1.12         3.75        32.05        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
        3.78         3.42        13.78        50.53        19.10        13.28 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
       10.29         9.14        21.24         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.66        14.27         3.39         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.65        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        18.08        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2506 
        7.63         8.48         1.22         1.55         2.83         6.74 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
       22.78        25.18        12.59        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6573 
        0.20        15.12        12.46         4.08         1.45         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       120.56                        127.59 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        10.67                         12.41 
[1] "0.1 - 120.6 (10.7)" "0.1 - 127.6 (12.4)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    30  36
  DEL PEAK 18(8P23.2) WILD-TYPE 194 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     30   36
  DEL PEAK 18(8P23.2) WILD-TYPE  194  311
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                          30                           194
  MALE                            36                           311
[1] 2 2
[1] FALSE
D43V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     7  56
  DEL PEAK 18(8P23.2) WILD-TYPE  67 418
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      7   56
  DEL PEAK 18(8P23.2) WILD-TYPE   67  418
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                            7                            67
  YES                          56                           418
[1] 2 2
[1] FALSE
D43V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 18(8P23.2) MUTATED                               3
  DEL PEAK 18(8P23.2) WILD-TYPE                            25
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 18(8P23.2) MUTATED                     1
  DEL PEAK 18(8P23.2) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 18(8P23.2) MUTATED                                62
  DEL PEAK 18(8P23.2) WILD-TYPE                             463
D43V6, multiclass
                                 clus
vv                                DEL PEAK 18(8P23.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          62
                                 clus
vv                                DEL PEAK 18(8P23.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              25
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED       5                         4    53
  DEL PEAK 18(8P23.2) WILD-TYPE     8                        46   432
D43V7, multiclass
                           clus
vv                          DEL PEAK 18(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              53
                           clus
vv                          DEL PEAK 18(8P23.2) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               432
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     0  57
  DEL PEAK 18(8P23.2) WILD-TYPE  12 416
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      0   57
  DEL PEAK 18(8P23.2) WILD-TYPE   12  416
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           416
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 19(9P21.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(9P21.3) MUTATED    72 345
  DEL PEAK 19(9P21.3) WILD-TYPE  28 125
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          417                           153 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          345                           125 
$`DEL PEAK 19(9P21.3) MUTATED`
TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       23.18        10.59        35.41        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0027 TCGA-02-0037 TCGA-02-0038 
       77.65        20.12        53.10        12.16         3.62        10.72 
TCGA-02-0043 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 
       18.31        14.73         3.22        15.09         6.54        19.86 
TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 TCGA-02-0071 TCGA-02-0080 TCGA-02-0083 
        8.35        19.73        26.43         5.49        89.72        22.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
       51.32         8.81        16.96         3.48        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        10.75         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90        10.62         7.33        15.91 
TCGA-02-0333 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0446 
        4.37        12.39        14.50        10.55        47.11         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0119 
       16.21        16.80        12.92        15.32        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 
       25.35        14.30        26.70        11.90        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       11.74         2.33        10.09        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0169 
       10.45        10.82         3.42        56.91         5.85         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 
       13.12         4.47         4.04         4.18        20.25        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0208 
       27.22        44.58        10.42        38.96         0.39         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.63         7.40        11.84        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       19.82        13.64        48.69        10.82         9.01        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        23.57        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       40.41        20.78        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
       11.84        15.32        13.61        15.32         1.08        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        0.43        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        8.55         2.73         3.75         4.57         5.23         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       17.72        22.68         4.18         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       12.16         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0390 TCGA-08-0392 
       37.58        22.29         3.39        12.23        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0620 
       10.75        15.98        18.41         7.56        15.35        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0707 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
        3.65        28.41         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       24.79        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       12.23        15.85        14.53         3.98         4.14        25.68 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        6.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        1.35         5.39         2.89        16.50        26.33        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        7.10         1.15         0.92         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       13.28         3.91         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0960 
       14.01         9.14        21.24        13.97        11.77         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
       12.95         4.64        25.38         3.65         7.17         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        0.13         9.67         4.87         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 
       12.10         1.78        22.49        14.07        16.80         3.98 
TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        5.49         1.58         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 
        9.86        24.23        40.54        30.05        14.04        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59         2.86        15.78         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        0.66         6.74         7.30         5.26        14.93        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 
        2.53        11.77        31.27        11.01        13.64        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
       19.50         4.67        12.69        16.93        20.78        15.02 
TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       15.95        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44         0.20        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29        11.38        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        4.83         5.03        23.90        36.20         1.61        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

$`DEL PEAK 19(9P21.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0011 TCGA-02-0025 TCGA-02-0026 
       11.77         4.73        18.35        20.71        42.74        24.59 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0052 
       90.58         2.83        14.14        10.52         6.87        12.59 
TCGA-02-0055 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 
        2.50         9.57         6.02        28.70        25.05        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0084 TCGA-02-0087 TCGA-02-0102 TCGA-02-0113 
       20.84        27.25        12.62        57.76        27.02        92.65 
TCGA-02-0271 TCGA-02-0324 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0440 
       14.47         7.73        25.71        25.12        10.59        11.34 
TCGA-02-0456 TCGA-02-2485 TCGA-06-0129 TCGA-06-0130 TCGA-06-0138 TCGA-06-0140 
        3.35        15.45        33.67        12.95        24.23         0.20 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0157 TCGA-06-0159 
       20.09        17.79         8.61        12.33         3.19         9.44 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 
       11.80        10.65        19.66         3.22        91.00        88.14 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
        3.65        69.90        15.42         4.67         7.40         5.56 
TCGA-06-0206 TCGA-06-0213 TCGA-06-0238 TCGA-06-0240 TCGA-06-0402 TCGA-06-0414 
        7.66         0.53        13.32        20.42         0.26        35.11 
TCGA-06-0686 TCGA-06-0749 TCGA-06-0881 TCGA-06-0939 TCGA-06-1805 TCGA-06-2558 
       14.20         2.70        16.57        26.76        33.90        12.49 
TCGA-06-2559 TCGA-06-2570 TCGA-06-5411 TCGA-06-5416 TCGA-06-5858 TCGA-06-6390 
        4.93        31.50         8.35         6.71         6.15         5.39 
TCGA-06-6698 TCGA-06-A7TK TCGA-08-0245 TCGA-08-0344 TCGA-08-0349 TCGA-08-0350 
        4.77        14.60        37.84       115.86         9.80        29.23 
TCGA-08-0351 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0512 TCGA-08-0521 
       65.33        14.93        18.02        15.35        42.15         4.80 
TCGA-08-0524 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0662 TCGA-12-0703 
        7.27        14.73        12.99        34.92        38.17        20.38 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 TCGA-12-0820 TCGA-12-1090 
       15.06        53.85        43.23         9.73        18.48         7.59 
TCGA-12-1096 TCGA-12-1598 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-14-0812 
        9.11        15.65        14.73        59.77        44.02         3.25 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1450 TCGA-14-1451 TCGA-14-1454 TCGA-14-1456 
        2.04        15.95        58.78        23.11        30.18        40.96 
TCGA-14-1794 TCGA-14-3477 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1460 
        0.99         3.78        17.59        26.07        16.37         6.41 
TCGA-19-0957 TCGA-19-1787 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-5960 
       21.90        12.66         1.08         7.53         0.16        14.96 
TCGA-19-A60I TCGA-26-1438 TCGA-26-5132 TCGA-26-5133 TCGA-26-5135 TCGA-26-5136 
       17.79        10.03         9.40        14.86         8.88        18.97 
TCGA-26-6173 TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2527 
        7.92        21.30        11.51        24.76        18.08        14.40 
TCGA-28-1746 TCGA-28-1752 TCGA-28-2509 TCGA-28-5207 TCGA-28-5214 TCGA-28-5218 
        0.20         8.48         4.77        11.28        23.44         5.16 
TCGA-28-5219 TCGA-32-1980 TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 TCGA-32-2632 
       22.68         1.18        14.86        12.23         7.36         8.84 
TCGA-32-2634 TCGA-41-2571 TCGA-41-3915 TCGA-41-5651 TCGA-76-6193 TCGA-76-6286 
       22.78         0.85        11.84        15.12         2.70        20.98 
TCGA-76-6662 TCGA-76-6663 TCGA-81-5911 
       34.45        18.64        17.72 

  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                         0.10                          0.16 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                       127.59                        115.86 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                        11.67                         14.47 
[1] "0.1 - 127.6 (11.7)" "0.2 - 115.9 (14.5)"
[1] "hr=" "1.2"
D44V2, continuous
D44V3, binary
                               cls
clus                              0   1
  DEL PEAK 19(9P21.3) MUTATED   168 250
  DEL PEAK 19(9P21.3) WILD-TYPE  56  97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED    168  250
  DEL PEAK 19(9P21.3) WILD-TYPE   56   97
        clus
vv       DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE
  FEMALE                         168                            56
  MALE                           250                            97
[1] 2 2
[1] FALSE
D44V4, binary
                               cls
clus                              0   1
  DEL PEAK 19(9P21.3) MUTATED    59 341
  DEL PEAK 19(9P21.3) WILD-TYPE  15 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED     59  341
  DEL PEAK 19(9P21.3) WILD-TYPE   15  133
     clus
vv    DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE
  NO                           59                            15
  YES                         341                           133
[1] 2 2
[1] FALSE
D44V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 19(9P21.3) MUTATED                              21
  DEL PEAK 19(9P21.3) WILD-TYPE                             7
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 19(9P21.3) MUTATED                    15
  DEL PEAK 19(9P21.3) WILD-TYPE                   3
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 19(9P21.3) MUTATED                               382
  DEL PEAK 19(9P21.3) WILD-TYPE                             143
D44V6, multiclass
                                 clus
vv                                DEL PEAK 19(9P21.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            21
  TREATED PRIMARY GBM                                      15
  UNTREATED PRIMARY (DE NOVO) GBM                         382
                                 clus
vv                                DEL PEAK 19(9P21.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               7
  TREATED PRIMARY GBM                                         3
  UNTREATED PRIMARY (DE NOVO) GBM                           143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9P21.3) MUTATED       9                        40   354
  DEL PEAK 19(9P21.3) WILD-TYPE     4                        10   131
D44V7, multiclass
                           clus
vv                          DEL PEAK 19(9P21.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          40
  WHITE                                             354
                           clus
vv                          DEL PEAK 19(9P21.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(9P21.3) MUTATED     8 343
  DEL PEAK 19(9P21.3) WILD-TYPE   4 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED      8  343
  DEL PEAK 19(9P21.3) WILD-TYPE    4  130
                        clus
vv                       DEL PEAK 19(9P21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         343
                        clus
vv                       DEL PEAK 19(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 20(9Q34.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(9Q34.2) MUTATED    11  67
  DEL PEAK 20(9Q34.2) WILD-TYPE  89 403
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           78                           492 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           67                           403 
$`DEL PEAK 20(9Q34.2) MUTATED`
TCGA-02-0006 TCGA-02-0015 TCGA-02-0016 TCGA-02-0034 TCGA-02-0070 TCGA-02-0107 
       18.35        20.61        87.06        14.14        25.05        17.65 
TCGA-02-0258 TCGA-02-0269 TCGA-02-0330 TCGA-02-2466 TCGA-02-2470 TCGA-06-0128 
       16.54        10.75        15.91        16.80        12.92        22.72 
TCGA-06-0132 TCGA-06-0141 TCGA-06-0162 TCGA-06-0173 TCGA-06-0177 TCGA-06-0208 
       25.35        10.29         3.42         4.47         4.18         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0237 TCGA-06-0409 TCGA-06-0412 TCGA-06-0743 
        7.63         7.40        13.64        72.36         9.57        26.40 
TCGA-06-0745 TCGA-06-0879 TCGA-06-1086 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
        7.86        40.41         6.84        15.32         1.08        17.65 
TCGA-06-2565 TCGA-06-5412 TCGA-06-6694 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0246 
       16.64         4.54         7.36         1.87         2.56         4.18 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0510 TCGA-12-0707 TCGA-12-0821 TCGA-12-0826 
        8.42        24.56         4.27        28.41        10.62        27.78 
TCGA-12-0827 TCGA-12-1091 TCGA-12-1093 TCGA-12-1602 TCGA-12-3648 TCGA-12-3652 
       38.76        33.21        15.98         6.77        26.93        34.92 
TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-1395 TCGA-14-1396 TCGA-14-1456 
       14.53        15.12        11.97         1.38         1.12        40.96 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
       13.78        50.53        53.19         3.91         4.31        29.03 
TCGA-16-1047 TCGA-19-0963 TCGA-19-2631 TCGA-19-5958 TCGA-19-A6J4 TCGA-26-1439 
        4.57        14.27         7.00        14.07         3.98        13.87 
TCGA-26-5136 TCGA-27-2521 TCGA-27-2528 TCGA-28-1757 TCGA-28-2506 TCGA-28-5220 
       18.97        10.39        15.78         0.13         6.74        10.49 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-4W-AA9S TCGA-RR-A6KC 
       21.14        19.86        10.85        13.35         1.45        20.55 

$`DEL PEAK 20(9Q34.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       82.59        77.65        20.12        53.10        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58         2.83         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        6.54         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        28.70         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       23.18        92.65        99.98        15.65        48.95        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 
       12.23         9.90         7.73        10.62         7.33        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 
       47.11        11.34         9.27        16.21         3.35        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 
        6.94         3.98        33.67        12.95        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90         0.20         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       11.80        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.12         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.66        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        7.17        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79        11.84        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93        12.56        30.64         5.95         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 
        0.43        31.50        11.74         3.55         8.35         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
       26.79         3.12        14.60        17.72        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 
       29.23        65.33         1.28        17.95        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 
       26.66        12.13         3.65        20.38        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        18.48        23.51         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82         7.59        21.73        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 
       59.77        44.02        15.22        10.95        12.69        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        0.79         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18         0.92         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-1446 TCGA-15-1449 
       17.49         7.96         3.78         3.42        19.10        13.28 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       17.59        26.07        16.37        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.66         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       14.96        17.79        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        18.08        16.08         7.59         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       14.40         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 TCGA-28-2509 
        8.48         1.22         1.55         2.83         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       22.68         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 
        8.84        22.78        25.18         3.72        12.59        19.23 
TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.08        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       36.20         1.61        17.72        26.30         5.92         6.28 

  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                        87.06                        127.59 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                       13.825                        12.000 
[1] "0.1 - 87.1 (13.8)"  "0.1 - 127.6 (12.0)"
[1] "hr=" "1"  
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 20(9Q34.2) MUTATED    30  49
  DEL PEAK 20(9Q34.2) WILD-TYPE 194 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED     30   49
  DEL PEAK 20(9Q34.2) WILD-TYPE  194  298
        clus
vv       DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE
  FEMALE                          30                           194
  MALE                            49                           298
[1] 2 2
[1] FALSE
D45V4, binary
                               cls
clus                              0   1
  DEL PEAK 20(9Q34.2) MUTATED     8  65
  DEL PEAK 20(9Q34.2) WILD-TYPE  66 409
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED      8   65
  DEL PEAK 20(9Q34.2) WILD-TYPE   66  409
     clus
vv    DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE
  NO                            8                            66
  YES                          65                           409
[1] 2 2
[1] FALSE
D45V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 20(9Q34.2) MUTATED                               8
  DEL PEAK 20(9Q34.2) WILD-TYPE                            20
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 20(9Q34.2) MUTATED                     3
  DEL PEAK 20(9Q34.2) WILD-TYPE                  15
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 20(9Q34.2) MUTATED                                68
  DEL PEAK 20(9Q34.2) WILD-TYPE                             457
D45V6, multiclass
                                 clus
vv                                DEL PEAK 20(9Q34.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             8
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          68
                                 clus
vv                                DEL PEAK 20(9Q34.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              20
  TREATED PRIMARY GBM                                        15
  UNTREATED PRIMARY (DE NOVO) GBM                           457
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(9Q34.2) MUTATED       1                        11    66
  DEL PEAK 20(9Q34.2) WILD-TYPE    12                        39   419
D45V7, multiclass
                           clus
vv                          DEL PEAK 20(9Q34.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              66
                           clus
vv                          DEL PEAK 20(9Q34.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            39
  WHITE                                               419
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(9Q34.2) MUTATED     0  71
  DEL PEAK 20(9Q34.2) WILD-TYPE  12 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED      0   71
  DEL PEAK 20(9Q34.2) WILD-TYPE   12  402
                        clus
vv                       DEL PEAK 20(9Q34.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK 20(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           402
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 21(10P15.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10P15.3) MUTATED    72 391
  DEL PEAK 21(10P15.3) WILD-TYPE  28  79
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           463                            107 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           391                             79 
$`DEL PEAK 21(10P15.3) MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
        4.73        18.35        10.59        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       53.10        12.16         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       10.52        18.31         6.87         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
        6.54         2.50        19.86         9.57        19.73        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0084 
       25.05         5.49        10.19        20.84        27.25        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 
       51.32         8.81        16.96         3.48        27.02        11.67 
TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 
       17.65        92.65        15.65        48.95        16.93        10.75 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62        15.91        25.71         4.37        25.12 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       20.38         6.94        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90         0.20        10.29        11.74         2.33 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
       17.79         8.61        19.46        46.59        12.33        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
        3.19        10.82         9.44         3.42        56.91         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
        4.18        20.25        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       48.69        10.82         0.26        72.36         4.70        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
       16.57        20.78        26.76        23.93         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 
       11.84        15.32        13.61         1.08        12.49        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        8.55         2.73         3.75         4.57         5.23         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 
        4.77        26.79         1.87         2.56        14.60        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        9.80         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97        12.56         4.27        42.15        11.08 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       10.75         4.80        18.41        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
       38.76         8.94        20.58        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 
       15.85         9.11        14.53         3.98        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       19.30         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 
       23.11         7.10         1.15        30.18         0.92        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
        7.17        17.49         7.96        13.78        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.91        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        9.14        21.24        13.97        11.77        21.90         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 
        4.64         3.65         7.17         3.25         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
        1.78        22.49        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03        13.87         9.73         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
       14.86         5.49         8.88        18.97         1.58         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       21.30        30.05        14.04        24.76        18.08        16.08 
TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2502 
        8.35         7.63         8.48         1.22         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
       13.64        22.68        10.49         5.42        15.39         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       14.86        12.23        20.78        15.02        15.95        22.78 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       18.64         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

$`DEL PEAK 21(10P15.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
       11.77        23.18        35.41        20.71        82.59        20.61 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 
       42.74        24.59        90.58        14.73         8.35         6.02 
TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 TCGA-02-0104 TCGA-02-0111 
       28.70        89.72        22.72        57.76        65.00        23.18 
TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 TCGA-02-0326 TCGA-02-0338 
       99.98        16.54        17.72        14.47         7.33        10.59 
TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 
       12.39        47.11        12.92        47.61         3.98        22.72 
TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0154 TCGA-06-0160 
       33.67         2.20        20.09        10.09        13.94        11.80 
TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0213 TCGA-06-0240 
       10.65        91.00        88.14         3.65         0.53        20.42 
TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 TCGA-06-1806 
        9.01         9.57         3.16         6.84        33.90        15.32 
TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 TCGA-06-6389 
        4.93         0.43        31.50         6.71         6.15         7.79 
TCGA-06-6391 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A7TL TCGA-08-0344 TCGA-08-0350 
        1.48         4.96         3.12        17.72       115.86        29.23 
TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0524 
       65.33         0.72        19.59        58.68        19.33         7.27 
TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       15.98         7.56        43.23       127.59         5.82         7.59 
TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-3477 
       21.73         4.14         1.12        40.96         6.67         3.78 
TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        3.42        50.53        53.19        26.07        16.37         4.31 
TCGA-16-1460 TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
        6.41         8.61        25.38        12.66         0.13         9.67 
TCGA-19-5958 TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 TCGA-27-1838 TCGA-27-2521 
       14.07        31.33         7.13         7.92        11.51        10.39 
TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1991 
        2.86         1.55         2.83         5.16        21.07        16.93 
TCGA-32-2616 TCGA-32-2632 TCGA-32-4208 TCGA-41-5651 TCGA-76-6664 
        7.36         8.84        21.14        15.12        36.20 

  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                         11.97                          14.07 
[1] "0.1 - 120.6 (12.0)" "0.1 - 127.6 (14.1)"
[1] "hr=" "1.7"
D46V2, continuous
D46V3, binary
                                cls
clus                               0   1
  DEL PEAK 21(10P15.3) MUTATED   175 289
  DEL PEAK 21(10P15.3) WILD-TYPE  49  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED    175  289
  DEL PEAK 21(10P15.3) WILD-TYPE   49   58
        clus
vv       DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE
  FEMALE                          175                             49
  MALE                            289                             58
[1] 2 2
[1] FALSE
D46V4, binary
                                cls
clus                               0   1
  DEL PEAK 21(10P15.3) MUTATED    62 382
  DEL PEAK 21(10P15.3) WILD-TYPE  12  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED     62  382
  DEL PEAK 21(10P15.3) WILD-TYPE   12   92
     clus
vv    DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE
  NO                            62                             12
  YES                          382                             92
[1] 2 2
[1] FALSE
D46V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 21(10P15.3) MUTATED                              20
  DEL PEAK 21(10P15.3) WILD-TYPE                             8
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 21(10P15.3) MUTATED                    11
  DEL PEAK 21(10P15.3) WILD-TYPE                   7
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 21(10P15.3) MUTATED                               433
  DEL PEAK 21(10P15.3) WILD-TYPE                              92
D46V6, multiclass
                                 clus
vv                                DEL PEAK 21(10P15.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             20
  TREATED PRIMARY GBM                                       11
  UNTREATED PRIMARY (DE NOVO) GBM                          433
                                 clus
vv                                DEL PEAK 21(10P15.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                8
  TREATED PRIMARY GBM                                          7
  UNTREATED PRIMARY (DE NOVO) GBM                             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10P15.3) MUTATED       8                        40   396
  DEL PEAK 21(10P15.3) WILD-TYPE     5                        10    89
D46V7, multiclass
                           clus
vv                          DEL PEAK 21(10P15.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           40
  WHITE                                              396
                           clus
vv                          DEL PEAK 21(10P15.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(10P15.3) MUTATED     8 379
  DEL PEAK 21(10P15.3) WILD-TYPE   4  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED      8  379
  DEL PEAK 21(10P15.3) WILD-TYPE    4   94
                        clus
vv                       DEL PEAK 21(10P15.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          379
                        clus
vv                       DEL PEAK 21(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             94
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 22(10P13) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(10P13) MUTATED    72 392
  DEL PEAK 22(10P13) WILD-TYPE  28  78
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         464                          106 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         392                           78 
$`DEL PEAK 22(10P13) MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
        4.73        18.35        10.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       20.12        53.10        42.74        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 
        3.62        10.72        10.52        18.31         6.87         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 
       15.09        12.59         6.54         2.50        19.86         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 
       27.25        12.62        51.32         8.81        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       27.02        11.67        17.65        92.65        15.65        48.95 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 
       12.23         9.90         7.73        10.62        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
        4.37        25.12        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 
        2.70         6.15        20.38         6.94        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
       10.29        11.74         2.33        17.79         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         3.42        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.12         4.47         3.22         4.04         4.18        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        8.42         7.63         7.40        11.84        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.64        13.32        48.69        10.82 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 
        0.26        72.36         4.70         9.57        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
       15.32        13.61         1.08        12.49        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95        16.64         5.98         4.37        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6693 
        2.73         3.75         4.57         5.23         5.39       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        1.87         2.56        14.60        22.68        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0520 TCGA-08-0521 
       12.56         4.27        42.15        11.08        10.75         4.80 
TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       18.41        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        14.86        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.98        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       30.18         0.92        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
       13.78        19.10        13.28        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 
       10.29        14.01         9.14        21.24        13.97        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
        5.95        12.95         4.64         3.65         7.17         3.25 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        22.49        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
       24.23        40.54        21.30        14.04        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         7.59        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01        13.64        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84         0.20        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        36.85        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       34.45        18.64         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

