[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-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/10005922/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/10015649/transformed.cor.cli.txt"

nPatients in clinical file=582, in cluster file=571, common to both=560
[1]  71 560
[1] "AMP PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            469 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            469 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          155                           405 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          155                           405 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         97                         463 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         97                         463 
[1] "AMP PEAK  4(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           48                           512 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           48                           512 
[1] "AMP PEAK  5(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            452 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            452 
[1] "AMP PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           512 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           512 
[1] "AMP PEAK  7(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        105                         455 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        105                         455 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          492                            68 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          492                            68 
[1] "AMP PEAK  9(7Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           450                            110 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           450                            110 
[1] "AMP PEAK 10(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          465                            95 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          465                            95 
[1] "AMP PEAK 11(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          458                           102 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          458                           102 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            490 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            490 
[1] "AMP PEAK 13(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          29                          531 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          29                          531 
[1] "AMP PEAK 14(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             82                             478 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             82                             478 
[1] "AMP PEAK 15(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           131                            429 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           131                            429 
[1] "AMP PEAK 16(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          91                          469 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          91                          469 
[1] "AMP PEAK 17(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          528 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          528 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          29                          531 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          29                          531 
[1] "AMP PEAK 19(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             524 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             524 
[1] "AMP PEAK 20(17P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            50                            510 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            50                            510 
[1] "AMP PEAK 21(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            81                            479 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            81                            479 
[1] "AMP PEAK 22(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           236                            324 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           236                            324 
[1] "AMP PEAK 23(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           241                            319 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           241                            319 
[1] "AMP PEAK 24(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         209                          351 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         209                          351 
[1] "AMP PEAK 25(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            68                            492 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            68                            492 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            464 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            464 
[1] "DEL PEAK  2(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           130                            430 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           130                            430 
[1] "DEL PEAK  3(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           500 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           500 
[1] "DEL PEAK  4(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           513 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           513 
[1] "DEL PEAK  5(1Q42.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            48                            512 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            48                            512 
[1] "DEL PEAK  6(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         526 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         526 
[1] "DEL PEAK  7(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           45                           515 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           45                           515 
[1] "DEL PEAK  8(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           54                           506 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           54                           506 
[1] "DEL PEAK  9(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           52                           508 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           52                           508 
[1] "DEL PEAK 10(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            58                            502 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            58                            502 
[1] "DEL PEAK 11(3Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           502 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           502 
[1] "DEL PEAK 12(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         495 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         495 
[1] "DEL PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           76                           484 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           76                           484 
[1] "DEL PEAK 14(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           89                           471 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           89                           471 
[1] "DEL PEAK 15(5Q35.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                           52                           508 
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                           52                           508 
[1] "DEL PEAK 16(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           156                            404 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           156                            404 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        177                         383 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        177                         383 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           65                           495 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           65                           495 
[1] "DEL PEAK 19(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          409                           151 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          409                           151 
[1] "DEL PEAK 20(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           76                           484 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           76                           484 
[1] "DEL PEAK 21(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           454                            106 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           454                            106 
[1] "DEL PEAK 22(10P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         456                          104 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         456                          104 
[1] "DEL PEAK 23(10P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            461                              99 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            461                              99 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            497                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            497                              63 
[1] "DEL PEAK 25(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           498                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           498                             62 
[1] "DEL PEAK 26(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           127                            433 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           127                            433 