$`DEL PEAK 22(10P13) WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0026 
       11.77        23.18        35.41        20.71        82.59        24.59 
TCGA-02-0028 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 
       90.58        14.73         8.35         6.02        28.70        89.72 
TCGA-02-0083 TCGA-02-0087 TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 
       22.72        57.76        65.00        23.18        99.98        16.54 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 
       17.72        14.47         7.33        10.59        12.39        47.11 
TCGA-02-2470 TCGA-06-0125 TCGA-06-0127 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 
       12.92        47.61         3.98        33.67         2.20        20.09 
TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 
       10.09        11.80        10.65        91.00        88.14         3.65 
TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 
        0.53        20.42         9.01         3.16         6.84        33.90 
TCGA-06-1806 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 
       15.32         4.93         0.43        31.50         6.71         6.15 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TL 
        7.79         1.48         4.96        26.79         3.12        17.72 
TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 
      115.86        29.23        65.33         0.72        19.59        58.68 
TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 TCGA-12-0818 
       19.33         7.27        15.98         7.56        43.23        91.76 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 
      127.59         5.82         7.59        21.73         4.14         1.12 
TCGA-14-1456 TCGA-14-1458 TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 
       40.96         6.67         3.78         3.42        50.53        53.19 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-0960 
        3.91        26.07        16.37         4.31         6.41         8.61 
TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-5958 TCGA-26-1442 
       25.38        12.66         0.13         9.67        14.07        31.33 
TCGA-26-1443 TCGA-26-6173 TCGA-27-1836 TCGA-27-1838 TCGA-27-2526 TCGA-28-1755 
        7.13         7.92        30.05        11.51         2.86         1.55 
TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1976 TCGA-32-1991 TCGA-32-2616 
        2.83         5.16        21.07         0.49        16.93         7.36 
TCGA-32-2632 TCGA-32-4208 TCGA-41-5651 TCGA-76-6664 
        8.84        21.14        15.12        36.20 

  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                        0.10                         0.13 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                      120.56                       127.59 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                      12.035                       14.270 
[1] "0.1 - 120.6 (12.0)" "0.1 - 127.6 (14.3)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                              cls
clus                             0   1
  DEL PEAK 22(10P13) MUTATED   173 292
  DEL PEAK 22(10P13) WILD-TYPE  51  55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED    173  292
  DEL PEAK 22(10P13) WILD-TYPE   51   55
        clus
vv       DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE
  FEMALE                        173                           51
  MALE                          292                           55
[1] 2 2
[1] FALSE
D47V4, binary
                              cls
clus                             0   1
  DEL PEAK 22(10P13) MUTATED    60 385
  DEL PEAK 22(10P13) WILD-TYPE  14  89
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED     60  385
  DEL PEAK 22(10P13) WILD-TYPE   14   89
     clus
vv    DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE
  NO                          60                           14
  YES                        385                           89
[1] 2 2
[1] FALSE
D47V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 22(10P13) MUTATED                              19
  DEL PEAK 22(10P13) WILD-TYPE                             9
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 22(10P13) MUTATED                    11
  DEL PEAK 22(10P13) WILD-TYPE                   7
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 22(10P13) MUTATED                               435
  DEL PEAK 22(10P13) WILD-TYPE                              90
D47V6, multiclass
                                 clus
vv                                DEL PEAK 22(10P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           19
  TREATED PRIMARY GBM                                     11
  UNTREATED PRIMARY (DE NOVO) GBM                        435
                                 clus
vv                                DEL PEAK 22(10P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              9
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                           90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P13) MUTATED       8                        39   398
  DEL PEAK 22(10P13) WILD-TYPE     5                        11    87
D47V7, multiclass
                           clus
vv                          DEL PEAK 22(10P13) MUTATED
  ASIAN                                              8
  BLACK OR AFRICAN AMERICAN                         39
  WHITE                                            398
                           clus
vv                          DEL PEAK 22(10P13) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                              cls
clus                             0   1
  DEL PEAK 22(10P13) MUTATED     8 380
  DEL PEAK 22(10P13) WILD-TYPE   4  93
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED      8  380
  DEL PEAK 22(10P13) WILD-TYPE    4   93
                        clus
vv                       DEL PEAK 22(10P13) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                        380
                        clus
vv                       DEL PEAK 22(10P13) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           93
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 23(10P11.23) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 23(10P11.23) MUTATED    73 396
  DEL PEAK 23(10P11.23) WILD-TYPE  27  74
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            469                             101 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            396                              74 
$`DEL PEAK 23(10P11.23) MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
        4.73        18.35        10.59        87.06        77.65        20.12 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
       18.31         6.87         3.22        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        2.50        19.86         9.57        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        20.84        27.25        12.62        51.32 
TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
        8.81        16.96         3.48        27.02        11.67        17.65 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 
       92.65        15.65        48.95        16.93        10.75         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 
       10.62        15.91        25.71         4.37        25.12        14.50 
TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       10.55        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 
       47.61         6.94         3.98        22.72        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       11.74         2.33        17.79         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        4.47         3.22         4.04         4.18        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        8.42         7.63         7.40        11.84        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.64        13.32        48.69        10.82 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 
        0.26        72.36         4.70         9.57        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
       15.32        13.61         1.08        12.49        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95        16.64         5.98         4.37        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6693 
        2.73         3.75         4.57         5.23         5.39       120.56 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 
       12.85         4.77         1.55         4.77         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        2.56        14.60        22.68        37.84         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16         9.80         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       12.23        14.93        18.02        15.35        13.97        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        4.27        42.15        11.08        19.33        10.75         4.80 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85         7.63         9.73        14.93        14.86 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        8.94        20.58        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        0.79         1.38         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 
        7.10         1.15        30.18         0.92        12.43         0.99 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 
        7.96        13.78        19.10        13.28        17.59        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 
       10.75         9.07         5.95        12.95         4.64         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        7.17         3.25         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
       10.03        13.87         9.73         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88        18.97         1.58         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 
       30.05        14.04        24.76        18.08        10.39         7.59 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        7.63         8.48         1.22         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
        2.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         5.42        15.39         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.02        15.95        22.78        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       18.64         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

$`DEL PEAK 23(10P11.23) WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
       11.77        23.18        35.41        20.71        82.59        20.61 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 TCGA-02-0058 
       53.10        42.74        24.59        90.58        14.73         8.35 
TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 TCGA-02-0104 
        6.02        28.70        89.72        22.72        57.76        65.00 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 TCGA-02-0326 
       23.18        99.98        16.54        17.72        14.47         7.33 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0129 TCGA-06-0142 
       10.59        12.39        47.11        12.92        33.67         2.20 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 
       20.09        10.09        11.80        10.65        91.00        88.14 
TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 
        0.53        20.42         9.01         3.16         6.84        33.90 
TCGA-06-1806 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 
       15.32         4.93         0.43        31.50         6.71         6.15 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6701 TCGA-06-A5U0 
        7.79         1.48         7.36         8.32         4.96        26.79 
TCGA-06-A7TL TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 
       17.72       115.86        29.23        65.33         0.72        19.59 
TCGA-08-0517 TCGA-08-0524 TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 
       58.68         7.27        43.23        91.76       127.59         5.82 
TCGA-12-1090 TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 
        7.59        21.73         4.14         1.12        40.96         6.67 
TCGA-14-1821 TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 
       17.79         3.78         3.42        50.53        53.19         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-1390 TCGA-19-1787 
       26.07        16.37         4.31         6.41        25.38        12.66 
TCGA-19-1791 TCGA-19-5956 TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 TCGA-27-1838 
        0.13        22.49        31.33         7.13         7.92        11.51 
TCGA-27-2523 TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 
       16.08         2.86         1.55         2.83         5.16        21.07 
TCGA-32-1991 TCGA-32-2616 TCGA-32-2632 TCGA-32-4208 TCGA-76-6664 
       16.93         7.36         8.84        21.14        36.20 

  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                           0.10                            0.13 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                         120.56                          127.59 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                          11.84                           16.08 
[1] "0.1 - 120.6 (11.8)" "0.1 - 127.6 (16.1)"
[1] "hr=" "1.9"
D48V2, continuous
D48V3, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10P11.23) MUTATED   177 293
  DEL PEAK 23(10P11.23) WILD-TYPE  47  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED    177  293
  DEL PEAK 23(10P11.23) WILD-TYPE   47   54
        clus
vv       DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE
  FEMALE                           177                              47
  MALE                             293                              54
[1] 2 2
[1] FALSE
D48V4, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10P11.23) MUTATED    62 389
  DEL PEAK 23(10P11.23) WILD-TYPE  12  85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED     62  389
  DEL PEAK 23(10P11.23) WILD-TYPE   12   85
     clus
vv    DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE
  NO                             62                              12
  YES                           389                              85
[1] 2 2
[1] FALSE
D48V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 23(10P11.23) MUTATED                              20
  DEL PEAK 23(10P11.23) WILD-TYPE                             8
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 23(10P11.23) MUTATED                    10
  DEL PEAK 23(10P11.23) WILD-TYPE                   8
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 23(10P11.23) MUTATED                               440
  DEL PEAK 23(10P11.23) WILD-TYPE                              85
D48V6, multiclass
                                 clus
vv                                DEL PEAK 23(10P11.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              20
  TREATED PRIMARY GBM                                        10
  UNTREATED PRIMARY (DE NOVO) GBM                           440
                                 clus
vv                                DEL PEAK 23(10P11.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 8
  TREATED PRIMARY GBM                                           8
  UNTREATED PRIMARY (DE NOVO) GBM                              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10P11.23) MUTATED       8                        42   399
  DEL PEAK 23(10P11.23) WILD-TYPE     5                         8    86
D48V7, multiclass
                           clus
vv                          DEL PEAK 23(10P11.23) MUTATED
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            42
  WHITE                                               399
                           clus
vv                          DEL PEAK 23(10P11.23) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                               8
  WHITE                                                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10P11.23) MUTATED     8 386
  DEL PEAK 23(10P11.23) WILD-TYPE   4  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED      8  386
  DEL PEAK 23(10P11.23) WILD-TYPE    4   87
                        clus
vv                       DEL PEAK 23(10P11.23) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           386
                        clus
vv                       DEL PEAK 23(10P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              87
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED    83 424
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  46
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            507                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            424                              46 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 
       82.59        20.61        87.06        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       18.31         6.87         3.22        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
       19.86         9.57        19.73        26.43        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        20.84        27.25        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
        8.81        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        92.65        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 
       12.23         9.90         7.73        10.62        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
        4.37        25.12        10.59        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 
        9.27        16.21         3.35        16.80        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       26.70        24.23        11.90         0.20        10.29        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         3.42        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.12         4.47         3.22         4.04         4.18        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         0.26        72.36         4.70         9.57 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
       40.41        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 
       12.49         4.93        17.65        12.56         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        5.98         4.37        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 
        8.81         8.98         8.55         2.73         3.75         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        4.77         1.55         4.77        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        2.56        14.60        17.72        22.68        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 
        0.72        12.56         4.27        42.15        11.08        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.38         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        1.15        30.18         0.92        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 
        3.78        13.78        50.53        19.10        13.28        17.59 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
        9.14        21.24        13.97        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
        9.73         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        1.55         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01        13.64        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06         8.35        20.98         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0047 TCGA-02-0051 
       11.77        53.10        42.74        90.58        14.73        15.09 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0087 TCGA-02-0114 
        8.35         6.02        28.70        89.72        57.76        99.98 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0326 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 
       17.72        14.47         7.33        12.39        47.11        12.92 
TCGA-06-0142 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0240 
        2.20        11.80        10.65        91.00        88.14        20.42 
TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1806 TCGA-06-2563 TCGA-06-2569 
        9.01         3.16         6.84        15.32        30.64         0.43 
TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 TCGA-06-6389 TCGA-06-6391 TCGA-06-6701 
       31.50         6.71         6.15         7.79         1.48         4.96 
TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 
      115.86        29.23        65.33        19.59        58.68         7.27 
TCGA-12-0773 TCGA-12-0818 TCGA-12-1090 TCGA-12-1098 TCGA-14-1396 TCGA-14-1456 
       43.23        91.76         7.59         3.98         1.12        40.96 
TCGA-14-1458 TCGA-14-1821 TCGA-14-4157 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
        6.67        17.79         3.42        53.19         3.91        26.07 
TCGA-16-1460 TCGA-19-1390 TCGA-19-1787 TCGA-19-5958 TCGA-26-1442 TCGA-28-1756 
        6.41        25.38        12.66        14.07        31.33         2.83 
TCGA-28-5218 TCGA-32-2616 TCGA-76-6656 
        5.16         7.36         4.83 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.10                            0.43 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         127.59                          115.86 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          12.10                           14.07 
[1] "0.1 - 127.6 (12.1)" "0.4 - 115.9 (14.1)"
[1] "hr=" "1.9"
D49V2, continuous
D49V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   198 310
  DEL PEAK 24(10Q23.31) WILD-TYPE  26  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    198  310
  DEL PEAK 24(10Q23.31) WILD-TYPE   26   37
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                           198                              26
  MALE                             310                              37
[1] 2 2
[1] FALSE
D49V4, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    67 420
  DEL PEAK 24(10Q23.31) WILD-TYPE   7  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     67  420
  DEL PEAK 24(10Q23.31) WILD-TYPE    7   54
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                             67                               7
  YES                           420                              54
[1] 2 2
[1] FALSE
D49V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 24(10Q23.31) MUTATED                              23
  DEL PEAK 24(10Q23.31) WILD-TYPE                             5
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 24(10Q23.31) MUTATED                    13
  DEL PEAK 24(10Q23.31) WILD-TYPE                   5
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 24(10Q23.31) MUTATED                               472
  DEL PEAK 24(10Q23.31) WILD-TYPE                              53
D49V6, multiclass
                                 clus
vv                                DEL PEAK 24(10Q23.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              23
  TREATED PRIMARY GBM                                        13
  UNTREATED PRIMARY (DE NOVO) GBM                           472
                                 clus
vv                                DEL PEAK 24(10Q23.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 5
  TREATED PRIMARY GBM                                           5
  UNTREATED PRIMARY (DE NOVO) GBM                              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED      10                        45   432
  DEL PEAK 24(10Q23.31) WILD-TYPE     3                         5    53
D49V7, multiclass
                           clus
vv                          DEL PEAK 24(10Q23.31) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            45
  WHITE                                               432
                           clus
vv                          DEL PEAK 24(10Q23.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    10 420
  DEL PEAK 24(10Q23.31) WILD-TYPE   2  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     10  420
  DEL PEAK 24(10Q23.31) WILD-TYPE    2   53
                        clus
vv                       DEL PEAK 24(10Q23.31) MUTATED
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           420
                        clus
vv                       DEL PEAK 24(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              53
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 25(10Q26.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q26.3) MUTATED    85 423
  DEL PEAK 25(10Q26.3) WILD-TYPE  15  47
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           508                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           423                             47 
$`DEL PEAK 25(10Q26.3) MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       10.52        18.31         6.87         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 
        6.54         2.50        19.86         8.35         9.57        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       26.43        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32         8.81        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 
       27.02        65.00        11.67        17.65        92.65        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 
       48.95        16.54        16.93        10.75         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 
       15.91        25.71         4.37        25.12        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
       10.29        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
        3.19        10.82         9.44         3.42        56.91         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        4.18        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 
       13.64        13.32        48.69        10.82         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95        16.64         5.98         4.37        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6693 
        2.73         3.75         4.57         5.23         5.39       120.56 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 
        8.32        12.85         4.77         1.55         4.77        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56        14.60        17.72        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        9.80         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       11.08        58.68        19.33        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       53.85         7.63         9.73        14.93        14.86        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       12.23        15.85         9.11        14.53         3.98        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        5.39         2.89        16.50        26.33         2.04        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       19.30         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 
       23.11         7.10         1.15        30.18         0.92        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 
       19.10        13.28         3.91        17.59        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       13.97        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        3.39         9.07         5.95         4.64        25.38         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        7.17         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
        3.98        28.54        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 
        1.58         7.92         2.33        19.33         5.06         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        10.39         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        8.48         1.22         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       16.93        12.23        20.78        15.02        15.95        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

$`DEL PEAK 25(10Q26.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0028 TCGA-02-0047 TCGA-02-0060 TCGA-02-0069 
       11.77        53.10        90.58        14.73         6.02        28.70 
TCGA-02-0080 TCGA-02-0087 TCGA-02-0111 TCGA-02-0114 TCGA-02-0266 TCGA-02-0271 
       89.72        57.76        23.18        99.98        17.72        14.47 
TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-2470 TCGA-06-0142 TCGA-06-0160 
        7.33        10.59        12.39        12.92         2.20        11.80 
TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 
       10.65        91.00        88.14        20.42         9.01         3.16 
TCGA-06-1086 TCGA-06-1806 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 
        6.84        15.32         0.43        31.50         6.71         6.15 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6694 TCGA-06-6701 TCGA-08-0245 TCGA-08-0350 
        7.79         1.48         7.36         4.96        37.84        29.23 
TCGA-08-0351 TCGA-08-0516 TCGA-08-0524 TCGA-12-0773 TCGA-12-0818 TCGA-12-1090 
       65.33        19.59         7.27        43.23        91.76         7.59 
TCGA-12-1099 TCGA-14-0871 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 
        4.14        28.93         1.12        40.96         6.67        17.79 
TCGA-15-1447 TCGA-16-0849 TCGA-16-1460 TCGA-19-1385 TCGA-19-1388 TCGA-19-1787 
       53.19        26.07         6.41        10.75        12.95        12.66 
TCGA-26-1442 TCGA-27-1831 TCGA-27-2523 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 
       31.33        16.60        16.08         1.55         2.83         5.16 
TCGA-32-2616 TCGA-32-2632 
        7.36         8.84 

  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                          0.10                           0.43 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                        127.59                          99.98 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                        12.145                         12.790 
[1] "0.1 - 127.6 (12.1)" "0.4 - 100.0 (12.8)"
[1] "hr=" "1.6"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED   198 311
  DEL PEAK 25(10Q26.3) WILD-TYPE  26  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED    198  311
  DEL PEAK 25(10Q26.3) WILD-TYPE   26   36
        clus
vv       DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  FEMALE                          198                             26
  MALE                            311                             36
[1] 2 2
[1] FALSE
D50V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED    69 421
  DEL PEAK 25(10Q26.3) WILD-TYPE   5  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     69  421
  DEL PEAK 25(10Q26.3) WILD-TYPE    5   53
     clus
vv    DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  NO                            69                              5
  YES                          421                             53
[1] 2 2
[1] FALSE
D50V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 25(10Q26.3) MUTATED                              23
  DEL PEAK 25(10Q26.3) WILD-TYPE                             5
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 25(10Q26.3) MUTATED                    14
  DEL PEAK 25(10Q26.3) WILD-TYPE                   4
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 25(10Q26.3) MUTATED                               472
  DEL PEAK 25(10Q26.3) WILD-TYPE                              53
D50V6, multiclass
                                 clus
vv                                DEL PEAK 25(10Q26.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             23
  TREATED PRIMARY GBM                                       14
  UNTREATED PRIMARY (DE NOVO) GBM                          472
                                 clus
vv                                DEL PEAK 25(10Q26.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                5
  TREATED PRIMARY GBM                                          4
  UNTREATED PRIMARY (DE NOVO) GBM                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q26.3) MUTATED       9                        46   433
  DEL PEAK 25(10Q26.3) WILD-TYPE     4                         4    52
D50V7, multiclass
                           clus
vv                          DEL PEAK 25(10Q26.3) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                           46
  WHITE                                              433
                           clus
vv                          DEL PEAK 25(10Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED    10 421
  DEL PEAK 25(10Q26.3) WILD-TYPE   2  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     10  421
  DEL PEAK 25(10Q26.3) WILD-TYPE    2   52
                        clus
vv                       DEL PEAK 25(10Q26.3) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          421
                        clus
vv                       DEL PEAK 25(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             52
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 26(11P15.5) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11P15.5) MUTATED    22 107
  DEL PEAK 26(11P15.5) WILD-TYPE  78 363
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            441 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           107                            363 
$`DEL PEAK 26(11P15.5) MUTATED`
TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0024 TCGA-02-0033 
       35.41        82.59        20.61        87.06        53.10         2.83 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 
       14.73         3.22        15.09        12.59         2.50         8.35 
TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0084 TCGA-02-0086 
        9.57        28.70        10.19        20.84        12.62         8.81 
TCGA-02-0087 TCGA-02-0099 TCGA-02-0104 TCGA-02-0113 TCGA-02-0114 TCGA-02-0281 
       57.76         3.48        65.00        92.65        99.98         3.98 
TCGA-02-0332 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 
       25.71         3.35        16.80        15.32        22.72        33.67 
TCGA-06-0146 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 
       20.09         9.44         5.85         3.22         4.18        69.90 
TCGA-06-0192 TCGA-06-0197 TCGA-06-0213 TCGA-06-0216 TCGA-06-0221 TCGA-06-0238 
       38.96         5.56         0.53        24.16        19.82        13.32 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-1086 
       72.36         4.70        35.11         2.10        14.20         6.84 
TCGA-06-1800 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2569 TCGA-06-2570 
       26.79        33.90        15.32        12.49         0.43        31.50 
TCGA-06-5408 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-06-A7TK TCGA-06-A7TL 
       11.74         3.75         7.79         7.36        14.60        17.72 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0348 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 
       37.84         4.18        12.16        65.33         8.42        24.56 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0510 TCGA-08-0517 TCGA-12-0616 TCGA-12-0619 
       12.23        14.93         4.27        58.68        14.73        34.92 
TCGA-12-0691 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 
       12.13        53.85        24.79        23.51        38.76         4.14 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0813 
        6.77        44.02        14.53        11.97         6.21         1.35 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1454 
        5.39        16.50         2.04        28.93         1.15        30.18 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 TCGA-14-3477 TCGA-15-1444 
       12.43         0.99        17.79        17.85         3.78        50.53 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-1045 
       53.19        13.28         3.91        17.59        16.37        29.03 
TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 TCGA-19-5960 
        5.95        25.38         3.65         7.53        16.80        14.96 
TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1442 TCGA-26-5133 TCGA-27-1830 TCGA-27-2521 
        3.98        13.87        31.33        14.86         5.06        10.39 
TCGA-28-1756 TCGA-28-2502 TCGA-28-2509 TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 
        2.83         0.66         4.77        13.64        21.07         0.49 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 
       15.95         8.84        21.14         3.72        10.85        11.84 
TCGA-74-6584 TCGA-76-4934 TCGA-76-6286 
        7.50         2.53        20.98 