[1] "DEL PEAK 27(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           103                            457 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           103                            457 
[1] "DEL PEAK 28(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            95                            465 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            95                            465 
[1] "DEL PEAK 29(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            489 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            489 
[1] "DEL PEAK 30(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          74                          486 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          74                          486 
[1] "DEL PEAK 31(12Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          76                          484 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          76                          484 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           234                            326 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           234                            326 
[1] "DEL PEAK 33(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                           174                            386 
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                           174                            386 
[1] "DEL PEAK 34(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                           170                            390 
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                           170                            390 
[1] "DEL PEAK 35(15Q14) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                         147                          413 
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                         147                          413 
[1] "DEL PEAK 36(16P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                            92                            468 
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                            92                            468 
[1] "DEL PEAK 37(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                            95                            465 
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                            95                            465 
[1] "DEL PEAK 38(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                            82                            478 
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                            82                            478 
[1] "DEL PEAK 39(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            92                            468 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            92                            468 
[1] "DEL PEAK 40(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            68                            492 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            68                            492 
[1] "DEL PEAK 41(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            80                            480 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            80                            480 
[1] "DEL PEAK 42(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             98                             462 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             98                             462 
[1] "DEL PEAK 43(21Q22.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                             46                             514 
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                             46                             514 
[1] "DEL PEAK 44(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            210                             350 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            210                             350 
[1] "DEL PEAK 45(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          115                           445 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          115                           445 
[1] "DEL PEAK 46(XQ23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                        106                         454 
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                        106                         454 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 560 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
         279          144          558          705          322         1077 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
         630         2512          627         1699         2362          612 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
        1615         1300          748          315         2755           86 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
         430          110          326          320          557          209 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
         448           98          459          383          199           76 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
         604          254          291          183          600          804 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
         873          762          167          310          634          829 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
        2729          691            7         1561          268         1757 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
         516          106          822         1977          355          537 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
         705         2818         3041          476         1489          503 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
         515          539          327          440          121          422 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
         432          485          372          301          235          323 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
           5          484          782          133          764          322 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
         377          441          321         1433          345          282 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
         493          102          511          393          466          470 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
         493           NA            8          123         1439            3 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
         109          691          989          320          570          428 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
         702          674          327           NA          280           NA 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
         357           71          611          508          298          239 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
          NA           NA          359          389          263           97 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
         166           NA           NA           78         1730           NA 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
         161          579           95          396            7           67 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
          83         2768           61         1642          578           77 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        1228         2246          801          866          454          313 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
         557          142          214           79           12          197 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
         167          119          151          360            6          378 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
         684           11          548          315          359           NA 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
         455          314          168            8         2145          143 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
         245            5         1065          375           98          136 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
         294           62          717          286          679          595 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
         164           82           66           28         1322         1405 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
         204          218          699          178          165          637 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
         226          193          109          815          263          240 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
         414         1031           NA           33           23          150 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
         282           86          932          181          207          182 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
         133           13          958          342          108          254 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
         138          268          273          260          204           83 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
         114          187          139          120          237          164 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
          45           15          224          253          391          145 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
          47          145          151           NA           NA           NA 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
         690         1057          119         3310           53          132 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
         419          316          231          104         1637           39 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