$`DEL PEAK 26(11P15.5) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       77.65        20.12        42.74        24.59        12.16        90.58 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        6.54        19.86         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0089 
        5.49        27.25        89.72        22.72        51.32        16.96 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0115 TCGA-02-0116 
       27.02        11.67        17.65        23.18        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
       47.61         6.94         3.98        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.12         4.47         4.04        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        3.65        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         7.40         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 
        7.40        11.84        15.02         0.72        13.64        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       48.69        10.82         9.01         0.26         9.57         3.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 
       12.62         5.75         5.75         9.80        23.57        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93         4.04        11.84        15.32        13.61 
TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
       16.64         5.98         4.37         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        4.57         5.23         5.39         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 
        1.87         3.12         2.56        22.68       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0354 
        8.42        25.71         9.80        29.23         1.28        17.95 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 
       31.10        37.58        22.29         3.39        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        7.56        15.35        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 
       14.86        91.76        18.48        10.62        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       15.12         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        3.25         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1825 
        7.10         0.92        40.96         6.67         1.97         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.42        13.78 
TCGA-15-1446 TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       19.10        26.07         4.31         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A60I 
        4.73        12.10         1.78        22.49        14.07        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03         9.73         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
       19.33        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        18.08        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.13         6.74         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 
        5.16        22.68        10.49         5.42        15.39         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.02         7.36        22.78 
TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       25.18        12.59        19.86        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 
        8.94         9.53         0.99         4.44         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06         8.35         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                         99.98                         127.59 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                         13.87                          11.77 
[1] "0.4 - 100.0 (13.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D51V2, continuous
D51V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    57  72
  DEL PEAK 26(11P15.5) WILD-TYPE 167 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     57   72
  DEL PEAK 26(11P15.5) WILD-TYPE  167  275
        clus
vv       DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  FEMALE                           57                            167
  MALE                             72                            275
[1] 2 2
[1] FALSE
D51V4, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    16 107
  DEL PEAK 26(11P15.5) WILD-TYPE  58 367
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     16  107
  DEL PEAK 26(11P15.5) WILD-TYPE   58  367
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  NO                            16                             58
  YES                          107                            367
[1] 2 2
[1] FALSE
D51V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 26(11P15.5) MUTATED                               6
  DEL PEAK 26(11P15.5) WILD-TYPE                            22
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 26(11P15.5) MUTATED                     6
  DEL PEAK 26(11P15.5) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 26(11P15.5) MUTATED                               117
  DEL PEAK 26(11P15.5) WILD-TYPE                             408
D51V6, multiclass
                                 clus
vv                                DEL PEAK 26(11P15.5) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          117
                                 clus
vv                                DEL PEAK 26(11P15.5) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               22
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            408
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11P15.5) MUTATED       3                        11   110
  DEL PEAK 26(11P15.5) WILD-TYPE    10                        39   375
D51V7, multiclass
                           clus
vv                          DEL PEAK 26(11P15.5) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              110
                           clus
vv                          DEL PEAK 26(11P15.5) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                375
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED     2 105
  DEL PEAK 26(11P15.5) WILD-TYPE  10 368
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      2  105
  DEL PEAK 26(11P15.5) WILD-TYPE   10  368
                        clus
vv                       DEL PEAK 26(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          105
                        clus
vv                       DEL PEAK 26(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            368
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 27(11P11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11P11.2) MUTATED    18  87
  DEL PEAK 27(11P11.2) WILD-TYPE  82 383
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           105                            465 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                            87                            383 
$`DEL PEAK 27(11P11.2) MUTATED`
TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       35.41        53.10         2.83        14.73         3.22        12.59 
TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0084 
        2.50         9.57        28.70        10.19        20.84        12.62 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0266 
        8.81        57.76        92.65        99.98        15.65        17.72 
TCGA-02-0281 TCGA-02-0332 TCGA-02-0456 TCGA-02-2466 TCGA-06-0128 TCGA-06-0159 
        3.98        25.71         3.35        16.80        22.72         9.44 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 
        5.85         3.22         4.18        69.90        44.58        38.96 
TCGA-06-0197 TCGA-06-0216 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
        5.56        24.16        13.32        72.36         4.70        35.11 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1805 
        2.10        14.20        46.19         6.84        26.79        33.90 
TCGA-06-1806 TCGA-06-2570 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-06-A7TK 
       15.32        31.50         3.75         7.79         7.36        14.60 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0353 TCGA-08-0510 TCGA-12-0616 TCGA-12-0619 
       17.72        37.84         8.42         4.27        14.73        34.92 
TCGA-12-0670 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 
       25.97        53.85        24.79        23.51        38.76         4.14 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0817 
        6.77        44.02        14.53        11.97         6.21         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 
       16.50         2.04        28.93        30.18        12.43         0.99 
TCGA-14-1821 TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       17.79        17.85         3.78        53.19        13.28         3.91 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 
       16.37         4.31        29.03         5.95        25.38         3.65 
TCGA-19-2623 TCGA-19-5951 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 
        7.53         8.02        16.80        14.96         3.98        13.87 
TCGA-26-5133 TCGA-27-1830 TCGA-27-2521 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 
       14.86         5.06        10.39         4.77        13.64         0.49 
TCGA-32-1986 TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 
       12.69        15.95         8.84         3.72        10.85        11.84 
TCGA-74-6584 TCGA-76-4934 TCGA-76-6286 
        7.50         2.53        20.98 

$`DEL PEAK 27(11P11.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16        90.58        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 
       10.52        18.31         6.87        15.09         6.54        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        8.35         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0089 TCGA-02-0099 
       27.25        89.72        22.72        51.32        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0116 
       27.02        65.00        11.67        17.65        23.18        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.21        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.61         6.94         3.98        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         4.47         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       88.14        20.25         3.65        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       10.42         4.67         7.40         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        7.63         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.64        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.80        23.57        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 
       16.57        20.78        26.76        23.93         4.04        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       15.32        13.61         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        7.56        15.35        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 
       14.86        91.76        18.48        10.62        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       15.12         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 
        3.25         1.35         2.89        26.33        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.67 
TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
        1.97         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 TCGA-16-0849 
        3.42        13.78        50.53        19.10        17.59        26.07 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 
        3.39        10.75         9.07        12.95         4.64         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
       17.19        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       14.07        17.79        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33        19.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
        2.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
       22.68        10.49         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 
       15.85        19.50         1.18         4.67        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.02         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       21.14        12.59        19.86        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 
        8.94         9.53         0.99         4.44         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06         8.35         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                         99.98                         127.59 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                         13.64                          11.84 
[1] "0.5 - 100.0 (13.6)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    47  58
  DEL PEAK 27(11P11.2) WILD-TYPE 177 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     47   58
  DEL PEAK 27(11P11.2) WILD-TYPE  177  289
        clus
vv       DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  FEMALE                           47                            177
  MALE                             58                            289
[1] 2 2
[1] FALSE
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    13  87
  DEL PEAK 27(11P11.2) WILD-TYPE  61 387
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     13   87
  DEL PEAK 27(11P11.2) WILD-TYPE   61  387
     clus
vv    DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  NO                            13                             61
  YES                           87                            387
[1] 2 2
[1] FALSE
D52V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 27(11P11.2) MUTATED                               5
  DEL PEAK 27(11P11.2) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 27(11P11.2) MUTATED                     6
  DEL PEAK 27(11P11.2) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 27(11P11.2) MUTATED                                94
  DEL PEAK 27(11P11.2) WILD-TYPE                             431
D52V6, multiclass
                                 clus
vv                                DEL PEAK 27(11P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                           94
                                 clus
vv                                DEL PEAK 27(11P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(11P11.2) MUTATED       2                        11    88
  DEL PEAK 27(11P11.2) WILD-TYPE    11                        39   397
D52V7, multiclass
                           clus
vv                          DEL PEAK 27(11P11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               88
                           clus
vv                          DEL PEAK 27(11P11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                397
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED     2  84
  DEL PEAK 27(11P11.2) WILD-TYPE  10 389
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED      2   84
  DEL PEAK 27(11P11.2) WILD-TYPE   10  389
                        clus
vv                       DEL PEAK 27(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 27(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            389
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 28(11Q14.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(11Q14.1) MUTATED     9  87
  DEL PEAK 28(11Q14.1) WILD-TYPE  91 383
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            474 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            87                            383 
$`DEL PEAK 28(11Q14.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0048 
       11.77        23.18        35.41        53.10         2.83         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 
       12.59         2.50         9.57        28.70        10.19        20.84 
TCGA-02-0086 TCGA-02-0111 TCGA-02-0113 TCGA-02-0266 TCGA-02-0281 TCGA-02-0332 
        8.81        23.18        92.65        17.72         3.98        25.71 
TCGA-02-0339 TCGA-02-0456 TCGA-02-2466 TCGA-06-0130 TCGA-06-0159 TCGA-06-0166 
       12.39         3.35        16.80        12.95         9.44         5.85 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 
        3.22         4.18        69.90        44.58        10.42        38.96 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0216 TCGA-06-0238 TCGA-06-0241 TCGA-06-0409 
        7.40         5.56        24.16        13.32        48.69        72.36 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1800 
        4.70        35.11         2.10        14.20        46.19        26.79 
TCGA-06-1806 TCGA-06-5856 TCGA-06-6390 TCGA-06-6694 TCGA-06-A7TK TCGA-08-0245 
       15.32         3.75         5.39         7.36        14.60        37.84 
TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 TCGA-12-0772 TCGA-12-0819 
        4.27        10.75        14.73        34.92        53.85        24.79 
TCGA-12-0822 TCGA-12-1091 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 
       23.51        33.21         4.14        15.65         6.77        44.02 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 
       14.53         6.21         5.39        16.50         2.04        28.93 
TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-1449 
       30.18        12.43         0.99        17.85         3.78        13.28 
TCGA-16-0846 TCGA-16-0850 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 
        3.91        16.37        29.03         5.95        25.38         3.65 
TCGA-19-5959 TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-28-2509 TCGA-28-5216 
       16.80        13.87         5.06        10.39         4.77        13.64 
TCGA-32-1976 TCGA-32-1986 TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 
        0.49        12.69        15.95         8.84         3.72        10.85 
TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 TCGA-76-6286 TCGA-76-6661 TCGA-81-5910 
       11.84         7.50         2.53        20.98        23.90         1.61 

$`DEL PEAK 28(11Q14.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
        4.73        18.35        10.59        20.71        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
       90.58        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        6.87        14.73        15.09         6.54        19.86         8.35 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 
        6.02        19.73        26.43        25.05         5.49        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 
        3.48        27.02        65.00        11.67        17.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.54        16.93        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
       10.62         7.33        15.91         4.37        25.12        10.59 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.66         3.29        13.12         4.47         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       15.42         4.67         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       13.64        20.42        10.82         9.01         0.26         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
        3.16        12.62         5.75         5.75         9.80        23.57 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84         4.04        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        4.57         5.23         7.79         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 
        1.87         3.12         2.56        17.72        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       18.02        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        58.68        19.33         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        15.35        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
       12.13         3.65        20.38        28.41        15.06        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 
        7.63         9.73        14.93        14.86        91.76        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
        9.11        14.53         3.98        25.68        14.73        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        2.24        11.24        13.78         3.25         1.35         2.89 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       26.33        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        0.92        40.96         6.67         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 
       50.53        19.10        53.19        17.59        26.07         4.31 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 
        3.39        10.75         9.07        12.95         4.64         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
        1.78        22.49        14.07        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33        19.33        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       18.08        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        23.44        11.01         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
       10.49         5.42        15.39        21.07         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02         7.36        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17        36.85        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 
       17.06         8.35         4.83         5.03        34.45        18.64 
TCGA-76-6664 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       36.20        17.72        26.30         5.92         6.28        20.55 

  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                        12.820                         12.035 
[1] "0.5 - 92.7 (12.8)"  "0.1 - 127.6 (12.0)"
[1] "hr=" "1"  
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    42  54
  DEL PEAK 28(11Q14.1) WILD-TYPE 182 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     42   54
  DEL PEAK 28(11Q14.1) WILD-TYPE  182  293
        clus
vv       DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  FEMALE                           42                            182
  MALE                             54                            293
[1] 2 2
[1] FALSE
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    14  79
  DEL PEAK 28(11Q14.1) WILD-TYPE  60 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     14   79
  DEL PEAK 28(11Q14.1) WILD-TYPE   60  395
     clus
vv    DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  NO                            14                             60
  YES                           79                            395
[1] 2 2
[1] FALSE
D53V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 28(11Q14.1) MUTATED                               3
  DEL PEAK 28(11Q14.1) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 28(11Q14.1) MUTATED                     5
  DEL PEAK 28(11Q14.1) WILD-TYPE                  13
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 28(11Q14.1) MUTATED                                88
  DEL PEAK 28(11Q14.1) WILD-TYPE                             437
D53V6, multiclass
                                 clus
vv                                DEL PEAK 28(11Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        5
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 28(11Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         13
  UNTREATED PRIMARY (DE NOVO) GBM                            437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11Q14.1) MUTATED       2                         7    83
  DEL PEAK 28(11Q14.1) WILD-TYPE    11                        43   402
D53V7, multiclass
                           clus
vv                          DEL PEAK 28(11Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               83
                           clus
vv                          DEL PEAK 28(11Q14.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED     1  78
  DEL PEAK 28(11Q14.1) WILD-TYPE  11 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED      1   78
  DEL PEAK 28(11Q14.1) WILD-TYPE   11  395
                        clus
vv                       DEL PEAK 28(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 28(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            395
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 29(12P13.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(12P13.1) MUTATED    17  54
  DEL PEAK 29(12P13.1) WILD-TYPE  83 416
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            499 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            54                            416 
$`DEL PEAK 29(12P13.1) MUTATED`
TCGA-02-0014 TCGA-02-0026 TCGA-02-0034 TCGA-02-0038 TCGA-02-0055 TCGA-02-0071 
       82.59        24.59        14.14        10.72         2.50         5.49 
TCGA-02-0075 TCGA-02-0085 TCGA-02-0087 TCGA-02-0104 TCGA-02-0113 TCGA-06-0129 
       20.84        51.32        57.76        65.00        92.65        33.67 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0175 TCGA-06-0190 TCGA-06-0195 
       17.79         8.61         9.44         4.04        10.42         7.40 
TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0414 TCGA-06-0646 TCGA-06-1801 
        5.56        19.82        13.64        35.11         5.75        11.84 
TCGA-06-2570 TCGA-06-5415 TCGA-06-5859 TCGA-06-6390 TCGA-06-6694 TCGA-06-6697 
       31.50         8.55         4.57         5.39         7.36        12.85 
TCGA-06-6700 TCGA-08-0245 TCGA-08-0348 TCGA-08-0349 TCGA-08-0359 TCGA-08-0386 
        4.77        37.84        12.16         9.80         3.39        18.02 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-12-0619 TCGA-12-1598 TCGA-12-1600 
        4.27        11.08        19.33        34.92        15.65        14.73 
TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 
       44.02         6.21         5.39         2.04        28.93        23.11 
TCGA-14-1794 TCGA-14-3477 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1055 
        0.99         3.78        26.07        16.37         4.31        10.29 
TCGA-19-0960 TCGA-19-1385 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-4065 
        8.61        10.75        12.95        25.38         7.53         7.04 
TCGA-26-5132 TCGA-26-5136 TCGA-27-1836 TCGA-28-2514 TCGA-28-5204 TCGA-32-1978 
        9.40        18.97        30.05         5.26        14.93        15.85 
TCGA-32-2494 TCGA-32-4208 TCGA-76-4935 TCGA-76-6193 TCGA-76-6664 
       20.78        21.14        36.85         2.70        36.20 

$`DEL PEAK 29(12P13.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0039 
       42.74        12.16        90.58         2.83         3.62        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        6.54        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 
       26.43        28.70        25.05        10.19        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       22.72        12.62         8.81        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       11.74         2.33        20.09        10.09        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       12.33        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
       13.12         4.47         3.22        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       15.42        38.96         4.67         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        72.36         4.70         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 
       26.76        23.93         6.84         4.04        26.79        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37         0.43        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         6.71         2.73         3.75         6.15 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6698 
        5.23         7.79         1.48       120.56         8.32         4.77 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       14.60        17.72        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
       17.95        24.56        31.10        37.58        22.29        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       19.59        58.68        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       18.41         7.56        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
        3.98         4.14        25.68         6.77        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        2.24        11.24        13.78         3.25         1.35         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       16.50        26.33        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1453 
        1.12         3.75        32.05        58.78         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 
       13.28         3.91        17.59        29.03         4.57        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
        0.66        14.27         3.39         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         0.16         4.08        24.23         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
        7.13         9.37        14.86         5.49         8.88         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        40.54        21.30        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        6.74         4.77         7.30        11.28        17.88         2.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        9.17         2.53        16.70         3.29        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       18.64         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                          0.99                           0.10 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                         12.85                          12.16 
[1] "1.0 - 92.7 (12.8)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.3"
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED    31  40
  DEL PEAK 29(12P13.1) WILD-TYPE 193 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED     31   40
  DEL PEAK 29(12P13.1) WILD-TYPE  193  307
        clus
vv       DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  FEMALE                           31                            193
  MALE                             40                            307
[1] 2 2
[1] FALSE
D54V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED     7  61
  DEL PEAK 29(12P13.1) WILD-TYPE  67 413
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      7   61
  DEL PEAK 29(12P13.1) WILD-TYPE   67  413
     clus
vv    DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  NO                             7                             67
  YES                           61                            413
[1] 2 2
[1] FALSE
D54V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 29(12P13.1) MUTATED                               1
  DEL PEAK 29(12P13.1) WILD-TYPE                            27
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 29(12P13.1) MUTATED                     1
  DEL PEAK 29(12P13.1) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 29(12P13.1) MUTATED                                69
  DEL PEAK 29(12P13.1) WILD-TYPE                             456
D54V6, multiclass
                                 clus
vv                                DEL PEAK 29(12P13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           69
                                 clus
vv                                DEL PEAK 29(12P13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            456
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(12P13.1) MUTATED       2                         2    64
  DEL PEAK 29(12P13.1) WILD-TYPE    11                        48   421
D54V7, multiclass
                           clus
vv                          DEL PEAK 29(12P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               64
                           clus
vv                          DEL PEAK 29(12P13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             48
  WHITE                                                421
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED     1  59
  DEL PEAK 29(12P13.1) WILD-TYPE  11 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      1   59
  DEL PEAK 29(12P13.1) WILD-TYPE   11  414
                        clus
vv                       DEL PEAK 29(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 29(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            414
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 30(12Q12) MUTATION ANALYSIS
D55V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 30(12Q12) MUTATED    14  62
  DEL PEAK 30(12Q12) WILD-TYPE  86 408
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          76                          494 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          62                          408 
$`DEL PEAK 30(12Q12) MUTATED`
TCGA-02-0034 TCGA-02-0046 TCGA-02-0055 TCGA-02-0071 TCGA-02-0075 TCGA-02-0084 
       14.14         6.87         2.50         5.49        20.84        12.62 
TCGA-02-0087 TCGA-02-0102 TCGA-02-0104 TCGA-02-0113 TCGA-06-0146 TCGA-06-0147 
       57.76        27.02        65.00        92.65        20.09        17.79 
TCGA-06-0149 TCGA-06-0159 TCGA-06-0173 TCGA-06-0175 TCGA-06-0184 TCGA-06-0190 
        8.61         9.44         4.47         4.04        69.90        10.42 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 
        7.40         5.56        19.82        13.64         4.70        35.11 
TCGA-06-0875 TCGA-06-5856 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 TCGA-06-A7TL 
       43.46         3.75         7.79         5.39         7.36        17.72 
TCGA-08-0245 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0386 TCGA-08-0510 
       37.84        12.16         9.80        65.33        18.02         4.27 
TCGA-08-0514 TCGA-12-0619 TCGA-12-0662 TCGA-12-1600 TCGA-12-3646 TCGA-14-0740 
       11.08        34.92        38.17        14.73        44.02        11.97 
TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 
        6.21         1.35         5.39         2.04        28.93        23.11 
TCGA-14-1453 TCGA-14-1458 TCGA-14-1794 TCGA-14-1821 TCGA-14-3477 TCGA-16-0849 
        1.15         6.67         0.99        17.79         3.78        26.07 
TCGA-16-0850 TCGA-16-1056 TCGA-19-0957 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 
       16.37        14.01        21.90        12.95        25.38         7.53 
TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5136 TCGA-28-1746 
        7.04        14.96        10.03         9.40        18.97         0.20 
TCGA-28-1756 TCGA-32-1978 TCGA-32-2494 TCGA-32-4208 TCGA-32-4210 TCGA-41-2571 
        2.83        15.85        20.78        21.14         3.72         0.85 
TCGA-41-5651 TCGA-76-4935 TCGA-76-6193 TCGA-RR-A6KA 
       15.12        36.85         2.70         6.28 