         195          458          685          447         1084          594 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
          29          279          330          478           97          322 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
           9           17          107          358          259          561 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
        1770           39          327          146          199          486 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
         527          168          426          439           50          316 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
         181          218         2005            3         1161          790 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
         734          186           80          551           NA          378 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
        1615         1311          167          277          452          434 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
        2791          754          562          323          715          845 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
        1179          272          626         3881          177          190 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
         929          658          364          346          482          277 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
         442          121          104          287          769          414 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
         195         1807         1315          784          351          333 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
         358         1050          357          399           98           62 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
         460          364           29          189          701           68 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
         342          419           99           41          164           88 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
         502          801           62          880          485          587 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
          24           42           34          114          975         1788 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
         703          216           35          918           28         1246 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
         187          378           30           60          541          543 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
         232          179          218          532          242          115 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
         104          300           NA          581         1618          168 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
         119          302          793          496          131          883 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
          25          301          406          111          556          425 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
         195          358          666          262           13          434 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
         103          327          276          181          394          141 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
         772          106          218          385           99            4 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
         294          148           33          229            5          124 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
         501          213          214          202          343          244 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
         567          144          242           54          198          164 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
         161          165           NA          504          305          422 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
         296          953          217          285          286          452 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
         167          270           37           48          241           71 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
         146          505           NA          555         1008          648 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
         914          427          350          753          316          316 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
         489          231           87          438          480            6 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
          77          280          254          232          258           37 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
          47           86            4           20          205          145 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
         222          160          119          275          474          442 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
         358          951          432          237          415          128 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
         690          319          165          468          641           15 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
           3          482          593           36          142          386 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
         452          515          372          632          457          485 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
         224          269          693          644          643          113 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
         383          604          330          323           26          406 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
         272          290           30          135          360            6 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
         351          236          105          636          132          436 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
         250          228          146          138           94          111 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
         279           77          328          508          100           82 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
         346          519          254          638          147          153 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
           7          282          235          237           49          539 
TCGA-87-5896 TCGA-OX-A56R 
         800           NA 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=369,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=397,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 560 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, 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    12  79
  AMP PEAK  1(1P36.21) WILD-TYPE  86 383
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            91                            469 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            79                            383 
$`AMP PEAK  1(1P36.21) MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 
        9.17        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        10.52 
TCGA-06-0133 TCGA-06-0152 TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 
       14.07        11.80         0.23         2.01         2.53        26.33 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0213 
       28.47        18.31         7.04         6.48         3.91         0.20 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       22.49        10.36         4.70        35.01        12.33         3.22 
TCGA-06-0649 TCGA-06-2557 TCGA-06-5856 TCGA-06-6698 TCGA-08-0349 TCGA-08-0350 
        2.04         1.08         3.75         4.77         7.59         3.42 
TCGA-08-0386 TCGA-08-0520 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0769 
       15.72        10.75         5.52        10.39        38.17        12.43 
TCGA-12-0776 TCGA-12-0820 TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 
        9.11        18.48        27.78         6.25         3.98         3.42 
TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-12-5295 TCGA-14-0783 TCGA-14-0813 
        9.44        43.23        11.74        13.12         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         5.52 
TCGA-16-1056 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 
       13.35         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         1.22         8.48         4.77 
TCGA-28-5207 TCGA-28-5216 TCGA-28-6450 TCGA-32-1970 TCGA-32-1987 TCGA-32-2616 
        9.04        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 
       21.17         3.72        10.62         9.53         7.76         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 
        0.10         3.58        22.72        32.52        18.74        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.12        13.02         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       19.00        40.37        73.84        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 
        2.60         0.39         5.49         4.96        11.84        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 
        5.52         0.26        70.52         8.05         0.16         4.47 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.67        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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 
        3.95         7.79         5.39         1.48         0.49         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
        8.32        12.85         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 
        1.74         4.34        13.78        10.39        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
        1.28         4.80         6.54        15.98        17.33        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.10        43.10         5.49        14.86        14.27        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-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.85         9.11        14.53        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
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-14-0862 TCGA-14-0865 
        2.24        11.24        13.78         3.25         2.89        16.50 
TCGA-14-0866 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       26.33        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       32.05        58.78        23.11         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1829 
        6.15        12.43         1.97        17.79         7.63         7.17 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42         9.86        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         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        0.82         9.90         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
       10.75         5.95         4.64         3.48         7.17         3.25 
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-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       16.47         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
        5.42         3.98        16.57        10.03        13.87        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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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 
       10.39        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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79         4.21        22.68        10.49 
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-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
       15.95         8.84        22.78        21.14        12.59        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-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       11.84         0.20        11.54         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  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 
                          9.40                          10.36 
[1] "0.1 - 92.7 (9.4)"   "0.1 - 127.6 (10.4)"
[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 181 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     39   52
  AMP PEAK  1(1P36.21) WILD-TYPE  181  288
        clus
vv       AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           39                            181
  MALE                             52                            288
[1] 2 2
[1] FALSE
D1V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  1(1P36.21) MUTATED                               0
  AMP PEAK  1(1P36.21) WILD-TYPE                            17
                                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
D1V5, 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)                               17
  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"
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED    63  28
  AMP PEAK  1(1P36.21) WILD-TYPE 319 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     63   28
  AMP PEAK  1(1P36.21) WILD-TYPE  319  150
     clus
vv    AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  NO                            63                            319
  YES                           28                            150
[1] 2 2
[1] FALSE
                                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                        35   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                             35
  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   9 393
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED      3   69
  AMP PEAK  1(1P36.21) WILD-TYPE    9  393
                        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                            393
[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    28 127
  AMP PEAK  2(1Q32.1) WILD-TYPE  70 335
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          155                           405 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          127                           335 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0014 TCGA-02-0024 TCGA-02-0028 TCGA-02-0052 
        9.17        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        10.52        14.07 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 
       11.74         2.33         7.86        11.80        12.79         3.19 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0177 TCGA-06-0182 TCGA-06-0185 
        2.56         5.29        19.04         2.01         2.53        73.84 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0210 
       28.47        18.31         7.04         6.48         3.91         4.96 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0240 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       22.49        10.36        20.42        70.52         4.70         8.05 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0750 TCGA-06-1084 TCGA-06-1087 TCGA-06-1804 
       35.01         3.22         0.92         7.43         3.58        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-A6S0 TCGA-08-0244 TCGA-08-0349 TCGA-08-0350 TCGA-08-0353 
        1.55         3.12        22.68         7.59         3.42         6.41 
TCGA-08-0357 TCGA-08-0386 TCGA-08-0514 TCGA-08-0524 TCGA-08-0531 TCGA-12-0615 
       35.64        15.72         8.52         6.54         5.52        14.01 
TCGA-12-0619 TCGA-12-0670 TCGA-12-0692 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 
       10.39        25.97         2.63        12.43        43.10         5.49 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1090 TCGA-12-1092 
       10.62        27.78        38.76        20.58         6.25        21.63 
TCGA-12-1096 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-3649 TCGA-12-3653 
        9.11         3.98         3.42         9.44        11.54        11.74 
TCGA-14-0783 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 
        6.21         2.24         1.35         5.39        16.50         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1401 TCGA-14-1452 TCGA-14-1454 TCGA-14-1459 
       28.93        19.30         3.75         7.10        30.18        12.43 
TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
        0.99        17.85         3.78         9.86        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-19-0962 TCGA-19-0963 TCGA-19-1387 
        3.91         9.93         4.31         0.43        14.27         5.95 
TCGA-19-1786 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2625 TCGA-19-4065 
        7.17         0.13         9.67         1.08         4.08         7.04 
TCGA-19-5952 TCGA-19-5954 TCGA-19-A6J4 TCGA-26-1440 TCGA-26-6173 TCGA-27-1834 
       18.64         7.96         3.98         9.73         7.92        33.14 
TCGA-27-2518 TCGA-27-2524 TCGA-27-2528 TCGA-28-1750 TCGA-28-1752 TCGA-28-2509 
       24.76         7.59        15.78         8.35         8.48         4.77 
TCGA-28-5207 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 TCGA-32-1979 
        9.04        13.64         4.21        10.49        15.39        19.50 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 
       14.86        16.93         8.84        22.78         3.72        19.86 
TCGA-32-5222 TCGA-41-2573 TCGA-41-3392 TCGA-41-5651 TCGA-41-6646 TCGA-74-6577 
       10.62         8.94         0.99        11.54         7.76         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4934 TCGA-76-4935 TCGA-76-6662 
       14.33         7.50         2.53        10.78         9.27 

$`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 
       55.86        77.65        20.12        42.74        24.59        10.36 
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 
        0.23        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         0.16 
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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 
        4.04        47.31         0.10         3.58        32.52        18.74 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         2.20 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0155 
       20.09        16.70         9.80        19.46        46.59         8.65 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0169 
        5.46         9.44        11.80        56.88        10.65         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.02         0.23         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       19.00        40.37        26.33        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        2.60         0.39         5.49        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.36        18.02        11.80        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.26         0.16        12.33         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17        43.46        46.19         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
        5.85         5.42        20.94         6.35        26.79         8.65 
TCGA-06-1802 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
        7.89        33.90         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95         6.81         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.24         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         7.36         8.32        12.85 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0246 
        4.77         4.96         1.87         2.56        34.75         3.91 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 
      108.82         1.74         4.34        13.78        10.39        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0359 
        1.28        15.06        22.52        14.70        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        3.52        11.77        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
        4.80        15.98        17.33        14.43         1.64         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 
        7.17        65.92         0.10        38.17        24.13         6.12 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       18.12        28.41        53.10         9.11        14.86        14.27 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0828 TCGA-12-1088 