$`DEL PEAK 30(12Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0047 TCGA-02-0048 
        3.62        10.72        10.52        18.31        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 
        6.02        19.73        26.43        28.70        25.05        10.19 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 
       27.25        89.72        22.72        51.32         8.81        16.96 
TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
        3.48        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 
       10.29         2.20        11.74         2.33        10.09        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        3.29        13.12         3.22        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        73.84        27.22        44.58        15.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       38.96         4.67         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       72.36         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         2.70         0.92        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        4.57         5.23         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        14.60        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 
        1.74         8.42        25.71        29.23         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 
       12.99        10.45         7.59        94.78         0.10        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       14.53         3.98         4.14        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       14.53        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
       23.05         2.24        11.24        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       16.50        26.33        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 
        1.12         3.75        32.05        58.78         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
        0.92        40.96        12.43         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19        13.28         3.91        17.59 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 
        4.31        29.03         4.57        10.29         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       13.97         6.41        11.77         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 
        3.39        10.75         9.07         5.95         4.64         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        1.08         0.16         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       22.49        14.07        16.80        17.79         3.98        28.54 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.37        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 
        5.42        15.39        21.07         0.49         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        10.85        19.23        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        9.53         0.99         4.44        11.84         0.20        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 
        3.65         9.17         2.53        16.70         3.29        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KC 
        5.92        20.55 

  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                       92.65                       127.59 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                      12.390                       12.195 
[1] "0.2 - 92.7 (12.4)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    32  44
  DEL PEAK 30(12Q12) WILD-TYPE 192 303
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     32   44
  DEL PEAK 30(12Q12) WILD-TYPE  192  303
        clus
vv       DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  FEMALE                         32                          192
  MALE                           44                          303
[1] 2 2
[1] FALSE
D55V4, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    13  58
  DEL PEAK 30(12Q12) WILD-TYPE  61 416
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     13   58
  DEL PEAK 30(12Q12) WILD-TYPE   61  416
     clus
vv    DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  NO                          13                           61
  YES                         58                          416
[1] 2 2
[1] FALSE
D55V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 30(12Q12) MUTATED                               3
  DEL PEAK 30(12Q12) WILD-TYPE                            25
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 30(12Q12) MUTATED                     2
  DEL PEAK 30(12Q12) WILD-TYPE                  16
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 30(12Q12) MUTATED                                71
  DEL PEAK 30(12Q12) WILD-TYPE                             454
D55V6, multiclass
                                 clus
vv                                DEL PEAK 30(12Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            3
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 30(12Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             25
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q12) MUTATED       0                         6    67
  DEL PEAK 30(12Q12) WILD-TYPE    13                        44   418
D55V7, multiclass
                           clus
vv                          DEL PEAK 30(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             67
                           clus
vv                          DEL PEAK 30(12Q12) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           44
  WHITE                                              418
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED     2  60
  DEL PEAK 30(12Q12) WILD-TYPE  10 413
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED      2   60
  DEL PEAK 30(12Q12) WILD-TYPE   10  413
                        clus
vv                       DEL PEAK 30(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       DEL PEAK 30(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          413
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 31(12Q15) MUTATION ANALYSIS
D56V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(12Q15) MUTATED    14  64
  DEL PEAK 31(12Q15) WILD-TYPE  86 406
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          78                          492 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          64                          406 
$`DEL PEAK 31(12Q15) MUTATED`
TCGA-02-0034 TCGA-02-0052 TCGA-02-0055 TCGA-02-0071 TCGA-02-0075 TCGA-02-0084 
       14.14        12.59         2.50         5.49        20.84        12.62 
TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 TCGA-02-0113 TCGA-02-0266 TCGA-02-2466 
       57.76         3.48        27.02        92.65        17.72        16.80 
TCGA-06-0140 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 
        0.20        20.09        17.79         8.61        12.33         9.44 
TCGA-06-0162 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0190 
        3.42         4.47         3.22         4.18        69.90        10.42 
TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
        5.56        19.82        13.64         4.70        35.11         2.10 
TCGA-06-0875 TCGA-06-0939 TCGA-06-6389 TCGA-06-6694 TCGA-06-6695 TCGA-06-A7TK 
       43.46        26.76         7.79         7.36         8.32        14.60 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0349 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 
       17.72        37.84         9.80        18.02         4.27        11.08 
TCGA-12-0616 TCGA-12-0619 TCGA-12-1088 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 
       14.73        34.92       127.59        14.73         6.77        44.02 
TCGA-14-0740 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
       11.97         6.21         1.35         5.39         2.04        28.93 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1794 TCGA-14-3477 TCGA-15-1447 TCGA-16-0849 
       23.11         1.15         0.99         3.78        53.19        26.07 
TCGA-16-0850 TCGA-19-0957 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-2624 
       16.37        21.90        12.95        25.38         7.53         0.16 
TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        7.04        14.96        10.03         9.40         8.88        18.97 
TCGA-28-5214 TCGA-32-4210 TCGA-32-4211 TCGA-41-2571 TCGA-74-6584 TCGA-76-6193 
       23.44         3.72        12.59         0.85         7.50         2.70 

$`DEL PEAK 31(12Q15) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
        3.22        15.09         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 
        6.02        19.73        26.43        28.70        25.05        10.19 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 
       27.25        89.72        22.72        51.32         8.81        16.96 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       65.00        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       48.95        16.54        16.93        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        9.27        16.21         3.35        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       26.70        24.23        11.90        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        2.33        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19        10.82        11.80        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       19.66         3.29        13.12         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        73.84        27.22        44.58        15.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         7.40         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26        72.36         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         2.70         0.92        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 
        7.17        40.41        16.57        20.78        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6697 
        4.57         5.23         5.39         1.48       120.56        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        8.42        25.71        12.16        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       12.56        42.15        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       12.99        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 
       27.78        38.76         8.94        20.58         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 
       14.53         3.98         4.14        15.65        25.68        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 
       14.93         3.22         2.04        15.12         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
        2.24        11.24        13.78         3.25         2.89        16.50 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       26.33        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
        3.75        32.05        58.78         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
       40.96         6.67        12.43         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       13.78        50.53        19.10        13.28         3.91        17.59 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 
       21.24        13.97         6.41        11.77         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        4.87         1.08         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       22.49        14.07        16.80        17.79         3.98        28.54 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.37        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
        5.49         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       22.78        25.18        21.14        19.86        10.85        19.23 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 
        3.45        20.91         4.34        14.33         8.22         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                        0.16                         0.10 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                      127.59                       120.56 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                      12.150                       12.195 
[1] "0.2 - 127.6 (12.2)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    34  44
  DEL PEAK 31(12Q15) WILD-TYPE 190 303
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     34   44
  DEL PEAK 31(12Q15) WILD-TYPE  190  303
        clus
vv       DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  FEMALE                         34                          190
  MALE                           44                          303
[1] 2 2
[1] FALSE
D56V4, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    14  59
  DEL PEAK 31(12Q15) WILD-TYPE  60 415
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     14   59
  DEL PEAK 31(12Q15) WILD-TYPE   60  415
     clus
vv    DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  NO                          14                           60
  YES                         59                          415
[1] 2 2
[1] FALSE
D56V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 31(12Q15) MUTATED                               4
  DEL PEAK 31(12Q15) WILD-TYPE                            24
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 31(12Q15) MUTATED                     3
  DEL PEAK 31(12Q15) WILD-TYPE                  15
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 31(12Q15) MUTATED                                71
  DEL PEAK 31(12Q15) WILD-TYPE                             454
D56V6, multiclass
                                 clus
vv                                DEL PEAK 31(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            4
  TREATED PRIMARY GBM                                      3
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 31(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             24
  TREATED PRIMARY GBM                                       15
  UNTREATED PRIMARY (DE NOVO) GBM                          454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(12Q15) MUTATED       0                         5    68
  DEL PEAK 31(12Q15) WILD-TYPE    13                        45   417
D56V7, multiclass
                           clus
vv                          DEL PEAK 31(12Q15) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             68
                           clus
vv                          DEL PEAK 31(12Q15) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           45
  WHITE                                              417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED     3  62
  DEL PEAK 31(12Q15) WILD-TYPE   9 411
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED      3   62
  DEL PEAK 31(12Q15) WILD-TYPE    9  411
                        clus
vv                       DEL PEAK 31(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         62
                        clus
vv                       DEL PEAK 31(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          411
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(13Q14.2) MUTATED    38 201
  DEL PEAK 32(13Q14.2) WILD-TYPE  62 269
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           239                            331 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           201                            269 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0023 
       11.77        18.35        23.18        35.41        20.71        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0051 
       53.10        24.59         2.83        14.14        10.52        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
       12.59         6.54         2.50         9.57        19.73        26.43 
TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
       28.70        20.84        27.25         3.48        65.00        11.67 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0321 TCGA-02-0325 TCGA-02-0330 
       92.65        99.98        15.65         9.90        10.62        15.91 
TCGA-02-0339 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 TCGA-02-2483 
       12.39        10.55        11.34         9.27         3.35        15.32 
TCGA-06-0122 TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0140 TCGA-06-0143 
        6.15        22.72        12.95        24.23         0.20        11.74 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       17.79         8.61        12.33        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 
       56.91         5.85         4.18         3.65        69.90        44.58 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         7.40         5.56         0.39         7.66 
TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        7.63         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 
        0.26         4.70         3.16        35.11         9.80         2.10 
TCGA-06-0745 TCGA-06-0875 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        7.86        43.46        16.57        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
        1.08        12.49         4.93         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 
       11.74         4.54         8.98         6.71         3.75         4.57 
TCGA-06-6389 TCGA-06-6694 TCGA-06-6701 TCGA-06-A7TK TCGA-08-0245 TCGA-08-0246 
        7.79         7.36         4.96        14.60        37.84         4.18 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0354 TCGA-08-0357 
       25.71        12.16         9.80        29.23        17.95        37.58 
TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
        3.39        18.02        15.35         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-12-0615 
       42.15        11.08        19.59        58.68        10.75        15.35 
TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 
       10.45        38.17        25.97        12.13        15.06        53.85 
TCGA-12-0776 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
        9.73        24.79        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
      127.59        33.21        21.73        15.98        12.23         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       14.53         4.14        15.65         6.77        59.77        44.02 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 
       34.92        14.53        14.93        15.12        11.97         6.21 
TCGA-14-0787 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 
        2.24         3.25         5.39         2.89        16.50         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 
       15.95        19.30         1.12        23.11         1.15        30.18 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-15-0742 
       40.96         6.67        17.85         7.63         3.78        13.78 
TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       50.53        53.19        13.28         3.91        26.07        16.37 
TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 
       29.03        10.29         9.14        10.75         5.95         4.64 
TCGA-19-1392 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 
        3.65         1.08         7.53         4.08        24.23         7.04 
TCGA-19-5947 TCGA-19-5955 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-5132 
        6.64         1.78        17.79        10.03        13.87         9.40 
TCGA-26-5133 TCGA-26-5136 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 
       14.86        18.97         7.92        19.33         5.06         9.86 
TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 
       40.54        18.08        10.39         7.59         8.35         8.48 
TCGA-28-2502 TCGA-28-2509 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-32-1970 
        0.66         4.77        11.01        13.64        22.68        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 
       21.07         0.49         0.10        14.86        12.23         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
        8.84        22.78         3.72        19.86        10.85         0.85 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9R TCGA-4W-AA9S 
        8.94         0.99        11.84         0.20         4.08         1.45 
TCGA-74-6573 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 
        3.45         3.65         2.53        36.85         3.29         2.70 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-76-6662 TCGA-81-5911 
        8.35        20.98        23.90        34.45        17.72 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-02-0003 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
        4.73        10.59        82.59        20.61        87.06        77.65 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       42.74        12.16        90.58         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 
        6.87        14.73         3.22        19.86         8.35         6.02 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       25.05         5.49        10.19        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0107 
       51.32         8.81        57.76        16.96        27.02        17.65 
TCGA-02-0111 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       23.18        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.73         7.33        25.71         4.37        25.12        10.59 
TCGA-02-0422 TCGA-02-0432 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 
       14.50        47.11        16.21        16.80        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
       20.32         2.70        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 
       33.67        25.35        14.30        26.70        11.90        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
        2.20         2.33        20.09        10.09        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 
       13.94        10.45         3.19        11.80        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0194 
       88.14        20.25        73.84        27.22        15.42         4.67 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        8.42         7.40        11.84        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 
       48.69        10.82         9.01        72.36         9.57        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         5.75        23.57        14.20        26.40        46.88 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.70         0.92        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1086 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       40.41        20.78         6.84        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2569 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 
        5.95        16.64         0.43         3.55         8.35         8.81 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        8.55         2.73         6.15         5.23         5.39         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
      120.56         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0244 
       26.79         1.87         3.12         2.56        17.72        22.68 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
      115.86         1.74         8.42        65.33         1.28         8.42 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 
       24.56        31.10        22.29        12.23        14.93        13.97 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       19.33         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        34.92         7.59        94.78         0.10 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 
       26.66         3.65        20.38        28.41        43.23         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        91.76        18.48        10.62        23.51 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 
        5.82         7.59        15.85         3.98        25.68        14.73 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 
       26.93        15.22        10.95        12.69         3.22         2.04 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0866 
        0.95        23.05        11.24        13.78         1.35        26.33 
TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       28.93         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1452 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
        7.10         0.92        12.43         0.99         1.97        17.79 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 
        5.88         7.17        17.49         7.96         3.42        19.10 
TCGA-16-0848 TCGA-16-0861 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
       17.59         4.31         4.57        14.01        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        3.39         9.07        12.95        25.38         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 
        3.25         0.13         9.67         4.87         0.16         7.00 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5956 
       17.19         8.02        18.90         4.73        12.10        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 
       14.07        16.80        14.96         3.98        28.54         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
       31.33         7.13         9.37         5.49         8.88         1.58 
TCGA-26-6174 TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        2.33        16.60        24.23        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       11.51        24.76        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
        0.20         2.53         9.21         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         6.74         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
        5.16        10.49         5.42        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
        4.67        12.69        16.93        20.78        15.02        15.95 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 
       25.18        21.14        12.59        19.23        13.35         9.53 
TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6575 TCGA-74-6577 
        4.44        15.12        12.46        25.58        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4931 TCGA-76-6191 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 
        9.17        16.70        11.38        17.06         4.83         5.03 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       18.64        36.20         1.61        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                         11.84                          12.56 
[1] "0.1 - 127.6 (11.8)" "0.1 - 120.6 (12.6)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED    90 149
  DEL PEAK 32(13Q14.2) WILD-TYPE 134 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     90  149
  DEL PEAK 32(13Q14.2) WILD-TYPE  134  198
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                           90                            134
  MALE                            149                            198
[1] 2 2
[1] FALSE
D57V4, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED    38 193
  DEL PEAK 32(13Q14.2) WILD-TYPE  36 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     38  193
  DEL PEAK 32(13Q14.2) WILD-TYPE   36  281
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  NO                            38                             36
  YES                          193                            281
[1] 2 2
[1] FALSE
D57V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 32(13Q14.2) MUTATED                               9
  DEL PEAK 32(13Q14.2) WILD-TYPE                            19
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 32(13Q14.2) MUTATED                     6
  DEL PEAK 32(13Q14.2) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 32(13Q14.2) MUTATED                               224
  DEL PEAK 32(13Q14.2) WILD-TYPE                             301
D57V6, multiclass
                                 clus
vv                                DEL PEAK 32(13Q14.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              9
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          224
                                 clus
vv                                DEL PEAK 32(13Q14.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               19
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED       5                        17   211
  DEL PEAK 32(13Q14.2) WILD-TYPE     8                        33   274
D57V7, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              211
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             33
  WHITE                                                274
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED     5 202
  DEL PEAK 32(13Q14.2) WILD-TYPE   7 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      5  202
  DEL PEAK 32(13Q14.2) WILD-TYPE    7  271
                        clus
vv                       DEL PEAK 32(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          202
                        clus
vv                       DEL PEAK 32(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 33(13Q22.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(13Q22.1) MUTATED    36 191
  DEL PEAK 33(13Q22.1) WILD-TYPE  64 279
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           227                            343 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           191                            279 
$`DEL PEAK 33(13Q22.1) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0023 
       11.77        18.35        23.18        35.41        20.71        20.12 
TCGA-02-0026 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0051 
       24.59        90.58         2.83        14.14        10.52        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
       12.59         6.54         2.50         9.57        19.73        26.43 
TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
       28.70        20.84        27.25         3.48        65.00        11.67 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 TCGA-02-0321 TCGA-02-0325 TCGA-02-0330 
       92.65        15.65        16.54         9.90        10.62        15.91 
TCGA-02-0339 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 TCGA-02-2483 TCGA-06-0122 
       12.39        11.34         9.27         3.35        15.32         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0139 
       20.38        47.61        22.72        12.95        24.23        11.90 
TCGA-06-0140 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
        0.20        11.74        20.09        17.79        10.09         8.61 
TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
       12.33        10.82         9.44         3.42        56.91         5.85 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 
        4.18         3.65        69.90        44.58        38.96         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 
        5.56         0.39         7.66         7.63         0.53        15.02 
TCGA-06-0219 TCGA-06-0402 TCGA-06-0410 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 
        0.72         0.26         4.70        35.11         9.80         2.10 
TCGA-06-0745 TCGA-06-0875 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        7.86        43.46        16.57        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2567 TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 
        1.08        12.49         4.37        11.74         4.54         8.98 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6694 TCGA-06-6701 
        6.71         3.75         4.57         7.79         7.36         4.96 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 
        2.56        14.60        37.84         4.18        25.71         9.80 
TCGA-08-0354 TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 
       17.95        37.58         3.39        18.02        15.35         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 
       12.56         4.27        42.15        19.59        58.68        10.75 
TCGA-12-0615 TCGA-12-0619 TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 
       15.35        34.92        10.45        38.17        25.97        12.13 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0776 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 
       15.06        53.85         9.73        24.79        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
        8.94        20.58       127.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 
       12.23         9.11        14.53         4.14        15.65         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 
       59.77        44.02        14.93        15.12        11.97         6.21 
TCGA-14-0787 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
        2.24        13.78         3.25         5.39         2.89        16.50 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 
        2.04        15.95        19.30         1.12        23.11         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 
       30.18        40.96         6.67        17.85         7.63         3.78 
TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       13.78        53.19        13.28         3.91        26.07        16.37 
TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-19-1385 TCGA-19-1387 
       29.03        10.29         9.14        21.24        10.75         5.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        4.64         3.65         1.08         7.53         4.08        24.23 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5955 TCGA-19-A60I TCGA-26-1439 TCGA-26-5133 
        7.04         6.64         1.78        17.79        13.87        14.86 
TCGA-26-5136 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 
       18.97         7.92        19.33         5.06         9.86        40.54 
TCGA-27-2519 TCGA-27-2521 TCGA-28-1746 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 
       18.08        10.39         0.20         8.35         8.48         0.66 
TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
        4.77        11.28        11.01        13.64        22.68        10.49 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 TCGA-32-2634 
       15.39         0.49        14.86        12.23         7.36        22.78 
TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 
        3.72        19.86        10.85         8.94         0.99        11.84 
TCGA-41-4097 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 
        0.20         4.08         1.45         3.65         2.53        36.85 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-81-5911 
        2.70         8.35        20.98        23.90        17.72 