       91.76        24.79        18.48        23.51         8.94       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
        5.82        30.54        11.97        11.38        15.85        14.53 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 
       15.12        11.97         0.95        23.05        11.24        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1043 TCGA-14-1395 
        3.25         2.89        26.33        15.95         0.79         1.38 
TCGA-14-1396 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 
        1.12        32.05        58.78        23.11         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       40.96         6.15         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 
        7.17        17.49         7.96         3.42        50.53        53.19 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07        16.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        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-19-1787 TCGA-19-1789 TCGA-19-2620 TCGA-19-2623 
       25.38         3.48        12.66         3.25         4.87         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16        16.47         7.00         6.64        11.28         8.02 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03        13.87        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         1.22         1.58 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        2.33         4.80        16.60         9.86        18.25        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        10.39        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
        2.86        14.40         0.20         2.53         9.21         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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5219 TCGA-28-6450 TCGA-32-1973 
       31.27        14.20         7.79        22.68         5.42        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-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2638 
       12.23        20.78        15.02        15.95         7.36        21.17 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       21.14        12.59        10.85         0.85        13.35         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-74-6573 TCGA-74-6575 TCGA-74-6581 
        4.44        11.84         0.20         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         0.23         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  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 
                         9.27                         10.39 
[1] "0.1 - 92.7 (9.3)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    61  94
  AMP PEAK  2(1Q32.1) WILD-TYPE 159 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     61   94
  AMP PEAK  2(1Q32.1) WILD-TYPE  159  246
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          61                           159
  MALE                            94                           246
[1] 2 2
[1] FALSE
D2V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  2(1Q32.1) MUTATED                               4
  AMP PEAK  2(1Q32.1) WILD-TYPE                            13
                               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
D2V5, multiclass
                                 clus
vv                                AMP PEAK  2(1Q32.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             4
  TREATED PRIMARY GBM                                       5
  UNTREATED PRIMARY (DE NOVO) GBM                         146
                                 clus
vv                                AMP PEAK  2(1Q32.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              13
  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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED   107  48
  AMP PEAK  2(1Q32.1) WILD-TYPE 275 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED    107   48
  AMP PEAK  2(1Q32.1) WILD-TYPE  275  130
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                          107                           275
  YES                          48                           130
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED       3                        12   134
  AMP PEAK  2(1Q32.1) WILD-TYPE    10                        27   351
D2V7, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             134
                           clus
vv                          AMP PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            27
  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     2 127
  AMP PEAK  2(1Q32.1) WILD-TYPE  10 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      2  127
  AMP PEAK  2(1Q32.1) WILD-TYPE   10  335
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           335
[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    16  81
  AMP PEAK  3(1Q44) WILD-TYPE  82 381
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         97                         463 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         81                         381 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0028 TCGA-02-0052 TCGA-02-0055 TCGA-02-0104 
        9.17        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        14.07        11.80 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 
        2.56         5.29        19.04         0.23         2.01         2.53 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       28.47        18.31         7.04         6.48         3.91        22.49 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-1084 
       10.36        70.52         4.70        35.01         3.22         7.43 
TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-2561 TCGA-06-2569 TCGA-06-5856 
        3.58         8.65         1.08         9.27         0.43         3.75 
TCGA-06-6698 TCGA-08-0349 TCGA-08-0350 TCGA-08-0354 TCGA-08-0380 TCGA-08-0386 
        4.77         7.59         3.42        15.06        10.85        15.72 
TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0619 TCGA-12-0657 TCGA-12-0773 
        6.54        17.33         5.52        10.39         0.10        43.10 
TCGA-12-0826 TCGA-12-0827 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       27.78        38.76         6.25         3.98         3.42         9.44 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 
       11.74         6.21         1.35         5.39        16.50         2.04 
TCGA-14-0871 TCGA-14-1452 TCGA-14-1454 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 
       28.93         7.10        30.18         0.99        17.85         3.78 
TCGA-15-0742 TCGA-15-1449 TCGA-19-0962 TCGA-19-1786 TCGA-19-1791 TCGA-19-2625 
        9.86         5.52         0.43         7.17         0.13         4.08 
TCGA-19-4065 TCGA-26-1440 TCGA-26-6173 TCGA-27-2524 TCGA-28-2509 TCGA-28-5214 
        7.04         9.73         7.92         7.59         4.77        14.20 
TCGA-28-5216 TCGA-28-5218 TCGA-32-1970 TCGA-32-1987 TCGA-32-2632 TCGA-32-2634 
       13.64         4.21        15.39        14.86         8.84        22.78 
TCGA-32-4210 TCGA-32-4719 TCGA-32-5222 TCGA-41-5651 TCGA-74-6578 TCGA-74-6584 
        3.72        10.85        10.62        11.54        14.33         7.50 
TCGA-76-4934 
        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        55.86        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        10.36         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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       18.74        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        46.59        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0169 
        5.46         9.44        11.80        56.88        10.65         3.12 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.02         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       40.37        73.84        26.33        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        2.60         0.39         5.49         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       12.43         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.32         5.52         0.26         8.05         0.16        12.33 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       20.94         6.35        26.79         7.89        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       15.32         0.76         4.93         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        6.81         5.98         4.37        31.50        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
       10.39        53.82         1.28         6.41        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0389 TCGA-08-0390 
       35.64        19.53         0.95         9.17         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.30         0.56         3.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-12-0615 
       58.19         1.28        10.75         4.80        15.98        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 
       14.43         1.64         5.95         7.17        65.92        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        53.10         5.49         9.11        14.86        14.27 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 
       91.76        24.79        18.48        10.62        23.51         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        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 
       11.38        15.85         9.11        14.53        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-0866 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-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        1.15         0.92        40.96         6.15        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-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 
        3.42        50.53        19.10        53.19         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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-19-1787 