$`DEL PEAK 33(13Q22.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
        4.73        10.59        82.59        20.61        87.06        77.65 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       53.10        42.74        12.16         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 
        6.87        14.73         3.22        19.86         8.35         6.02 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       25.05         5.49        10.19        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0107 
       51.32         8.81        57.76        16.96        27.02        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       23.18        99.98        48.95        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.73         7.33        25.71         4.37        25.12        10.59 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
       14.50        10.55        47.11        16.21        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
       15.45        20.32         2.70         6.94         3.98        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 
       25.35        14.30        26.70        10.29         2.20         2.33 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 
       19.46        46.59        13.94        10.45         3.19        11.80 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       10.65        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 
        4.04        91.00        88.14        20.25        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
       15.42        10.42         4.67         8.42         7.40        11.84 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.82         9.01        72.36         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         5.75        23.57        14.20        26.40        46.88 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.70         0.92        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1086 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       40.41        20.78         6.84         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         5.98         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 
        3.55         8.35         8.81         8.55         2.73         6.15 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        4.77         1.55         4.77        26.79         1.87         3.12 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       17.72        22.68       115.86         1.74         8.42        12.16 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         1.28         8.42        24.56        31.10 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0514 TCGA-08-0518 
       22.29        12.23        14.93        13.97        11.08        19.33 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
        4.80         7.27        15.98        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0692 
       12.99         7.59        94.78         0.10        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       20.38        28.41        43.23         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-1089 TCGA-12-1090 
       91.76        18.48        10.62        23.51         5.82         7.59 
TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
       15.85         3.98        25.68        14.73        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.53         3.22         2.04 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0813 TCGA-14-0866 TCGA-14-0871 
        0.95        23.05        11.24         1.35        26.33        28.93 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
        0.79         1.38         3.75        32.05        58.78         7.10 
TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 
        0.92        12.43         0.99         1.97        17.79         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 
        7.17        17.49         7.96         3.42        50.53        19.10 
TCGA-16-0848 TCGA-16-0861 TCGA-16-1047 TCGA-16-1056 TCGA-16-1063 TCGA-16-1460 
       17.59         4.31         4.57        14.01        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        9.07        12.95        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-5950 
        0.13         9.67         4.87         0.16         7.00        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 
        8.02        18.90         4.73        12.10        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       16.80        14.96         3.98        28.54        10.03         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 
       31.33         7.13         9.37         9.40         5.49         8.88 
TCGA-26-5139 TCGA-26-6174 TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        1.58         2.33        16.60        24.23        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       14.04        11.51        24.76        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 
       14.40        15.78         2.53         9.21         7.63         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         6.74         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       14.93        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5218 TCGA-28-6450 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.16         5.42        21.07         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
        1.18         4.67        12.69        16.93        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 
       15.95         8.84        25.18        21.14        12.59        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 
        0.85        13.35         9.53         4.44        15.12        12.46 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-6191 
        7.50         4.80         4.54         3.09         9.17        16.70 
TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 
        3.29        11.38        17.06         4.83         5.03        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
       18.64        36.20         1.61        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           0.2                            0.1 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                         11.97                          12.23 
[1] "0.2 - 127.6 (12.0)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q22.1) MUTATED    88 139
  DEL PEAK 33(13Q22.1) WILD-TYPE 136 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED     88  139
  DEL PEAK 33(13Q22.1) WILD-TYPE  136  208
        clus
vv       DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE
  FEMALE                           88                            136
  MALE                            139                            208
[1] 2 2
[1] FALSE
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q22.1) MUTATED    36 185
  DEL PEAK 33(13Q22.1) WILD-TYPE  38 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED     36  185
  DEL PEAK 33(13Q22.1) WILD-TYPE   38  289
     clus
vv    DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE
  NO                            36                             38
  YES                          185                            289
[1] 2 2
[1] FALSE
D58V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 33(13Q22.1) MUTATED                               9
  DEL PEAK 33(13Q22.1) WILD-TYPE                            19
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 33(13Q22.1) MUTATED                     5
  DEL PEAK 33(13Q22.1) WILD-TYPE                  13
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 33(13Q22.1) MUTATED                               213
  DEL PEAK 33(13Q22.1) WILD-TYPE                             312
D58V6, multiclass
                                 clus
vv                                DEL PEAK 33(13Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              9
  TREATED PRIMARY GBM                                        5
  UNTREATED PRIMARY (DE NOVO) GBM                          213
                                 clus
vv                                DEL PEAK 33(13Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               19
  TREATED PRIMARY GBM                                         13
  UNTREATED PRIMARY (DE NOVO) GBM                            312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q22.1) MUTATED       5                        18   199
  DEL PEAK 33(13Q22.1) WILD-TYPE     8                        32   286
D58V7, multiclass
                           clus
vv                          DEL PEAK 33(13Q22.1) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              199
                           clus
vv                          DEL PEAK 33(13Q22.1) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             32
  WHITE                                                286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q22.1) MUTATED     3 190
  DEL PEAK 33(13Q22.1) WILD-TYPE   9 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED      3  190
  DEL PEAK 33(13Q22.1) WILD-TYPE    9  283
                        clus
vv                       DEL PEAK 33(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          190
                        clus
vv                       DEL PEAK 33(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 34(14Q13.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q13.1) MUTATED    37 139
  DEL PEAK 34(14Q13.1) WILD-TYPE  63 331
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           176                            394 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           139                            331 
$`DEL PEAK 34(14Q13.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 
       11.77        23.18        35.41        20.71        87.06        53.10 
TCGA-02-0025 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 
       42.74        14.14        10.72        10.52        14.73         3.22 
TCGA-02-0051 TCGA-02-0055 TCGA-02-0074 TCGA-02-0086 TCGA-02-0099 TCGA-02-0107 
       15.09         2.50        10.19         8.81         3.48        17.65 
TCGA-02-0113 TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 
       92.65         3.98         7.73        10.62        15.91        25.71 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 
       11.34         9.27        16.21         3.35        16.80        15.32 
TCGA-02-2486 TCGA-06-0125 TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 
       20.32        47.61        22.72        12.95        24.23        10.29 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0162 TCGA-06-0166 TCGA-06-0188 TCGA-06-0194 
       11.74        20.09         3.42         5.85        44.58         4.67 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0397 TCGA-06-0409 
       24.16         0.72        19.82        48.69         9.01        72.36 
TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0749 
        4.70        12.62         5.75         2.10         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-1084 TCGA-06-2561 
        0.92        43.46        46.19         7.17        23.93        17.65 
TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 TCGA-06-6388 
       11.74         8.35         8.81         6.71         3.75         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6697 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 
        7.79         5.39        12.85         1.55         1.87         2.56 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0347 TCGA-08-0352 TCGA-08-0380 TCGA-08-0390 
       17.72        37.84        25.71         1.28        14.93        13.97 
TCGA-08-0392 TCGA-08-0512 TCGA-08-0520 TCGA-08-0524 TCGA-12-0616 TCGA-12-0654 
        0.72        42.15        10.75         7.27        14.73         7.59 
TCGA-12-0662 TCGA-12-0692 TCGA-12-0703 TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 
       38.17         3.65        20.38         7.63        10.62       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1096 TCGA-12-1099 
        5.82        33.21        21.73        15.98         9.11         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
       15.65        25.68         6.77        12.69        14.53        14.93 
TCGA-14-0736 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       15.12         6.21         1.35         5.39         2.89        16.50 
TCGA-14-1455 TCGA-14-1459 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
        0.92        12.43        17.85         7.63         7.17        17.49 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1447 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 
        3.78        13.78        53.19        17.59         4.31        29.03 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1791 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        4.64        25.38         0.13         7.53         4.08        24.23 
TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 
        6.64        22.49        14.96         3.98        10.03        13.87 
TCGA-26-1440 TCGA-26-5133 TCGA-26-5134 TCGA-26-6173 TCGA-27-1832 TCGA-27-1834 
        9.73        14.86         5.49         7.92         9.86        40.54 
TCGA-27-1835 TCGA-27-2519 TCGA-27-2527 TCGA-28-1750 TCGA-28-1756 TCGA-28-2506 
       21.30        18.08        14.40         8.35         2.83         6.74 
TCGA-28-2509 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
        4.77         5.26        11.28        31.27        11.01        13.64 
TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 TCGA-32-2615 TCGA-32-2634 TCGA-32-4210 
       10.49         0.49         1.18        15.95        22.78         3.72 
TCGA-32-5222 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       19.23         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-4W-AA9R TCGA-74-6575 TCGA-74-6581 TCGA-74-6584 TCGA-76-4928 
        0.20         4.08        20.91         8.22         7.50         3.09 
TCGA-76-4929 TCGA-76-4934 TCGA-76-6191 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
        3.65         2.53        16.70         2.70        17.06         8.35 
TCGA-76-6664 TCGA-OX-A56R 
       36.20         5.92 

$`DEL PEAK 34(14Q13.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0021 
        4.73        18.35        10.59        82.59        20.61        77.65 
TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 
       20.12        24.59        12.16        90.58         2.83         3.62 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       18.31         6.87        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       51.32        57.76        16.96        27.02        65.00        11.67 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
       12.23         9.90         7.33         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-2470 TCGA-02-2485 
       12.39        14.50        10.55        47.11        12.92        15.45 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
        2.70         6.15        20.38         6.94         3.98        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       25.35        14.30        26.70        11.90         0.20         2.20 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       11.80        56.91        10.65        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0402 TCGA-06-0412 
       13.64        13.32        20.42        10.82         0.26         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        3.16        35.11         5.75         9.80        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 
       26.40        46.88         2.70         5.65        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 
        4.37         0.43        31.50         3.55         4.54         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6391 TCGA-06-6693 
        8.55         2.73         6.15         4.57         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
        7.36         8.32         4.77         4.77         4.96        26.79 
TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12        14.60        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 
        8.42        12.16         9.80        29.23        65.33         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       12.23        18.02        15.35        12.56         4.27        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 
       19.59        58.68        19.33         4.80        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 
        7.56        15.35        12.99        34.92        10.45        94.78 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0707 TCGA-12-0769 
        0.10        25.97        26.66        12.13        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1090 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 
       20.58         7.59        12.23        15.85        14.53         3.98 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       14.73        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
       34.92         3.22         2.04        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-0867 
        2.24        11.24        13.78         3.25        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       30.18        40.96         6.67         0.99         1.97        17.79 
TCGA-14-1827 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
        5.88         7.96         3.42        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.91        26.07        16.37         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95        12.95         3.65         7.17        12.66         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 
        9.67         4.87         1.08         0.16         7.00         7.04 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1442 TCGA-26-1443 
       14.07        16.80        17.79        28.54        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
        9.37         9.40         8.88        18.97         1.58         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 
       19.33         5.06        16.60        24.23        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        16.08         7.59         2.86 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-5204 
        1.22         1.55         0.13         0.66         7.30        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       17.88         2.53        11.77        23.44         5.16        22.68 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39        21.07         0.10        15.85        19.50 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.02         7.36         8.84        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-5651 TCGA-41-6646 
       19.86        10.85         0.85        13.35        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 
        1.45        25.58         3.45         4.34        14.33         4.80 
TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 TCGA-76-6192 TCGA-76-6280 TCGA-76-6286 
        4.54         9.17        36.85         3.29        11.38        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 
        4.83         5.03        23.90        34.45        18.64         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         6.28        20.55 

  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                         10.67                          12.56 
[1] "0.1 - 127.6 (10.7)" "0.1 - 120.6 (12.6)"
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED    78  98
  DEL PEAK 34(14Q13.1) WILD-TYPE 146 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED     78   98
  DEL PEAK 34(14Q13.1) WILD-TYPE  146  249
        clus
vv       DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE
  FEMALE                           78                            146
  MALE                             98                            249
[1] 2 2
[1] FALSE
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED    26 145
  DEL PEAK 34(14Q13.1) WILD-TYPE  48 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED     26  145
  DEL PEAK 34(14Q13.1) WILD-TYPE   48  329
     clus
vv    DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE
  NO                            26                             48
  YES                          145                            329
[1] 2 2
[1] FALSE
D59V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 34(14Q13.1) MUTATED                               6
  DEL PEAK 34(14Q13.1) WILD-TYPE                            22
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 34(14Q13.1) MUTATED                     6
  DEL PEAK 34(14Q13.1) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 34(14Q13.1) MUTATED                               164
  DEL PEAK 34(14Q13.1) WILD-TYPE                             361
D59V6, multiclass
                                 clus
vv                                DEL PEAK 34(14Q13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          164
                                 clus
vv                                DEL PEAK 34(14Q13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               22
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            361
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q13.1) MUTATED       2                        19   147
  DEL PEAK 34(14Q13.1) WILD-TYPE    11                        31   338
D59V7, multiclass
                           clus
vv                          DEL PEAK 34(14Q13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           19
  WHITE                                              147
                           clus
vv                          DEL PEAK 34(14Q13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             31
  WHITE                                                338
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED     1 145
  DEL PEAK 34(14Q13.1) WILD-TYPE  11 328
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED      1  145
  DEL PEAK 34(14Q13.1) WILD-TYPE   11  328
                        clus
vv                       DEL PEAK 34(14Q13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 34(14Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            328
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 35(14Q24.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(14Q24.2) MUTATED    33 138
  DEL PEAK 35(14Q24.2) WILD-TYPE  67 332
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           171                            399 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           138                            332 
$`DEL PEAK 35(14Q24.2) MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 
       23.18        35.41        20.71        87.06        53.10        42.74 
TCGA-02-0026 TCGA-02-0034 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       24.59        14.14        10.52        14.73         3.22        15.09 
TCGA-02-0055 TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0074 TCGA-02-0086 
        2.50         8.35         6.02        28.70        10.19         8.81 
TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0113 TCGA-02-0258 TCGA-02-0266 
        3.48        65.00        17.65        92.65        16.54        17.72 
TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0432 
        3.98         7.73        10.62        15.91        25.71        47.11 
TCGA-02-0446 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 
        9.27         3.35        16.80        15.32        22.72        33.67 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 TCGA-06-0146 TCGA-06-0155 
       12.95        24.23        10.29        11.74        20.09        10.45 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0171 TCGA-06-0188 TCGA-06-0194 TCGA-06-0214 
        3.42         5.85        13.12        44.58         4.67        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 
       24.16         0.72        19.82        48.69        72.36         4.70 
TCGA-06-0412 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0750 
        9.57        12.62         5.75         2.10         7.86         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-2561 TCGA-06-5408 TCGA-06-5411 
       43.46        46.19         7.17        17.65        11.74         8.35 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-6697 
        6.71         3.75         4.57         7.79         5.39        12.85 
TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0245 TCGA-08-0380 
        1.55         1.87         2.56        17.72        37.84        14.93 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 TCGA-12-0615 
       13.97         0.72        42.15        58.68        10.75        15.35 
TCGA-12-0616 TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0776 
       14.73         7.59        38.17        12.13         3.65         9.73 
TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 
       10.62        38.76       127.59         5.82        33.21        21.73 
TCGA-12-1096 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 
        9.11        15.65        14.73         6.77        12.69        14.53 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       14.93        15.12         6.21         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-1396 TCGA-14-1401 TCGA-14-1453 TCGA-14-1455 TCGA-14-1821 
       16.50         1.12         3.75         1.15         0.92        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-3477 TCGA-14-4157 TCGA-15-1447 
       17.85         7.63         7.17         3.78         3.42        53.19 
TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-19-0962 TCGA-19-1389 TCGA-19-1390 
       17.59         4.31        29.03         0.66         4.64        25.38 
TCGA-19-1791 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 
        0.13         7.53         4.08        24.23         6.64        22.49 
TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1440 TCGA-26-5133 TCGA-26-5134 
       14.96         3.98        13.87         9.73        14.86         5.49 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2527 TCGA-28-1750 
        9.86        40.54        21.30        18.08        14.40         8.35 
TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 
        2.83         6.74         4.77         5.26        11.28        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 TCGA-32-2494 
       11.01        13.64        10.49         0.49         1.18        20.78 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-4208 TCGA-41-2573 TCGA-41-2575 
       15.95         7.36        22.78        21.14         8.94         9.53 
TCGA-41-3392 TCGA-41-4097 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-6193 
        0.99         0.20         3.09         3.65         2.53         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-OX-A56R 
       17.06         8.35         5.92 

$`DEL PEAK 35(14Q24.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
       11.77         4.73        18.35        10.59        82.59        20.61 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 
       77.65        20.12        12.16        90.58         2.83         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       10.72        18.31         6.87        12.59         6.54        19.86 
TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 
        9.57        19.73        26.43        25.05         5.49        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 
       27.25        89.72        22.72        12.62        51.32        57.76 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       16.96        27.02        11.67        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       48.95        16.93        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 TCGA-02-0333 TCGA-02-0337 
       15.95        12.23         9.90         7.33         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0451 
       10.59        12.39        14.50        10.55        11.34        16.21 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       47.61         6.94         3.98        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
       11.90         0.20         2.20         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 
        8.61        19.46        46.59        12.33        13.94         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
       10.82         9.44        11.80        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42        38.96         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.64        13.32        20.42        10.82         9.01         0.26 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        3.16        35.11         5.75         9.80        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0877 TCGA-06-0879 
       26.40        46.88         2.70         2.70         5.65        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49         4.93        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 
       16.64         5.98         4.37         0.43        31.50         3.55 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 
        4.54         8.81         8.98         8.55         2.73         6.15 
TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 
        5.23         1.48       120.56         7.36         8.32         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 
        4.77         4.96        26.79         3.12        14.60        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 
       18.02        15.35        12.56         4.27        11.08        19.59 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       19.33         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 
       12.99        34.92        10.45        94.78         0.10        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
       26.66        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1093 
       23.51        27.78         8.94        20.58         7.59        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       12.23        15.85        14.53         3.98         4.14        25.68 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.77        44.02        26.93        15.22        10.95        34.92 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
       11.24        13.78         3.25        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1402 TCGA-14-1450 
       15.95        19.30         0.79         1.38        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
       23.11         7.10        30.18        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 
        0.99         1.97         5.88        17.49         7.96        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10        13.28         3.91        26.07        16.37 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         8.61        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07         5.95        12.95         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
       12.66         3.25         9.67         4.87         1.08         0.16 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         7.04        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 
       12.10         1.78        14.07        16.80        17.79        28.54 
TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       16.60        24.23        30.05        14.04        11.51        24.76 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         7.59         2.86        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        2.53         9.21         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        0.13         0.66         7.30        14.93        17.88         2.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 
       11.77        23.44         5.16        22.68         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 
       14.86        16.93        12.23        15.02         8.84        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
       13.35         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 
        8.22         7.50         4.80         4.54         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29        11.38        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         6.28        20.55 

  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                         10.75                          12.39 
[1] "0.1 - 127.6 (10.8)" "0.1 - 120.6 (12.4)"
[1] "hr=" "1"  
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q24.2) MUTATED    74  97
  DEL PEAK 35(14Q24.2) WILD-TYPE 150 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED     74   97
  DEL PEAK 35(14Q24.2) WILD-TYPE  150  250
        clus
vv       DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE
  FEMALE                           74                            150
  MALE                             97                            250
[1] 2 2
[1] FALSE
D60V4, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q24.2) MUTATED    29 139
  DEL PEAK 35(14Q24.2) WILD-TYPE  45 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED     29  139
  DEL PEAK 35(14Q24.2) WILD-TYPE   45  335
     clus
vv    DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE
  NO                            29                             45
  YES                          139                            335
[1] 2 2
[1] FALSE
D60V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 35(14Q24.2) MUTATED                               5
  DEL PEAK 35(14Q24.2) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 35(14Q24.2) MUTATED                     7
  DEL PEAK 35(14Q24.2) WILD-TYPE                  11
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 35(14Q24.2) MUTATED                               159
  DEL PEAK 35(14Q24.2) WILD-TYPE                             366
D60V6, multiclass
                                 clus
vv                                DEL PEAK 35(14Q24.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                          159
                                 clus
vv                                DEL PEAK 35(14Q24.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         11
  UNTREATED PRIMARY (DE NOVO) GBM                            366
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q24.2) MUTATED       5                        16   145
  DEL PEAK 35(14Q24.2) WILD-TYPE     8                        34   340
D60V7, multiclass
                           clus
vv                          DEL PEAK 35(14Q24.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              145
                           clus
vv                          DEL PEAK 35(14Q24.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             34
  WHITE                                                340
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q24.2) MUTATED     3 141
  DEL PEAK 35(14Q24.2) WILD-TYPE   9 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED      3  141
  DEL PEAK 35(14Q24.2) WILD-TYPE    9  332
                        clus
vv                       DEL PEAK 35(14Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK 35(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            332
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 36(15Q14) MUTATION ANALYSIS
D61V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(15Q14) MUTATED    24 127
  DEL PEAK 36(15Q14) WILD-TYPE  76 343
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         151                          419 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         127                          343 
$`DEL PEAK 36(15Q14) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0026 
       11.77         4.73        20.71        87.06        53.10        24.59 
TCGA-02-0034 TCGA-02-0038 TCGA-02-0047 TCGA-02-0048 TCGA-02-0054 TCGA-02-0074 
       14.14        10.72        14.73         3.22         6.54        10.19 
TCGA-02-0079 TCGA-02-0084 TCGA-02-0087 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 
       27.25        12.62        57.76        23.18        92.65        15.65 
TCGA-02-0258 TCGA-02-0269 TCGA-02-0281 TCGA-02-0321 TCGA-02-0324 TCGA-02-2470 
       16.54        10.75         3.98         9.90         7.73        12.92 
TCGA-02-2483 TCGA-06-0119 TCGA-06-0124 TCGA-06-0128 TCGA-06-0129 TCGA-06-0141 
       15.32         2.70        20.38        22.72        33.67        10.29 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 
        5.85         3.22         4.18        44.58        10.42        38.96 
TCGA-06-0201 TCGA-06-0209 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 
        0.39         7.63         0.53        24.16        13.64        13.32 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.26         4.70         5.75         5.75         9.80         2.10 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0875 TCGA-06-1801 TCGA-06-2558 TCGA-06-2562 
       14.20         7.86        43.46        11.84        12.49        12.56 
TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 TCGA-06-A5U1 TCGA-06-A6S0 
        8.81         6.71         3.75         7.36         1.87         3.12 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0246 TCGA-08-0344 TCGA-08-0348 TCGA-08-0349 
       14.60        17.72         4.18       115.86        12.16         9.80 
TCGA-08-0355 TCGA-08-0359 TCGA-08-0386 TCGA-08-0510 TCGA-08-0525 TCGA-12-0618 
       24.56         3.39        18.02         4.27        15.98        12.99 
TCGA-12-0619 TCGA-12-0707 TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 TCGA-12-1096 
       34.92        28.41         7.63        10.62       127.59         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 
       14.53         4.14        15.65        14.73         6.77        44.02 
TCGA-12-3648 TCGA-12-3651 TCGA-14-0736 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 
       26.93        12.69        15.12         6.21         5.39         2.04 
TCGA-14-1459 TCGA-14-1794 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       12.43         0.99        53.19        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1063 TCGA-19-0963 TCGA-19-1385 
       26.07        16.37        29.03        13.97        14.27        10.75 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 
        5.95        12.95        25.38         3.65        24.23         7.04 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-6174 
        1.78        22.49        14.96        10.03        13.87         2.33 
TCGA-27-1830 TCGA-27-1834 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 
        5.06        40.54        18.08         7.59         2.86         0.20 
TCGA-28-1750 TCGA-28-1756 TCGA-28-2513 TCGA-28-2514 TCGA-28-5215 TCGA-28-5219 
        8.35         2.83         7.30         5.26        11.01        22.68 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-2494 TCGA-32-2616 TCGA-32-2634 
       15.39        21.07         0.49        20.78         7.36        22.78 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 
        3.72        12.59        10.85         0.85         8.94         9.53 
TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6578 
        0.99        11.84        15.12         4.08         1.45        14.33 
TCGA-76-4925 TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 TCGA-76-6193 TCGA-76-6285 
        4.80         3.65        36.85        16.70         2.70         8.35 
TCGA-76-6286 
       20.98 

$`DEL PEAK 36(15Q14) WILD-TYPE`
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 
       18.35        23.18        10.59        35.41        82.59        20.61 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       77.65        20.12        42.74        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 
        3.62        10.52        18.31         6.87        15.09        12.59 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0080 
       26.43        28.70        25.05         5.49        20.84        89.72 
TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       22.72        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       65.00        11.67        17.65        99.98        48.95        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21         3.35        16.80        15.45        20.32 
TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 
        6.15        47.61         6.94         3.98        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       14.30        26.70        24.23        11.90         0.20         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         4.47         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 TCGA-06-0208 
       15.42         4.67         7.40         5.56         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 
        7.40        11.84        15.02         0.72        19.82        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       48.69        10.82         9.01        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.11        12.62        23.57        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        17.65        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        4.54         8.98         8.55         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        5.23         7.79         5.39         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        2.56        22.68        37.84         1.74         8.42        25.71 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 
       29.23        65.33         1.28         8.42        17.95        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       37.58        22.29        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 
       19.33        10.75         4.80         7.27        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       15.35        14.73        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85        43.23         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        18.48        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94        20.58         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-3644 
       15.98        12.23        15.85         3.98        25.68        59.77 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
        2.04        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         1.35         2.89        16.50        26.33 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 
       30.18         0.92        40.96         6.67         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0861 
        3.78         3.42        13.78        50.53        19.10         4.31 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 
        4.57        10.29        14.01         9.14        21.24         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0964 TCGA-19-1386 
       11.77        21.90         8.61         0.66         3.39         9.07 
TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        4.64         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 
       14.07        16.80        17.79         3.98        28.54         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1831 
        8.88        18.97         1.58         7.92        19.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       24.76        10.39        16.08        14.40        15.78         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        9.21         7.63         8.48         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        0.66         6.74         4.77        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        2.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       10.49         5.42         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 
        4.67        12.69        14.86        16.93        12.23        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 TCGA-32-5222 
       15.95         8.84        25.18        21.14        19.86        19.23 
TCGA-41-2572 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 
       13.35         4.44         0.20        12.46        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
       20.91         4.34         8.22         7.50         4.54         3.09 
TCGA-76-4931 TCGA-76-4934 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 
        9.17         2.53         3.29        11.38        17.06         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03        23.90        34.45        18.64        36.20         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                      127.59                       120.56 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                       11.77                        12.23 
[1] "0.2 - 127.6 (11.8)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED    57  95
  DEL PEAK 36(15Q14) WILD-TYPE 167 252
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED     57   95
  DEL PEAK 36(15Q14) WILD-TYPE  167  252
        clus
vv       DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE
  FEMALE                         57                          167
  MALE                           95                          252
[1] 2 2
[1] FALSE
D61V4, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED    24 122
  DEL PEAK 36(15Q14) WILD-TYPE  50 352
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED     24  122
  DEL PEAK 36(15Q14) WILD-TYPE   50  352
     clus
vv    DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE
  NO                          24                           50
  YES                        122                          352
[1] 2 2
[1] FALSE
D61V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 36(15Q14) MUTATED                               8
  DEL PEAK 36(15Q14) WILD-TYPE                            20
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 36(15Q14) MUTATED                     4
  DEL PEAK 36(15Q14) WILD-TYPE                  14
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 36(15Q14) MUTATED                               140
  DEL PEAK 36(15Q14) WILD-TYPE                             385
D61V6, multiclass
                                 clus
vv                                DEL PEAK 36(15Q14) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            8
  TREATED PRIMARY GBM                                      4
  UNTREATED PRIMARY (DE NOVO) GBM                        140
                                 clus
vv                                DEL PEAK 36(15Q14) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             20
  TREATED PRIMARY GBM                                       14
  UNTREATED PRIMARY (DE NOVO) GBM                          385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q14) MUTATED       5                        11   129
  DEL PEAK 36(15Q14) WILD-TYPE     8                        39   356
D61V7, multiclass
                           clus
vv                          DEL PEAK 36(15Q14) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                         11
  WHITE                                            129
                           clus
vv                          DEL PEAK 36(15Q14) WILD-TYPE
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           39
  WHITE                                              356
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED     5 130
  DEL PEAK 36(15Q14) WILD-TYPE   7 343
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED      5  130
  DEL PEAK 36(15Q14) WILD-TYPE    7  343
                        clus
vv                       DEL PEAK 36(15Q14) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        130
                        clus
vv                       DEL PEAK 36(15Q14) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          343
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 37(16P12.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16P12.2) MUTATED    11  81
  DEL PEAK 37(16P12.2) WILD-TYPE  89 389
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            92                            478 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            81                            389 
$`DEL PEAK 37(16P12.2) MUTATED`
TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 TCGA-02-0116 TCGA-02-0258 
       42.74        12.59         2.50        10.19        48.95        16.54 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0337 TCGA-02-0456 TCGA-02-2486 TCGA-06-0132 
       17.72         3.98        25.12         3.35        20.32        25.35 
TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 TCGA-06-0216 
       56.91        19.66        13.12         4.18        15.02        24.16 
TCGA-06-0221 TCGA-06-0394 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-0649 
       19.82        10.82         4.70        35.11         5.75         2.10 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 
       14.20        26.40        46.88        40.41        20.78         4.04 
TCGA-06-2557 TCGA-06-2569 TCGA-06-5418 TCGA-06-6389 TCGA-06-6698 TCGA-06-6700 
        1.08         0.43         2.73         7.79         4.77         4.77 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0347 TCGA-08-0353 TCGA-08-0386 
        1.87         3.12         2.56        25.71         8.42        18.02 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0525 TCGA-12-0619 
        0.72        12.56         4.27        11.08        15.98        34.92 
TCGA-12-0620 TCGA-12-0776 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-1099 
       10.45         9.73        23.51        27.78        38.76         4.14 
TCGA-12-1600 TCGA-12-3649 TCGA-12-3651 TCGA-12-3653 TCGA-12-5301 TCGA-14-0736 
       14.73        15.22        12.69        14.53         2.04        15.12 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0871 TCGA-14-1823 TCGA-16-0861 TCGA-19-1389 
        3.25         1.35        28.93        17.85         4.31         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-2620 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 
        3.65         7.17         4.87         4.73         1.78        22.49 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 
       40.54        21.30        30.05        10.39         7.59         8.35 
TCGA-28-1753 TCGA-28-5204 TCGA-28-5216 TCGA-32-1978 TCGA-32-1980 TCGA-32-2494 
        1.22        14.93        13.64        15.85         1.18        20.78 
TCGA-32-4210 TCGA-41-3392 TCGA-41-3915 TCGA-74-6575 TCGA-76-4925 TCGA-76-4928 
        3.72         0.99        11.84        20.91         4.80         3.09 
TCGA-76-6191 TCGA-76-6282 
       16.70        17.06 

$`DEL PEAK 37(16P12.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
        3.22        15.09         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
       25.71         4.37        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
       47.11        11.34         9.27        16.21        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.32        15.45         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 
        6.94         3.98        22.72        33.67        12.95        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 
       10.82         9.44        11.80         3.42        10.65         5.85 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.29         4.47         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.53         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        9.01         0.26        72.36         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        5.75         9.80        23.57         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0881 
        0.92        43.46        46.19         5.65         7.17        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        5.23         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TK TCGA-06-A7TL 
       12.85         1.55         4.96        26.79        14.60        17.72 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       12.16         9.80        29.23        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       14.93        15.35        13.97        42.15        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 
       19.33        10.75         4.80         7.27        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       15.35        14.73        12.99         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        15.06        53.85        43.23         7.63        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0828 
       14.86        91.76        24.79        18.48        10.62         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68         6.77        59.77        44.02        26.93 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 
       10.95        34.92        14.93         3.22        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 
        6.21        23.05         2.24        11.24        13.78         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 
        2.89        16.50        26.33         2.04        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       17.59        26.07        16.37        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1787 TCGA-19-1789 
        9.07         5.95        12.95        25.38        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         9.67         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
       18.90        12.10        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       16.60         9.86        24.23        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       18.08        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1755 TCGA-28-1756 
        2.53         9.21         7.63         8.48         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01         5.16        22.68        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.49         0.10        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       14.86        16.93        12.23        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 
        4.54         3.65         9.17         2.53        36.85         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                         56.91                         127.59 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                        12.200                         12.195 
[1] "0.4 - 56.9 (12.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 37(16P12.2) MUTATED    32  60
  DEL PEAK 37(16P12.2) WILD-TYPE 192 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED     32   60
  DEL PEAK 37(16P12.2) WILD-TYPE  192  287
        clus
vv       DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE
  FEMALE                           32                            192
  MALE                             60                            287
[1] 2 2
[1] FALSE
D62V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(16P12.2) MUTATED    16  71
  DEL PEAK 37(16P12.2) WILD-TYPE  58 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED     16   71
  DEL PEAK 37(16P12.2) WILD-TYPE   58  403
     clus
vv    DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE
  NO                            16                             58
  YES                           71                            403
[1] 2 2
[1] FALSE
D62V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 37(16P12.2) MUTATED                               3
  DEL PEAK 37(16P12.2) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 37(16P12.2) MUTATED                     1
  DEL PEAK 37(16P12.2) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 37(16P12.2) MUTATED                                88
  DEL PEAK 37(16P12.2) WILD-TYPE                             437
D62V6, multiclass
                                 clus
vv                                DEL PEAK 37(16P12.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 37(16P12.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16P12.2) MUTATED       2                         9    77
  DEL PEAK 37(16P12.2) WILD-TYPE    11                        41   408
D62V7, multiclass
                           clus
vv                          DEL PEAK 37(16P12.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               77
                           clus
vv                          DEL PEAK 37(16P12.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             41
  WHITE                                                408
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(16P12.2) MUTATED     2  78
  DEL PEAK 37(16P12.2) WILD-TYPE  10 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED      2   78
  DEL PEAK 37(16P12.2) WILD-TYPE   10  395
                        clus
vv                       DEL PEAK 37(16P12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 37(16P12.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            395
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 38(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.1) MUTATED     9  90
  DEL PEAK 38(16Q23.1) WILD-TYPE  91 380
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            99                            471 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            90                            380 
$`DEL PEAK 38(16Q23.1) MUTATED`
TCGA-02-0009 TCGA-02-0026 TCGA-02-0038 TCGA-02-0039 TCGA-02-0052 TCGA-02-0055 
       10.59        24.59        10.72        10.52        12.59         2.50 
TCGA-02-0074 TCGA-02-0114 TCGA-02-0258 TCGA-02-0281 TCGA-02-0321 TCGA-02-0337 
       10.19        99.98        16.54         3.98         9.90        25.12 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 
        3.35        12.92        20.32        25.35        56.91        19.66 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0177 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       13.12         3.22         4.18        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
       19.82        35.11         5.75        14.20        26.40        46.88 
TCGA-06-0749 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 TCGA-06-2557 TCGA-06-2566 
        2.70        40.41        20.78         4.04         1.08         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-5418 TCGA-06-5859 TCGA-06-6389 TCGA-06-6693 
        4.37         0.43         2.73         4.57         7.79       120.56 
TCGA-06-6698 TCGA-06-6700 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0353 TCGA-08-0392 
        4.77         4.77         3.12         2.56         8.42         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0520 TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 
       12.56        42.15        10.75        15.98        12.99        34.92 
TCGA-12-0654 TCGA-12-0692 TCGA-12-0826 TCGA-12-1088 TCGA-12-1091 TCGA-12-1099 
        7.59         3.65        27.78       127.59        33.21         4.14 
TCGA-12-1600 TCGA-12-3649 TCGA-12-3653 TCGA-12-5295 TCGA-12-5301 TCGA-14-0736 
       14.73        15.22        14.53        14.93         2.04        15.12 
TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0871 TCGA-14-1453 
        2.24         3.25         1.35         2.89        28.93         1.15 
TCGA-14-1823 TCGA-14-2554 TCGA-16-1045 TCGA-19-1389 TCGA-19-1392 TCGA-19-5947 
       17.85        17.49        29.03         4.64         3.65         6.64 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-27-1832 TCGA-27-2521 TCGA-27-2524 
        4.73         1.78        22.49         9.86        10.39         7.59 
TCGA-28-1750 TCGA-28-1755 TCGA-28-5204 TCGA-28-5216 TCGA-32-1973 TCGA-32-1978 
        8.35         1.55        14.93        13.64        21.07        15.85 
TCGA-32-1980 TCGA-32-1987 TCGA-32-2494 TCGA-32-4210 TCGA-41-3915 TCGA-41-5651 
        1.18        14.86        20.78         3.72        11.84        15.12 
TCGA-74-6578 TCGA-76-4928 TCGA-OX-A56R 
       14.33         3.09         5.92 

$`DEL PEAK 38(16Q23.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 
       18.31         6.87        14.73         3.22        15.09         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       28.70        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       92.65        15.65        48.95        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 
       14.47        13.87        14.20        15.95        12.23         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 
       10.62         7.33        15.91        25.71         4.37        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 
       16.21        16.80        15.32        15.45         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       10.65         5.85         3.29         4.47         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       11.84         0.53        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        3.16        12.62         5.75         9.80         2.10        23.57 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
        7.17        16.57        26.76        23.93         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       11.84        15.32        13.61        33.90        15.32        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.98         8.55         6.71         3.75         6.15         5.23 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        5.39         1.48         7.36         8.32        12.85         1.55 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        4.96        26.79         1.87        14.60        17.72        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       12.16         9.80        29.23        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 TCGA-08-0514 
       14.93        18.02        15.35        13.97         4.27        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       19.59        58.68        19.33         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 
        7.56        15.35        14.73        10.45        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66        12.13        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
       38.76         8.94        20.58         5.82         7.59        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68         6.77        59.77        44.02        26.93 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 
       10.95        12.69        34.92         3.22        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0865 
        6.21        23.05        11.24        13.78         5.39        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 
        1.97        17.79         7.63         5.88         7.17         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 
        3.39        10.75         9.07         5.95        12.95        25.38 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        7.04        17.19         8.02        18.90        12.10        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 
        2.33        19.33         5.06        16.60        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1756 TCGA-28-1757 
        9.21         7.63         8.48         1.22         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 
        0.66         6.74         4.77         7.30         5.26        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88         2.53        11.77        31.27        23.44        11.01 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
        5.16        22.68        10.49         5.42        15.39         0.49 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
        0.10        19.50         4.67        12.69        16.93        12.23 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 
        4.34         8.22         7.50         4.80         4.54         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         6.28        20.55 

  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                        127.59                         115.86 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                         10.72                          12.23 
[1] "0.4 - 127.6 (10.7)" "0.1 - 115.9 (12.2)"
[1] "hr=" "1.2"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    40  59
  DEL PEAK 38(16Q23.1) WILD-TYPE 184 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     40   59
  DEL PEAK 38(16Q23.1) WILD-TYPE  184  288
        clus
vv       DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  FEMALE                           40                            184
  MALE                             59                            288
[1] 2 2
[1] FALSE
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    18  75
  DEL PEAK 38(16Q23.1) WILD-TYPE  56 399
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     18   75
  DEL PEAK 38(16Q23.1) WILD-TYPE   56  399
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  NO                            18                             56
  YES                           75                            399
[1] 2 2
[1] FALSE
D63V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 38(16Q23.1) MUTATED                               3
  DEL PEAK 38(16Q23.1) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 38(16Q23.1) MUTATED                     2
  DEL PEAK 38(16Q23.1) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 38(16Q23.1) MUTATED                                94
  DEL PEAK 38(16Q23.1) WILD-TYPE                             431
D63V6, multiclass
                                 clus
vv                                DEL PEAK 38(16Q23.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           94
                                 clus
vv                                DEL PEAK 38(16Q23.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16Q23.1) MUTATED       2                        11    84
  DEL PEAK 38(16Q23.1) WILD-TYPE    11                        39   401
D63V7, multiclass
                           clus
vv                          DEL PEAK 38(16Q23.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               84
                           clus
vv                          DEL PEAK 38(16Q23.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                401
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED     1  86
  DEL PEAK 38(16Q23.1) WILD-TYPE  11 387
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED      1   86
  DEL PEAK 38(16Q23.1) WILD-TYPE   11  387
                        clus
vv                       DEL PEAK 38(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 38(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            387
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 39(17P13.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P13.2) MUTATED    18  68
  DEL PEAK 39(17P13.2) WILD-TYPE  82 402
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                            86                            484 
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                            68                            402 
$`DEL PEAK 39(17P13.2) MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0079 
       11.77         2.83         2.50         9.57        28.70        27.25 
TCGA-02-0086 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 
        8.81        65.00        11.67        92.65        15.65        16.54 
TCGA-02-0269 TCGA-02-0321 TCGA-02-0325 TCGA-02-0339 TCGA-02-0456 TCGA-06-0130 
       10.75         9.90        10.62        12.39         3.35        12.95 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 TCGA-06-0177 TCGA-06-0184 
       17.79         8.61        12.33         9.44         4.18        69.90 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 
       27.22        44.58        15.42        10.42        38.96         5.56 
TCGA-06-0206 TCGA-06-0241 TCGA-06-0410 TCGA-06-0644 TCGA-06-0744 TCGA-06-1086 
        7.66        48.69         4.70        12.62        46.88         6.84 
TCGA-06-2561 TCGA-06-2569 TCGA-06-5408 TCGA-06-6700 TCGA-06-A5U0 TCGA-08-0245 
       17.65         0.43        11.74         4.77        26.79        37.84 
TCGA-08-0353 TCGA-08-0386 TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 TCGA-12-0780 
        8.42        18.02        13.97        34.92        53.85        14.86 
TCGA-12-0826 TCGA-12-1098 TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-14-0783 
       27.78         3.98        15.65        44.02        14.53         6.21 
TCGA-14-0871 TCGA-14-1453 TCGA-14-1794 TCGA-14-2555 TCGA-14-3477 TCGA-15-1449 
       28.93         1.15         0.99         7.96         3.78        13.28 
TCGA-16-0846 TCGA-16-1060 TCGA-19-0960 TCGA-19-2623 TCGA-19-2629 TCGA-19-4065 
        3.91         9.14         8.61         7.53        24.23         7.04 
TCGA-19-A60I TCGA-26-1442 TCGA-26-5133 TCGA-27-1835 TCGA-28-1756 TCGA-28-2509 
       17.79        31.33        14.86        21.30         2.83         4.77 
TCGA-28-5215 TCGA-32-1976 TCGA-32-2491 TCGA-32-2616 TCGA-41-2573 TCGA-41-3392 
       11.01         0.49        12.23         7.36         8.94         0.99 
TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-76-4925 TCGA-76-4934 
       11.84        15.12         4.08         1.45         4.80         2.53 
TCGA-76-6285 TCGA-76-6662 
        8.35        34.45 

$`DEL PEAK 39(17P13.2) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16        90.58        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 
       15.09        12.59         6.54        19.86         8.35         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 
        3.48        27.02        17.65        23.18        99.98        48.95 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       15.95        12.23         7.73         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
        4.37        25.12        10.59        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27        16.21        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        33.67        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       11.74         2.33        20.09        10.09        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 
       13.94        10.45         3.19        10.82        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 
        3.65        73.84         4.67         7.40         0.39         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 
        0.72        19.82        13.64        13.32        20.42        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26        72.36         9.57         3.16        35.11 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U1 
        8.32        12.85         4.77         1.55         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 
        3.12         2.56        14.60        17.72        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         1.28        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       18.41         7.56        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
       12.13         3.65        20.38        28.41        15.06        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 
       15.85         9.11        14.53         4.14        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        0.95        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
       40.96         6.67        12.43         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-4157 TCGA-15-0742 
        7.63         5.88         7.17        17.49         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10        53.19        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 
        4.31        29.03         4.57        10.29        14.01        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 
       13.97         6.41        11.77        21.90         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        9.67         4.87         1.08         0.16         4.08         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78        22.49        14.07        16.80        14.96         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.40         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       40.54        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.22         1.55         0.13         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88         2.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39        21.07         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 
        1.18         4.67        12.69        14.86        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T 
       13.35         9.53         4.44         0.20        12.46        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        11.38        17.06        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        5.03        23.90        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE 
                        11.705                         12.330 
[1] "0.4 - 92.7 (11.7)"  "0.1 - 127.6 (12.3)"
[1] "hr=" "1"  
D64V2, continuous
D64V3, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.2) MUTATED    38  48
  DEL PEAK 39(17P13.2) WILD-TYPE 186 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.2) MUTATED     38   48
  DEL PEAK 39(17P13.2) WILD-TYPE  186  299
        clus
vv       DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE
  FEMALE                           38                            186
  MALE                             48                            299
[1] 2 2
[1] FALSE
D64V4, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.2) MUTATED     9  76
  DEL PEAK 39(17P13.2) WILD-TYPE  65 398
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.2) MUTATED      9   76
  DEL PEAK 39(17P13.2) WILD-TYPE   65  398
     clus
vv    DEL PEAK 39(17P13.2) MUTATED DEL PEAK 39(17P13.2) WILD-TYPE
  NO                             9                             65
  YES                           76                            398
[1] 2 2
[1] FALSE
D64V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 39(17P13.2) MUTATED                               5
  DEL PEAK 39(17P13.2) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 39(17P13.2) MUTATED                     2
  DEL PEAK 39(17P13.2) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 39(17P13.2) MUTATED                                79
  DEL PEAK 39(17P13.2) WILD-TYPE                             446
D64V6, multiclass
                                 clus
vv                                DEL PEAK 39(17P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           79
                                 clus
vv                                DEL PEAK 39(17P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17P13.2) MUTATED       2                        10    73
  DEL PEAK 39(17P13.2) WILD-TYPE    11                        40   412
D64V7, multiclass
                           clus
vv                          DEL PEAK 39(17P13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               73
                           clus
vv                          DEL PEAK 39(17P13.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                412
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.2) MUTATED     2  74
  DEL PEAK 39(17P13.2) WILD-TYPE  10 399
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.2) MUTATED      2   74
  DEL PEAK 39(17P13.2) WILD-TYPE   10  399
                        clus
vv                       DEL PEAK 39(17P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       DEL PEAK 39(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            399
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 40(17P13.1) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P13.1) MUTATED    17  79
  DEL PEAK 40(17P13.1) WILD-TYPE  83 391
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                            96                            474 
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                            79                            391 
$`DEL PEAK 40(17P13.1) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0033 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
       11.77        53.10         2.83         2.50         9.57        28.70 
TCGA-02-0079 TCGA-02-0086 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 
       27.25         8.81        65.00        11.67        92.65        15.65 
TCGA-02-0258 TCGA-02-0269 TCGA-02-0281 TCGA-02-0321 TCGA-02-0325 TCGA-02-0339 
       16.54        10.75         3.98         9.90        10.62        12.39 
TCGA-02-0456 TCGA-06-0130 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 
        3.35        12.95        17.79         8.61        12.33         9.44 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        4.18        69.90        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 TCGA-06-0213 TCGA-06-0241 TCGA-06-0397 
       38.96         5.56         7.66         0.53        48.69         9.01 
TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0744 TCGA-06-0875 TCGA-06-1086 
        4.70        12.62         5.75        46.88        43.46         6.84 
TCGA-06-1087 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2569 TCGA-06-5408 
        4.04         1.08        12.49        17.65         0.43        11.74 
TCGA-06-6694 TCGA-06-A5U0 TCGA-08-0245 TCGA-08-0353 TCGA-08-0386 TCGA-08-0390 
        7.36        26.79        37.84         8.42        18.02        13.97 
TCGA-12-0619 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 TCGA-12-1598 TCGA-12-3646 
       34.92        53.85        27.78         3.98        15.65        44.02 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0871 TCGA-14-1034 TCGA-14-1396 TCGA-14-1453 
       14.53         6.21        28.93        15.95         1.12         1.15 
TCGA-14-1794 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 TCGA-19-0960 TCGA-19-1791 
        0.99         3.78        13.28         3.91         8.61         0.13 
TCGA-19-2623 TCGA-19-2629 TCGA-19-4065 TCGA-26-1442 TCGA-26-5133 TCGA-27-1835 
        7.53        24.23         7.04        31.33        14.86        21.30 
TCGA-28-1756 TCGA-28-2509 TCGA-28-5215 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 
        2.83         4.77        11.01         0.49        14.86        12.23 
TCGA-32-2616 TCGA-32-4210 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 
        7.36         3.72         8.94         0.99        11.84        15.12 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-76-4925 TCGA-76-4934 TCGA-76-6285 TCGA-76-6662 
        4.08         1.45         4.80         2.53         8.35        34.45 