        5.95        12.95         4.64        25.38         3.48        12.66 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       16.47         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
        5.42         3.98        16.57        10.03        13.87        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-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.22         1.58         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        10.39        16.08         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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 
       14.53        11.77        31.27         7.79        22.68        10.49 
TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        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        21.17        21.14        12.59 
TCGA-32-4213 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.86         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44        11.84         0.20         7.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        4.34         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  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 
                       9.17                       10.39 
[1] "0.1 - 92.7 (9.2)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    43  54
  AMP PEAK  3(1Q44) WILD-TYPE 177 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     43   54
  AMP PEAK  3(1Q44) WILD-TYPE  177  286
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        43                         177
  MALE                          54                         286
[1] 2 2
[1] FALSE
D3V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  3(1Q44) MUTATED                               0                   3
  AMP PEAK  3(1Q44) WILD-TYPE                            17                  15
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  3(1Q44) MUTATED                                94
  AMP PEAK  3(1Q44) WILD-TYPE                             431
D3V5, multiclass
                                 clus
vv                                AMP PEAK  3(1Q44) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           0
  TREATED PRIMARY GBM                                     3
  UNTREATED PRIMARY (DE NOVO) GBM                        94
                                 clus
vv                                AMP PEAK  3(1Q44) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            17
  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"
D3V6, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    69  28
  AMP PEAK  3(1Q44) WILD-TYPE 313 150
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     69   28
  AMP PEAK  3(1Q44) WILD-TYPE  313  150
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         69                         313
  YES                        28                         150
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       2                         8    80
  AMP PEAK  3(1Q44) WILD-TYPE    11                        31   405
D3V7, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         8
  WHITE                                            80
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                          31
  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  75
  AMP PEAK  3(1Q44) WILD-TYPE   9 387
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      3   75
  AMP PEAK  3(1Q44) WILD-TYPE    9  387
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        75                         387
[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     8  40
  AMP PEAK  4(2P24.3) WILD-TYPE  90 422
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           48                           512 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           40                           422 
$`AMP PEAK  4(2P24.3) MUTATED`
TCGA-02-0001 TCGA-02-0014 TCGA-02-0104 TCGA-02-0113 TCGA-02-0258 TCGA-02-0281 
        9.17        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 
       14.07        46.59        18.31        22.49        18.02         2.04 
TCGA-06-0877 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-2557 TCGA-06-2569 
        5.65         6.35         3.58         7.89         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         4.34        15.72         3.52        58.19 
TCGA-12-0619 TCGA-12-0773 TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0740 
       10.39        43.10        14.86         3.42        11.74        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        16.31 
TCGA-19-0957 TCGA-19-1786 TCGA-19-2629 TCGA-26-1439 TCGA-26-1442 TCGA-26-5133 
       21.90         7.17        16.47        13.87        31.33        14.86 
TCGA-27-1834 TCGA-27-1836 TCGA-28-5218 TCGA-32-4210 TCGA-41-2573 TCGA-74-6584 
       33.14        30.05         4.21         3.72         8.94         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        55.86        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        10.36        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 
        0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        3.58        22.72        32.52        10.52        18.74        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 
       26.33        28.47        14.93        10.29         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
       11.84         0.20        12.43         0.36        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       26.79         8.65        13.61        33.90        15.32         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.24         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         3.95         7.79         5.39         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91       108.82         1.74        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
        3.19        10.59         0.30         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       18.44         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       17.33         5.52        14.01        14.43         1.64         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        5.49         9.11        14.27        91.76        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-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0862 TCGA-14-0865 
       11.24        13.78         3.25         1.35         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-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.15        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
       53.19         5.52         9.93        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77         8.61         0.43        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-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.48        12.66         3.25         0.13         9.67         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-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1837 
        4.80        16.60         9.86        18.25        21.30        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        10.39        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-28-1752 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-28-2514 
        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79        13.64        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-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       20.78        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.17        21.14        12.59        19.86        10.85        10.62 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        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 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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 
                       11.855                         9.915 
[1] "0.4 - 92.7 (11.9)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED    22  26
  AMP PEAK  4(2P24.3) WILD-TYPE 198 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     22   26
  AMP PEAK  4(2P24.3) WILD-TYPE  198  314
        clus
vv       AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  FEMALE                          22                           198
  MALE                            26                           314
[1] 2 2
[1] FALSE
D4V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  4(2P24.3) MUTATED                               1
  AMP PEAK  4(2P24.3) WILD-TYPE                            16
                               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
D4V5, multiclass
                                 clus
vv                                AMP PEAK  4(2P24.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          46
                                 clus
vv                                AMP PEAK  4(2P24.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              16
  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"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED    34  14
  AMP PEAK  4(2P24.3) WILD-TYPE 348 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     34   14
  AMP PEAK  4(2P24.3) WILD-TYPE  348  164
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  NO                           34                           348
  YES                          14                           164
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.3) MUTATED       1                         5    40
  AMP PEAK  4(2P24.3) WILD-TYPE    12                        34   445
D4V7, multiclass
                           clus
vv                          AMP PEAK  4(2P24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              40
                           clus
vv                          AMP PEAK  4(2P24.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            34
  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  41
  AMP PEAK  4(2P24.3) WILD-TYPE  12 421
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      0   41
  AMP PEAK  4(2P24.3) WILD-TYPE   12  421
                        clus
vv                       AMP PEAK  4(2P24.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       AMP PEAK  4(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           421
[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    19  89
  AMP PEAK  5(3Q26.33) WILD-TYPE  79 373
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           108                            452 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                            89                            373 
$`AMP PEAK  5(3Q26.33) MUTATED`
TCGA-02-0001 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0047 TCGA-02-0048 
        9.17        10.59        55.86        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 
        5.29        28.47        18.31        11.84        10.36         0.26 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0648 TCGA-06-0649 
        4.70         0.16        35.01        12.33         9.67         2.04 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-2557 
        9.40        22.32         5.39         7.17         3.58         1.08 
TCGA-06-2563 TCGA-06-5408 TCGA-06-5416 TCGA-06-5856 TCGA-06-6389 TCGA-06-6391 
       30.64        11.24         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         4.34         6.41        19.53 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0618 
        0.30         3.52        10.75        15.98        14.01         1.64 
TCGA-12-0619 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 
       10.39         0.10        38.17         6.12         9.11        14.86 
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         6.25         3.42 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 
        9.44         6.41        59.41        43.23        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         5.52        14.27 
TCGA-19-1388 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 TCGA-26-6174 
       12.95         3.48        16.47         7.04         9.73         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-2521 TCGA-28-1752 
        4.80        16.60        33.14        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         9.04        31.27         7.79        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        10.36 
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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 
       73.84        26.33        14.93        10.29         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.20        12.43        22.49         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 
       20.42        14.96        10.32         5.52        70.52         8.05 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 
        3.22         4.47        23.57        19.56         2.70         2.17 
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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         6.35        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90        15.32         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        9.27         2.83         5.95         6.81         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         3.95 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.39         0.49        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        3.91       108.82        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28        15.06        22.52        14.70        35.64 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0620 
        4.80         6.54        17.33         5.52        14.43         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        7.17        65.92        25.97        24.13         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 
       28.41        12.43        53.10        43.10         5.49        14.27 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 
       91.76        24.79        18.48        10.62        27.78         8.94 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 
        9.11        14.53         3.98        25.28        13.61        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
       11.24        13.78         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-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       32.05        58.78         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 
        6.15        12.43         1.97        17.79        17.85         5.88 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       53.19         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1786 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-19-2631 TCGA-19-5947 
        1.08         7.53         0.16         4.08         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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         1.22         1.58         7.92 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
        9.86        18.25        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 
       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-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         0.66         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 
        3.91        15.58        14.53        11.77        14.20         4.21 
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-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         7.36        22.78        21.17        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        10.62         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 
       13.35         8.94         0.99         4.44        11.54         7.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
        3.45        20.91        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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38        17.06        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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                         108.82 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                          8.66                          10.59 
[1] "0.1 - 127.6 (8.7)"  "0.1 - 108.8 (10.6)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    40  68
  AMP PEAK  5(3Q26.33) WILD-TYPE 180 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     40   68
  AMP PEAK  5(3Q26.33) WILD-TYPE  180  272
        clus
vv       AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  FEMALE                           40                            180
  MALE                             68                            272
[1] 2 2
[1] FALSE
D5V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  5(3Q26.33) MUTATED                               0
  AMP PEAK  5(3Q26.33) WILD-TYPE                            17
                                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
D5V5, 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)                               17
  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"
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    73  35
  AMP PEAK  5(3Q26.33) WILD-TYPE 309 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     73   35
  AMP PEAK  5(3Q26.33) WILD-TYPE  309  143
     clus
vv    AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  NO                            73                            309
  YES                           35                            143
[1] 2 2
[1] FALSE
                                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                        32   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                             32
  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  11 380
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED      1   82
  AMP PEAK  5(3Q26.33) WILD-TYPE   11  380
                        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                            380
[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  91 421
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           512 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           41                           421 
$`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        47.31        10.52         3.19         7.04        70.52 
TCGA-06-0410 TCGA-06-0744 TCGA-06-0879 TCGA-06-6388 TCGA-06-6697 TCGA-08-0246 
        4.70        19.56        22.98         3.95        12.85         3.91 
TCGA-08-0510 TCGA-08-0531 TCGA-12-0616 TCGA-12-0691 TCGA-12-0820 TCGA-12-0826 
        3.52         5.52        14.43         6.12        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 
       13.35         5.95         3.48         6.64         5.39         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         7.79         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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        2.70         0.26         4.04         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       32.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       12.79         8.65         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29        18.31         4.67         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       20.42        14.96        10.32         5.52         0.26         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        2.04        23.57         9.40        22.32         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         0.49         7.36         8.32 
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-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.30         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        24.13         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
       14.86        14.27        91.76        24.79        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        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         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3651 
        6.41        59.41        43.23        25.78        11.54        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-1396 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         6.15 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         0.99        17.85         7.63         5.88         7.17 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        5.52         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        0.82         9.90         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 