$`DEL PEAK 40(17P13.1) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16        90.58        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 
       26.43        25.05         5.49        10.19        20.84        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       27.02        17.65        23.18        99.98        48.95        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       20.09        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.04        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        4.67         7.40         0.39         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       13.32        20.42        10.82         0.26        72.36         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        3.16        35.11         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40         7.86         2.70         2.70         0.92 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       33.90        15.32         4.93        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 
       16.64         5.98         4.37        31.50         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48       120.56         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       17.72        22.68         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       12.23        14.93        15.35         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       14.53         4.14        25.68        14.73         6.77        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 
        2.89        16.50        26.33         2.04        19.30         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.38         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        7.17        12.66         3.25         9.67         4.87         1.08 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16         4.08         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 
       13.87         9.73         7.13         9.37         9.40         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 
        5.06        16.60         9.86        24.23        40.54        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         6.74         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         5.16        22.68        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       21.07         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       12.69        16.93        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 
       19.23         0.85        13.35         9.53         4.44         0.20 
TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       12.46        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       36.85        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 
       20.98         4.83         5.03        23.90        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE 
                         10.88                          12.51 
[1] "0.1 - 92.7 (10.9)"  "0.1 - 127.6 (12.5)"
[1] "hr=" "1"  
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.1) MUTATED    45  51
  DEL PEAK 40(17P13.1) WILD-TYPE 179 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.1) MUTATED     45   51
  DEL PEAK 40(17P13.1) WILD-TYPE  179  296
        clus
vv       DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE
  FEMALE                           45                            179
  MALE                             51                            296
[1] 2 2
[1] FALSE
D65V4, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.1) MUTATED    13  80
  DEL PEAK 40(17P13.1) WILD-TYPE  61 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.1) MUTATED     13   80
  DEL PEAK 40(17P13.1) WILD-TYPE   61  394
     clus
vv    DEL PEAK 40(17P13.1) MUTATED DEL PEAK 40(17P13.1) WILD-TYPE
  NO                            13                             61
  YES                           80                            394
[1] 2 2
[1] FALSE
D65V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 40(17P13.1) MUTATED                               4
  DEL PEAK 40(17P13.1) WILD-TYPE                            24
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 40(17P13.1) MUTATED                     3
  DEL PEAK 40(17P13.1) WILD-TYPE                  15
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 40(17P13.1) MUTATED                                89
  DEL PEAK 40(17P13.1) WILD-TYPE                             436
D65V6, multiclass
                                 clus
vv                                DEL PEAK 40(17P13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                           89
                                 clus
vv                                DEL PEAK 40(17P13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P13.1) MUTATED       2                        10    82
  DEL PEAK 40(17P13.1) WILD-TYPE    11                        40   403
D65V7, multiclass
                           clus
vv                          DEL PEAK 40(17P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               82
                           clus
vv                          DEL PEAK 40(17P13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                403
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.1) MUTATED     2  83
  DEL PEAK 40(17P13.1) WILD-TYPE  10 390
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.1) MUTATED      2   83
  DEL PEAK 40(17P13.1) WILD-TYPE   10  390
                        clus
vv                       DEL PEAK 40(17P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       DEL PEAK 40(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            390
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 41(17Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q11.2) MUTATED    11  59
  DEL PEAK 41(17Q11.2) WILD-TYPE  89 411
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            70                            500 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            59                            411 
$`DEL PEAK 41(17Q11.2) MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0039 TCGA-02-0055 TCGA-02-0059 TCGA-02-0079 
       11.77         2.83        10.52         2.50         9.57        27.25 
TCGA-02-0086 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 TCGA-02-0269 
        8.81        11.67        92.65        15.65        16.54        10.75 
TCGA-02-0456 TCGA-06-0130 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 
        3.35        12.95        17.79         8.61        12.33         9.44 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0175 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
       56.91         5.85         4.04         4.18        69.90        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 TCGA-06-0644 
       15.42        10.42        38.96         5.56         7.66        12.62 
TCGA-06-0744 TCGA-06-0882 TCGA-06-2569 TCGA-06-5408 TCGA-06-6697 TCGA-08-0353 
       46.88        20.78         0.43        11.74        12.85         8.42 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0512 TCGA-12-0619 TCGA-12-0703 TCGA-12-0772 
       18.02        13.97        42.15        34.92        20.38        53.85 
TCGA-12-0775 TCGA-12-0826 TCGA-12-1098 TCGA-12-3653 TCGA-14-0862 TCGA-14-0871 
        7.63        27.78         3.98        14.53         2.89        28.93 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1453 TCGA-15-1447 TCGA-19-2623 TCGA-19-4065 
       15.95         1.12         1.15        53.19         7.53         7.04 
TCGA-19-5947 TCGA-19-5953 TCGA-19-A60I TCGA-26-5133 TCGA-27-2527 TCGA-28-2502 
        6.64         4.73        17.79        14.86        14.40         0.66 
TCGA-28-2509 TCGA-32-1986 TCGA-32-2491 TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 
        4.77        12.69        12.23         0.99         0.20        15.12 
TCGA-4W-AA9S TCGA-74-6573 TCGA-76-4934 TCGA-76-6285 
        1.45         3.45         2.53         8.35 

$`DEL PEAK 41(17Q11.2) WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16        90.58        14.14         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.72        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       26.43        28.70        25.05         5.49        10.19        20.84 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
        3.48        27.02        65.00        17.65        23.18        99.98 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       48.95        16.93        17.72        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       20.09        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0168 
        3.19        10.82        11.80         3.42        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 
        3.29        13.12         4.47         3.22        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0194 TCGA-06-0195 
       20.25         3.65        73.84        44.58         4.67         7.40 
TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57         3.16        35.11         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 
        9.80         2.10        23.57        14.20        26.40         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
        7.17        40.41        16.57        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56        14.60        17.72        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 
       15.35         0.72        12.56         4.27        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       18.41         7.56        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0776 
       12.13         3.65        28.41        15.06        43.23         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         1.35         5.39        16.50        26.33 
TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
        2.04        19.30         0.79         1.38         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
        3.42        13.78        50.53        19.10        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         0.16         4.08        24.23         7.00 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
       17.19         8.02        18.90        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         7.59         2.86        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         6.74         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 
       19.50         1.18         4.67        14.86        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         9.53         4.44        11.84 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       12.46         4.08        25.58        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17        36.85        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       18.64        36.20         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           0.2                            0.1 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                        11.705                         12.230 
[1] "0.2 - 92.7 (11.7)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED    26  44
  DEL PEAK 41(17Q11.2) WILD-TYPE 198 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     26   44
  DEL PEAK 41(17Q11.2) WILD-TYPE  198  303
        clus
vv       DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  FEMALE                           26                            198
  MALE                             44                            303
[1] 2 2
[1] FALSE
D66V4, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED    11  57
  DEL PEAK 41(17Q11.2) WILD-TYPE  63 417
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     11   57
  DEL PEAK 41(17Q11.2) WILD-TYPE   63  417
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  NO                            11                             63
  YES                           57                            417
[1] 2 2
[1] FALSE
D66V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 41(17Q11.2) MUTATED                               3
  DEL PEAK 41(17Q11.2) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 41(17Q11.2) MUTATED                     2
  DEL PEAK 41(17Q11.2) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 41(17Q11.2) MUTATED                                65
  DEL PEAK 41(17Q11.2) WILD-TYPE                             460
D66V6, multiclass
                                 clus
vv                                DEL PEAK 41(17Q11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           65
                                 clus
vv                                DEL PEAK 41(17Q11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            460
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(17Q11.2) MUTATED       2                         7    59
  DEL PEAK 41(17Q11.2) WILD-TYPE    11                        43   426
D66V7, multiclass
                           clus
vv                          DEL PEAK 41(17Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               59
                           clus
vv                          DEL PEAK 41(17Q11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                426
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED     1  59
  DEL PEAK 41(17Q11.2) WILD-TYPE  11 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      1   59
  DEL PEAK 41(17Q11.2) WILD-TYPE   11  414
                        clus
vv                       DEL PEAK 41(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 41(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            414
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 42(18Q22.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q22.3) MUTATED    18  64
  DEL PEAK 42(18Q22.3) WILD-TYPE  82 406
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                            82                            488 
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                            64                            406 
$`DEL PEAK 42(18Q22.3) MUTATED`
TCGA-02-0006 TCGA-02-0011 TCGA-02-0024 TCGA-02-0025 TCGA-02-0034 TCGA-02-0039 
       18.35        20.71        53.10        42.74        14.14        10.52 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0324 
       20.84        27.25        11.67        23.18        92.65         7.73 
TCGA-06-0129 TCGA-06-0151 TCGA-06-0173 TCGA-06-0206 TCGA-06-0237 TCGA-06-0648 
       33.67        46.59         4.47         7.66        13.64         9.80 
TCGA-06-0649 TCGA-06-0749 TCGA-06-1086 TCGA-06-1800 TCGA-06-1806 TCGA-06-2559 
        2.10         2.70         6.84        26.79        15.32         4.93 
TCGA-06-5413 TCGA-06-5859 TCGA-06-6388 TCGA-06-6694 TCGA-06-A5U0 TCGA-06-A5U1 
        8.81         4.57         5.23         7.36        26.79         1.87 
TCGA-08-0245 TCGA-08-0357 TCGA-08-0359 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
       37.84        37.58         3.39         4.27        11.08        19.33 
TCGA-08-0525 TCGA-12-0691 TCGA-12-0775 TCGA-12-0776 TCGA-12-0826 TCGA-12-1096 
       15.98        12.13         7.63         9.73        27.78         9.11 
TCGA-12-1098 TCGA-12-5301 TCGA-14-0812 TCGA-14-0817 TCGA-14-0865 TCGA-16-0846 
        3.98         2.04         3.25         5.39        16.50         3.91 
TCGA-16-0849 TCGA-19-0962 TCGA-19-1388 TCGA-19-1390 TCGA-19-2619 TCGA-19-4065 
       26.07         0.66        12.95        25.38         9.67         7.04 
TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-5133 TCGA-26-5136 TCGA-26-6173 
       14.96        10.03        13.87        14.86        18.97         7.92 
TCGA-27-1834 TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 
       40.54        11.51         8.35         5.26        11.28        31.27 
TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2634 
       13.64        21.07         0.49        14.86        12.23        22.78 
TCGA-32-4210 TCGA-41-3392 TCGA-4W-AA9S TCGA-74-6575 TCGA-76-4929 TCGA-76-4934 
        3.72         0.99         1.45        20.91         3.65         2.53 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6662 TCGA-81-5911 
        8.35        20.98        34.45        17.72 

$`DEL PEAK 42(18Q22.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
       11.77         4.73        23.18        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 
       20.61        87.06        77.65        20.12        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 
       90.58         2.83         3.62        10.72        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 
       28.70        25.05         5.49        10.19        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       27.02        65.00        17.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 
       13.87        14.20        15.95        12.23         9.90        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29        13.12         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.53        15.02        24.16         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        5.75        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
       40.41        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        4.54         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        6.15         7.79         5.39         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 
       12.85         4.77         1.55         4.77         4.96         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        2.56        14.60        17.72        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       22.29        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 
        0.72        12.56        42.15        19.59        58.68        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        4.80         7.27        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       15.06        53.85        43.23        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       15.98        12.23        15.85        14.53         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 
        2.24        11.24        13.78         1.35         2.89        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0850 
       50.53        19.10        53.19        13.28        17.59        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        3.65         7.17        12.66         3.25         0.13         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 
        1.78        22.49        14.07        16.80        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       28.54         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
        5.49         8.88         1.58         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        24.23        21.30        30.05        14.04 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       14.40        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        6.74         4.77         7.30        14.93        17.88         2.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       11.77        23.44        11.01         5.16        22.68        10.49 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
        5.42        15.39         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
        4.67        12.69        16.93        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        7.36         8.84        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.80         4.54         3.09         9.17        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 
        3.29         2.70        11.38        17.06         4.83         5.03 
TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R 
       23.90        18.64        36.20         1.61        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE 
                         11.59                          12.23 
[1] "0.5 - 92.7 (11.6)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.3) MUTATED    31  51
  DEL PEAK 42(18Q22.3) WILD-TYPE 193 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.3) MUTATED     31   51
  DEL PEAK 42(18Q22.3) WILD-TYPE  193  296
        clus
vv       DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE
  FEMALE                           31                            193
  MALE                             51                            296
[1] 2 2
[1] FALSE
D67V4, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.3) MUTATED    14  64
  DEL PEAK 42(18Q22.3) WILD-TYPE  60 410
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.3) MUTATED     14   64
  DEL PEAK 42(18Q22.3) WILD-TYPE   60  410
     clus
vv    DEL PEAK 42(18Q22.3) MUTATED DEL PEAK 42(18Q22.3) WILD-TYPE
  NO                            14                             60
  YES                           64                            410
[1] 2 2
[1] FALSE
D67V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 42(18Q22.3) MUTATED                               5
  DEL PEAK 42(18Q22.3) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 42(18Q22.3) MUTATED                     2
  DEL PEAK 42(18Q22.3) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 42(18Q22.3) MUTATED                                75
  DEL PEAK 42(18Q22.3) WILD-TYPE                             450
D67V6, multiclass
                                 clus
vv                                DEL PEAK 42(18Q22.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           75
                                 clus
vv                                DEL PEAK 42(18Q22.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q22.3) MUTATED       3                         9    67
  DEL PEAK 42(18Q22.3) WILD-TYPE    10                        41   418
D67V7, multiclass
                           clus
vv                          DEL PEAK 42(18Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               67
                           clus
vv                          DEL PEAK 42(18Q22.3) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             41
  WHITE                                                418
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.3) MUTATED     3  69
  DEL PEAK 42(18Q22.3) WILD-TYPE   9 404
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.3) MUTATED      3   69
  DEL PEAK 42(18Q22.3) WILD-TYPE    9  404
                        clus
vv                       DEL PEAK 42(18Q22.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 42(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            404
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 43(19Q13.41) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 43(19Q13.41) MUTATED    17  82
  DEL PEAK 43(19Q13.41) WILD-TYPE  83 388
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                             99                             471 
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                             82                             388 
$`DEL PEAK 43(19Q13.41) MUTATED`
TCGA-02-0026 TCGA-02-0028 TCGA-02-0034 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 
       24.59        90.58        14.14         2.50         8.35         9.57 
TCGA-02-0060 TCGA-02-0079 TCGA-02-0104 TCGA-02-0106 TCGA-02-0114 TCGA-02-0258 
        6.02        27.25        65.00        11.67        99.98        16.54 
TCGA-02-0260 TCGA-02-0281 TCGA-02-0321 TCGA-02-0325 TCGA-02-0432 TCGA-02-0456 
       16.93         3.98         9.90        10.62        47.11         3.35 
TCGA-02-2466 TCGA-06-0132 TCGA-06-0149 TCGA-06-0152 TCGA-06-0237 TCGA-06-0394 
       16.80        25.35         8.61        12.33        13.64        10.82 
TCGA-06-0745 TCGA-06-0875 TCGA-06-0878 TCGA-06-1084 TCGA-06-2561 TCGA-06-2562 
        7.86        43.46         7.17        23.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2569 TCGA-06-5411 TCGA-06-5415 TCGA-06-6693 TCGA-06-A5U0 
       30.64         0.43         8.35         8.55       120.56        26.79 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0346 TCGA-08-0348 
        2.56        22.68        37.84       115.86         8.42        12.16 
TCGA-08-0349 TCGA-08-0351 TCGA-08-0358 TCGA-08-0386 TCGA-08-0392 TCGA-08-0517 
        9.80        65.33        22.29        18.02         0.72        58.68 
TCGA-12-0619 TCGA-12-0656 TCGA-12-0827 TCGA-12-1088 TCGA-12-1094 TCGA-12-1095 
       34.92        94.78        38.76       127.59        12.23        15.85 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-3651 TCGA-14-0740 TCGA-14-0783 
       14.53         4.14        15.65        12.69        11.97         6.21 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1451 TCGA-14-1458 TCGA-14-4157 TCGA-15-1444 
        2.89        16.50        23.11         6.67         3.42        50.53 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-0960 TCGA-19-1388 TCGA-19-1390 
       16.37         4.31         6.41         8.61        12.95        25.38 
TCGA-19-2621 TCGA-19-2629 TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 
        1.08        24.23        18.97        40.54        18.08        10.39 
TCGA-28-1746 TCGA-28-2514 TCGA-28-5211 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        0.20         5.26        11.77        15.39        21.07         0.49 
TCGA-32-1978 TCGA-32-1987 TCGA-32-2491 TCGA-32-4208 TCGA-32-4210 TCGA-41-2575 
       15.85        14.86        12.23        21.14         3.72         9.53 
TCGA-41-5651 TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 TCGA-76-6193 TCGA-76-6285 
       15.12         4.80         3.65         9.17         2.70         8.35 
TCGA-76-6662 TCGA-76-6664 TCGA-87-5896 
       34.45        36.20        26.30 

$`DEL PEAK 43(19Q13.41) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 
       53.10        42.74        12.16         2.83         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       12.59         6.54        19.86        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        20.84        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       27.02        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
       12.23         7.73         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
       25.12        10.59        12.39        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        12.95        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       20.09        17.79        10.09        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.53        15.02        24.16         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       20.42        48.69         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.70         2.70         0.92        46.19         5.65        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       16.57        20.78        26.76         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.49         4.93         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 
        4.77         1.55         4.77         4.96         1.87         3.12 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0246 TCGA-08-0345 TCGA-08-0347 TCGA-08-0350 
       14.60        17.72         4.18         1.74        25.71        29.23 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
        3.39        12.23        14.93        15.35        13.97        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 
        4.27        42.15        11.08        19.59        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 
       14.73        12.99        10.45         7.59         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       27.78         8.94        20.58         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1096 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 
       21.73        15.98         9.11         3.98        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        0.95        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        1.35         5.39        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.78        13.78 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       13.97        11.77        21.90         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07         5.95         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       12.66         3.25         0.13         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 
        9.40        14.86         5.49         8.88         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 
       21.30        30.05        14.04        11.51        24.76        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        14.40        15.78         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 
        0.13         0.66         6.74         4.77         7.30        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       11.28        17.88         2.53        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 
       13.64         5.16        22.68        10.49         5.42         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 
       19.50         1.18         4.67        12.69        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        8.94         0.99         4.44        11.84         0.20        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 
       14.33         8.22         7.50         4.54         3.09         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 
       36.85        16.70         3.29        11.38        17.06        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 
        4.83         5.03        23.90        18.64         1.61        17.72 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                            0.2                             0.1 
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                         127.59                           92.65 
  DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE 
                          13.64                           11.84 
[1] "0.2 - 127.6 (13.6)" "0.1 - 92.7 (11.8)" 
[1] "hr=" "1.4"
D68V2, continuous
D68V3, binary
                                 cls
clus                                0   1
  DEL PEAK 43(19Q13.41) MUTATED    40  59
  DEL PEAK 43(19Q13.41) WILD-TYPE 184 288
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(19Q13.41) MUTATED     40   59
  DEL PEAK 43(19Q13.41) WILD-TYPE  184  288
        clus
vv       DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE
  FEMALE                            40                             184
  MALE                              59                             288
[1] 2 2
[1] FALSE
D68V4, binary
                                 cls
clus                                0   1
  DEL PEAK 43(19Q13.41) MUTATED     9  85
  DEL PEAK 43(19Q13.41) WILD-TYPE  65 389
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(19Q13.41) MUTATED      9   85
  DEL PEAK 43(19Q13.41) WILD-TYPE   65  389
     clus
vv    DEL PEAK 43(19Q13.41) MUTATED DEL PEAK 43(19Q13.41) WILD-TYPE
  NO                              9                              65
  YES                            85                             389
[1] 2 2
[1] FALSE
D68V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 43(19Q13.41) MUTATED                               3
  DEL PEAK 43(19Q13.41) WILD-TYPE                            25
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 43(19Q13.41) MUTATED                     4
  DEL PEAK 43(19Q13.41) WILD-TYPE                  14
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 43(19Q13.41) MUTATED                                92
  DEL PEAK 43(19Q13.41) WILD-TYPE                             433
D68V6, multiclass
                                 clus
vv                                DEL PEAK 43(19Q13.41) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               3
  TREATED PRIMARY GBM                                         4
  UNTREATED PRIMARY (DE NOVO) GBM                            92
                                 clus
vv                                DEL PEAK 43(19Q13.41) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                25
  TREATED PRIMARY GBM                                          14
  UNTREATED PRIMARY (DE NOVO) GBM                             433
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(19Q13.41) MUTATED       2                        11    83
  DEL PEAK 43(19Q13.41) WILD-TYPE    11                        39   402
D68V7, multiclass
                           clus
vv                          DEL PEAK 43(19Q13.41) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                                83
                           clus
vv                          DEL PEAK 43(19Q13.41) WILD-TYPE
  ASIAN                                                  11
  BLACK OR AFRICAN AMERICAN                              39
  WHITE                                                 402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                                 cls
clus                                0   1
  DEL PEAK 43(19Q13.41) MUTATED     2  82
  DEL PEAK 43(19Q13.41) WILD-TYPE  10 391
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(19Q13.41) MUTATED      2   82
  DEL PEAK 43(19Q13.41) WILD-TYPE   10  391
                        clus
vv                       DEL PEAK 43(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            82
                        clus
vv                       DEL PEAK 43(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             391
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 44(21Q21.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(21Q21.1) MUTATED    10  46
  DEL PEAK 44(21Q21.1) WILD-TYPE  90 424
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                            56                            514 
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                            46                            424 
$`DEL PEAK 44(21Q21.1) MUTATED`
TCGA-02-0011 TCGA-02-0015 TCGA-02-0051 TCGA-02-0080 TCGA-02-0106 TCGA-02-0114 
       20.71        20.61        15.09        89.72        11.67        99.98 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0339 TCGA-02-0451 TCGA-06-0126 TCGA-06-0150 
       17.72         3.98        12.39        16.21         6.94        19.46 
TCGA-06-0209 TCGA-06-0221 TCGA-06-0402 TCGA-06-0414 TCGA-06-0648 TCGA-06-0875 
        7.63        19.82         0.26        35.11         9.80        43.46 
TCGA-06-1801 TCGA-06-5856 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
       11.84         3.75         7.79       120.56         7.36         8.32 
TCGA-06-A7TL TCGA-08-0353 TCGA-08-0516 TCGA-12-0820 TCGA-12-0826 TCGA-12-0827 
       17.72         8.42        19.59        18.48        27.78        38.76 
TCGA-12-1099 TCGA-12-1600 TCGA-12-3653 TCGA-12-5295 TCGA-14-0740 TCGA-14-0817 
        4.14        14.73        14.53        14.93        11.97         5.39 
TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 
       17.85         3.78        13.78         3.91        17.59        16.37 
TCGA-16-1055 TCGA-19-0960 TCGA-19-1789 TCGA-19-2629 TCGA-19-5958 TCGA-19-A6J5 
       10.29         8.61         3.25        24.23        14.07        28.54 
TCGA-27-2521 TCGA-28-2514 TCGA-28-5219 TCGA-32-1978 TCGA-41-3392 TCGA-76-4925 
       10.39         5.26        22.68        15.85         0.99         4.80 
TCGA-76-4934 TCGA-76-6280 
        2.53        11.38 

$`DEL PEAK 44(21Q21.1) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       82.59        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        20.84        27.25        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        92.65        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 
       25.71         4.37        25.12        10.59        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       47.11        11.34         9.27         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.61         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        9.01        72.36         4.70         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         5.75         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       46.88         7.86         2.70         2.70         0.92        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84         4.04        26.79        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6697 TCGA-06-6698 
        4.57         5.23         5.39         1.48        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        2.56        14.60        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       65.33         1.28        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 
       91.76        24.79        10.62        23.51         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       12.23        15.85         9.11        14.53         3.98        15.65 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.68         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       10.95        12.69        34.92         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        7.96         3.42        50.53        19.10        53.19        13.28 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 
       26.07         4.31        29.03         4.57        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       21.24        13.97         6.41        11.77        21.90         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 
        4.64        25.38         3.65         7.17        12.66         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        22.49        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
       17.79         3.98        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 
        0.13         0.66         6.74         4.77         7.30        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88         2.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01        13.64         5.16        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       21.07         0.49         0.10        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.95         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
       13.35         8.94         9.53         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
       23.90        34.45        18.64        36.20         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                          0.26                           0.10 
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE 
                        13.925                         12.145 
[1] "0.3 - 120.6 (13.9)" "0.1 - 127.6 (12.1)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q21.1) MUTATED    23  33
  DEL PEAK 44(21Q21.1) WILD-TYPE 201 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q21.1) MUTATED     23   33
  DEL PEAK 44(21Q21.1) WILD-TYPE  201  314
        clus
vv       DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE
  FEMALE                           23                            201
  MALE                             33                            314
[1] 2 2
[1] FALSE
D69V4, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q21.1) MUTATED     7  46
  DEL PEAK 44(21Q21.1) WILD-TYPE  67 428
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q21.1) MUTATED      7   46
  DEL PEAK 44(21Q21.1) WILD-TYPE   67  428
     clus
vv    DEL PEAK 44(21Q21.1) MUTATED DEL PEAK 44(21Q21.1) WILD-TYPE
  NO                             7                             67
  YES                           46                            428
[1] 2 2
[1] FALSE
D69V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 44(21Q21.1) MUTATED                               3
  DEL PEAK 44(21Q21.1) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 44(21Q21.1) MUTATED                     1
  DEL PEAK 44(21Q21.1) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 44(21Q21.1) MUTATED                                52
  DEL PEAK 44(21Q21.1) WILD-TYPE                             473
D69V6, multiclass
                                 clus
vv                                DEL PEAK 44(21Q21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           52
                                 clus
vv                                DEL PEAK 44(21Q21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            473
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(21Q21.1) MUTATED       1                         4    50
  DEL PEAK 44(21Q21.1) WILD-TYPE    12                        46   435
D69V7, multiclass
                           clus
vv                          DEL PEAK 44(21Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               50
                           clus
vv                          DEL PEAK 44(21Q21.1) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                             46
  WHITE                                                435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q21.1) MUTATED     2  49
  DEL PEAK 44(21Q21.1) WILD-TYPE  10 424
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q21.1) MUTATED      2   49
  DEL PEAK 44(21Q21.1) WILD-TYPE   10  424
                        clus
vv                       DEL PEAK 44(21Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       DEL PEAK 44(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            424
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 45(22Q13.32) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(22Q13.32) MUTATED    33 179
  DEL PEAK 45(22Q13.32) WILD-TYPE  67 291
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            212                             358 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            179                             291 
$`DEL PEAK 45(22Q13.32) MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0015 TCGA-02-0016 TCGA-02-0026 TCGA-02-0027 
       23.18        35.41        20.61        87.06        24.59        12.16 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0054 TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 
       10.52        18.31         6.54        19.86         9.57         6.02 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0099 TCGA-02-0113 TCGA-02-0260 
       20.84        27.25         8.81         3.48        92.65        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 
       17.72        10.75        14.47         9.90        10.62         7.33 
TCGA-02-0333 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2486 TCGA-06-0129 
        4.37         3.35        16.80        15.32        20.32        33.67 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 TCGA-06-0147 TCGA-06-0152 TCGA-06-0158 
        0.20        10.29         2.33        17.79        12.33        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0175 
        9.44         3.42        56.91         5.85        19.66         4.04 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 
        3.65        73.84        27.22        44.58        15.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0211 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        7.40         5.56        11.84        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0744 
       13.64        48.69         9.01         0.26         4.70        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0875 TCGA-06-0878 TCGA-06-0882 TCGA-06-0939 
        7.86         2.70        43.46         7.17        20.78        26.76 
TCGA-06-1084 TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2562 TCGA-06-2565 
       23.93        13.61        15.32        12.49        12.56        16.64 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5418 TCGA-06-5856 
        4.37        11.74         8.35         8.81         2.73         3.75 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 
        7.79         5.39       120.56        12.85         4.77         1.87 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0349 TCGA-08-0350 
        2.56        22.68        37.84         4.18         9.80        29.23 
TCGA-08-0354 TCGA-08-0357 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       17.95        37.58        18.02        15.35         0.72        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0520 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 
       11.08        19.59        10.75        15.98        34.92        10.45 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0707 TCGA-12-0820 TCGA-12-0821 
       94.78        38.17        25.97        28.41        18.48        10.62 
TCGA-12-0826 TCGA-12-0827 TCGA-12-1088 TCGA-12-1091 TCGA-12-1096 TCGA-12-1097 
       27.78        38.76       127.59        33.21         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 
        3.98        15.65        14.73        44.02        12.69        14.53 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0862 
       14.93        15.12         6.21        23.05         2.24         2.89 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1402 
       16.50         2.04        28.93        15.95        19.30        32.05 
TCGA-14-1450 TCGA-14-1454 TCGA-14-1794 TCGA-14-1821 TCGA-14-2554 TCGA-14-3477 
       58.78        30.18         0.99        17.79        17.49         3.78 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-1056 TCGA-16-1062 TCGA-19-0962 
       13.78        50.53        53.19        14.01        21.24         0.66 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1389 TCGA-19-1392 TCGA-19-1791 TCGA-19-2620 
        3.39        10.75         4.64         3.65         0.13         4.87 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5956 
        7.53         4.08        24.23         7.00         6.64        22.49 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1442 TCGA-26-5132 
       14.07        14.96        17.79         3.98        31.33         9.40 
TCGA-26-5136 TCGA-26-6173 TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
       18.97         7.92         5.06         9.86        40.54        21.30 
TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-28-1746 
       11.51        18.08        10.39        16.08        14.40         0.20 
TCGA-28-1752 TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5208 
        8.48         2.83         6.74         4.77        11.28        17.88 
TCGA-28-5213 TCGA-28-5214 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 
       31.27        23.44        15.39        21.07         0.49        15.85 
TCGA-32-1980 TCGA-32-1986 TCGA-32-2491 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
        1.18        12.69        12.23        15.95         8.84        22.78 
TCGA-32-4208 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 
       21.14        13.35         8.94         9.53        11.84         0.20 
TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       12.46         1.45        20.91         8.22         4.80         4.54 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-6280 TCGA-76-6285 TCGA-76-6657 
        3.65         9.17         2.53        11.38         8.35         5.03 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

$`DEL PEAK 45(22Q13.32) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        18.35        10.59        20.71        82.59 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0033 
       77.65        20.12        53.10        42.74        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       14.14         3.62        10.72         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 
       15.09        12.59         2.50         8.35        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 
       28.70        25.05         5.49        10.19        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 
       12.62        51.32        57.76        16.96        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       16.54         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.73        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       12.92        15.45         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 
       26.70        24.23        11.90         2.20        11.74        20.09 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
        3.19        11.80        10.65         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 
        3.22        91.00         4.18        88.14        20.25        69.90 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       10.42        38.96         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 
        7.40         0.53        15.02        13.32        20.42        10.82 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       72.36         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 
        2.70         0.92        46.19         5.65        40.41        16.57 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1805 
        6.84         4.04        26.79        11.84        15.32        33.90 
TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 
        1.08         4.93        17.65        30.64         5.95         5.98 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 
        0.43        31.50         3.55         4.54         8.98         8.55 
TCGA-06-5416 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6391 TCGA-06-6694 
        6.71         6.15         4.57         5.23         1.48         7.36 
TCGA-06-6695 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 
        8.32         1.55         4.77         4.96        26.79         3.12 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       14.60        17.72       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
       12.16        65.33         1.28         8.42        24.56        31.10 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 
       22.29         3.39        12.23        14.93        13.97        12.56 
TCGA-08-0510 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
        4.27        58.68        19.33         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 TCGA-12-0657 
        7.56        15.35        14.73        12.99         7.59         0.10 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 
       26.66        12.13         3.65        20.38        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 
       24.79        23.51         8.94        20.58         5.82         7.59 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1099 TCGA-12-1599 
       21.73        15.98        12.23        15.85         4.14        25.68 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        6.77        59.77        26.93        15.22        10.95        34.92 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0789 TCGA-14-0790 
        3.22         2.04        11.97         0.95        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-1043 TCGA-14-1395 
        3.25         1.35         5.39        26.33         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 
        1.12         3.75        23.11         7.10         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
       40.96         6.67        12.43         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-15-1449 
        5.88         7.17         7.96         3.42        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
        4.57        10.29         9.14        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       21.90         8.61        14.27         9.07         5.95        12.95 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 
       25.38         7.17        12.66         3.25         9.67         1.08 
TCGA-19-2624 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        0.16         7.04        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       12.10         1.78        16.80        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        9.73         7.13         9.37        14.86         5.49         8.88 
TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 
        1.58         2.33        19.33        16.60        24.23        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 
       14.04        24.76         7.59         2.86        15.78         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        9.21         8.35         7.63         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5209 TCGA-28-5211 
        0.66         7.30         5.26        14.93         2.53        11.77 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        10.49         5.42 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 
        0.10        19.50         4.67        14.86        16.93        20.78 
TCGA-32-2495 TCGA-32-2616 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       15.02         7.36        25.18         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 
       10.85        19.23         0.85         0.99         4.44        15.12 
TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 
        4.08        25.58         3.45         4.34        14.33         7.50 
TCGA-76-4928 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        3.09        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
       20.98         4.83        23.90        34.45        18.64        36.20 
TCGA-81-5910 TCGA-81-5911 TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72         6.28        20.55 

  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                           0.13                            0.10 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                         127.59                          115.86 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                         12.625                          11.870 
[1] "0.1 - 127.6 (12.6)" "0.1 - 115.9 (11.9)"
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED    84 128
  DEL PEAK 45(22Q13.32) WILD-TYPE 140 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED     84  128
  DEL PEAK 45(22Q13.32) WILD-TYPE  140  219
        clus
vv       DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  FEMALE                            84                             140
  MALE                             128                             219
[1] 2 2
[1] FALSE
D70V4, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED    29 175
  DEL PEAK 45(22Q13.32) WILD-TYPE  45 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED     29  175
  DEL PEAK 45(22Q13.32) WILD-TYPE   45  299
     clus
vv    DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  NO                             29                              45
  YES                           175                             299
[1] 2 2
[1] FALSE
D70V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 45(22Q13.32) MUTATED                              10
  DEL PEAK 45(22Q13.32) WILD-TYPE                            18
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 45(22Q13.32) MUTATED                     6
  DEL PEAK 45(22Q13.32) WILD-TYPE                  12
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 45(22Q13.32) MUTATED                               196
  DEL PEAK 45(22Q13.32) WILD-TYPE                             329
D70V6, multiclass
                                 clus
vv                                DEL PEAK 45(22Q13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              10
  TREATED PRIMARY GBM                                         6
  UNTREATED PRIMARY (DE NOVO) GBM                           196
                                 clus
vv                                DEL PEAK 45(22Q13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                18
  TREATED PRIMARY GBM                                          12
  UNTREATED PRIMARY (DE NOVO) GBM                             329
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(22Q13.32) MUTATED       6                        13   184
  DEL PEAK 45(22Q13.32) WILD-TYPE     7                        37   301
D70V7, multiclass
                           clus
vv                          DEL PEAK 45(22Q13.32) MUTATED
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               184
                           clus
vv                          DEL PEAK 45(22Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              37
  WHITE                                                 301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED     4 180
  DEL PEAK 45(22Q13.32) WILD-TYPE   8 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED      4  180
  DEL PEAK 45(22Q13.32) WILD-TYPE    8  293
                        clus
vv                       DEL PEAK 45(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           180
                        clus
vv                       DEL PEAK 45(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             293
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 46(XP22.2) MUTATION ANALYSIS
D71V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 46(XP22.2) MUTATED    22  96
  DEL PEAK 46(XP22.2) WILD-TYPE  78 374
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          118                           452 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           96                           374 
$`DEL PEAK 46(XP22.2) MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 
       23.18        35.41        20.71        24.59        10.52         3.22 
TCGA-02-0058 TCGA-02-0099 TCGA-02-0111 TCGA-02-0258 TCGA-02-0330 TCGA-02-0339 
        8.35         3.48        23.18        16.54        15.91        12.39 
TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-02-2483 
       14.50        47.11        11.34         9.27        16.80        15.32 
TCGA-06-0138 TCGA-06-0152 TCGA-06-0158 TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 
       24.23        12.33        10.82        13.12         4.04        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0743 
       73.84        27.22        15.02         0.72        19.82        26.40 
TCGA-06-1800 TCGA-06-2558 TCGA-06-2561 TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 
       26.79        12.49        17.65        31.50        11.74         6.71 
TCGA-06-5418 TCGA-06-5859 TCGA-06-6693 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-06-A7TL 
        2.73         4.57       120.56        26.79         2.56        17.72 
TCGA-08-0245 TCGA-08-0348 TCGA-08-0354 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       37.84        12.16        17.95        15.35         0.72        42.15 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0818 TCGA-12-0821 
       58.68        10.75        15.98        15.35        91.76        10.62 
TCGA-12-0827 TCGA-12-1091 TCGA-12-1093 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 
       38.76        33.21        15.98        59.77        44.02        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0787 
       34.92        14.93        15.12        11.97         6.21         2.24 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 
        2.89        16.50        28.93         1.15        17.79         3.78 
TCGA-15-0742 TCGA-15-1444 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-19-0964 
       13.78        50.53        16.37         4.31        29.03         3.39 
TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-2619 TCGA-19-2621 
       12.95        25.38         3.65        12.66         9.67         1.08 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 
        7.53         4.08        24.23        22.49        14.96        13.87 
TCGA-26-5133 TCGA-27-1830 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-2514 
       14.86         5.06        10.39         7.59         8.35         5.26 
TCGA-28-5204 TCGA-28-5220 TCGA-32-1978 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 
       14.93        10.49        15.85        12.23        20.78        15.95 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 
       22.78        21.14         3.72        19.86        10.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-4W-AA9R TCGA-74-6575 TCGA-76-4929 TCGA-76-4931 
        9.53         0.99         4.08        20.91         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6285 TCGA-OX-A56R 
        2.53        36.85         8.35         5.92 

$`DEL PEAK 46(XP22.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
       11.77         4.73        18.35        10.59        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 
       87.06        77.65        20.12        53.10        42.74        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       90.58         2.83        14.14         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0114 
       27.02        65.00        11.67        17.65        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0430 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 
       10.59        10.55        16.21         3.35        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       26.70        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 
       46.59        13.94        10.45         3.19         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
        3.65        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 
        7.40        11.84         0.53        24.16        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84         4.04        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       33.90        15.32         1.08         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-5410 
        5.95        16.64         5.98         4.37         0.43         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5856 
        8.35         4.54         8.81         8.98         8.55         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 
        6.15         5.23         7.79         5.39         1.48         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        1.87         3.12        14.60        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74         8.42        25.71         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28         8.42        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 
        3.39        12.23        14.93        18.02        13.97        12.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
        4.27        11.08        19.59        19.33         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       18.41         7.56        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       43.23         7.63         9.73        14.93        14.86        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        23.51        27.78         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82         7.59        21.73        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3653 TCGA-12-5299 
        6.77        26.93        15.22        10.95        14.53         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        2.04         0.95        23.05        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 
        1.35         5.39        26.33         2.04        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-15-1447 
        7.17        17.49         7.96         3.42        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-1047 TCGA-16-1055 
       13.28         3.91        17.59        26.07         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 
       21.90         8.61         0.66        14.27        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        5.95         4.64         7.17         3.25         0.13         4.87 
TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       17.79         3.98        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33        19.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        18.08        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30        11.28        17.88         2.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 
       23.44        11.01        13.64         5.16        22.68         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
       15.39        21.07         0.49         0.10        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2495 TCGA-32-2616 
        4.67        12.69        14.86        16.93        15.02         7.36 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 
        8.84        25.18        12.59        19.23         0.85         8.94 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        4.80         4.54         3.09        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       34.45        18.64        36.20         1.61        17.72        26.30 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         0.72                          0.10 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                       120.56                        127.59 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                       14.680                        11.705 
[1] "0.7 - 120.6 (14.7)" "0.1 - 127.6 (11.7)"
[1] "hr=" "1.2"
D71V2, continuous
D71V3, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    46  72
  DEL PEAK 46(XP22.2) WILD-TYPE 178 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     46   72
  DEL PEAK 46(XP22.2) WILD-TYPE  178  275
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          46                           178
  MALE                            72                           275
[1] 2 2
[1] FALSE
D71V4, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    17  97
  DEL PEAK 46(XP22.2) WILD-TYPE  57 377
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     17   97
  DEL PEAK 46(XP22.2) WILD-TYPE   57  377
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                           17                            57
  YES                          97                           377
[1] 2 2
[1] FALSE
D71V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 46(XP22.2) MUTATED                               6
  DEL PEAK 46(XP22.2) WILD-TYPE                            22
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 46(XP22.2) MUTATED                     4
  DEL PEAK 46(XP22.2) WILD-TYPE                  14
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 46(XP22.2) MUTATED                               108
  DEL PEAK 46(XP22.2) WILD-TYPE                             417
D71V6, multiclass
                                 clus
vv                                DEL PEAK 46(XP22.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             6
  TREATED PRIMARY GBM                                       4
  UNTREATED PRIMARY (DE NOVO) GBM                         108
                                 clus
vv                                DEL PEAK 46(XP22.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              22
  TREATED PRIMARY GBM                                        14
  UNTREATED PRIMARY (DE NOVO) GBM                           417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(XP22.2) MUTATED       4                        10   100
  DEL PEAK 46(XP22.2) WILD-TYPE     9                        40   385
D71V7, multiclass
                           clus
vv                          DEL PEAK 46(XP22.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             100
                           clus
vv                          DEL PEAK 46(XP22.2) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            40
  WHITE                                               385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     1 100
  DEL PEAK 46(XP22.2) WILD-TYPE  11 373
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      1  100
  DEL PEAK 46(XP22.2) WILD-TYPE   11  373
                        clus
vv                       DEL PEAK 46(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       DEL PEAK 46(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           373
[1] 2 2
[1] FALSE