       10.75         9.07        12.95         4.64        25.38         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        16.47         7.00         7.04 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        6.51         5.29         5.42        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        33.14        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        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-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         4.77         7.30         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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-32-1986 
        0.49         0.10        15.85        19.50         1.18        12.69 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       14.86        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        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        0.99         4.44        11.54         7.76         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-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        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 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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 
                         9.86                         10.16 
[1] "0.2 - 92.7 (9.9)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED    22  26
  AMP PEAK  6(4P16.3) WILD-TYPE 198 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED     22   26
  AMP PEAK  6(4P16.3) WILD-TYPE  198  314
        clus
vv       AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          22                           198
  MALE                            26                           314
[1] 2 2
[1] FALSE
D6V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  6(4P16.3) MUTATED                               1
  AMP PEAK  6(4P16.3) WILD-TYPE                            16
                               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
D6V5, 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)                              16
  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"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED    34  14
  AMP PEAK  6(4P16.3) WILD-TYPE 348 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED     34   14
  AMP PEAK  6(4P16.3) WILD-TYPE  348  164
     clus
vv    AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  NO                           34                           348
  YES                          14                           164
[1] 2 2
[1] FALSE
                               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                        35   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                            35
  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  11 420
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED      1   42
  AMP PEAK  6(4P16.3) WILD-TYPE   11  420
                        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                           420
[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    18  87
  AMP PEAK  7(4Q12) WILD-TYPE  80 375
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        105                         455 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         87                         375 
$`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        10.52        22.16        11.74 
TCGA-06-0155 TCGA-06-0166 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
        8.65         5.29        13.02         0.23         2.20         2.01 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0221 
       18.31         7.04         4.96        11.84        12.43        18.02 
TCGA-06-0241 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0649 
       14.96         0.26        70.52         4.70         8.05         2.04 
TCGA-06-0743 TCGA-06-0875 TCGA-06-0879 TCGA-06-1802 TCGA-06-2559 TCGA-06-5408 
       22.32        43.46        22.98         7.89         4.93        11.24 
TCGA-06-5856 TCGA-06-6695 TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0353 
        3.75         8.32        34.75         3.91        13.78         6.41 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0524 TCGA-08-0531 TCGA-12-0616 
        3.52         8.52        18.44         6.54         5.52        14.43 
TCGA-12-0692 TCGA-12-0828 TCGA-12-1096 TCGA-12-1097 TCGA-12-3646 TCGA-14-0740 
        2.63         8.94         9.11        14.53        43.23        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         9.93        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         3.48         7.00 
TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 
        3.98        10.03        13.87         9.40         5.49         8.88 
TCGA-27-1830 TCGA-27-1834 TCGA-28-2506 TCGA-28-5211 TCGA-28-5215 TCGA-28-5216 
        4.80        33.14         6.74        11.77         7.79        13.64 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1991 TCGA-32-4210 TCGA-32-4211 
       21.07         0.49         0.10        16.93         3.72        12.59 
TCGA-32-5222 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-74-6575 TCGA-76-4928 
       10.62         9.53        11.84         0.20        20.91         3.09 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6193 
        2.53        10.78         2.70 

$`AMP PEAK  7(4Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       18.74        14.07        23.08        10.75         0.20         9.21 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
        2.20         2.33        20.09        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        11.80        12.79         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.12         2.73        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        0.20        22.49         0.36        10.36        11.80        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       10.32         5.52         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        4.47         9.67        23.57         9.40        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.17         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 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65        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 
        0.76         9.27         2.83        30.64         5.95         6.81 
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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         7.36        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 
        4.96         1.87         3.12         2.56        22.68       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74         4.34        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        0.30         0.56        11.77        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 
        4.80        15.98        17.33        14.01         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         6.12        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       11.97        11.38        15.85         3.98         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       25.28        13.61         6.41        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 
       11.24        13.78         1.35         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-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18        40.96         6.15        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
       17.85         5.88        17.49         7.96         3.42         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10        53.19         5.52        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0962 TCGA-19-0964 
       18.28        13.97         6.41        11.77         0.43         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       10.75         9.07         4.64         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        16.47         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.29         5.42        16.57         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5133 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        9.37        14.86         1.22         1.58         7.92         2.33 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        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        10.39        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-28-1752 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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 
        9.04        15.58        14.53        31.27        14.20         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1978 TCGA-32-1979 
       22.68        10.49         5.42        15.39        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-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        21.17 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       21.14        19.86        10.85         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 
        0.99         4.44        11.54         7.76         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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  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 
                       9.53                       10.36 
[1] "0.1 - 92.7 (9.5)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    37  68
  AMP PEAK  7(4Q12) WILD-TYPE 183 272
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     37   68
  AMP PEAK  7(4Q12) WILD-TYPE  183  272
        clus
vv       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  FEMALE                        37                         183
  MALE                          68                         272
[1] 2 2
[1] FALSE
D7V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  7(4Q12) MUTATED                               1                   2
  AMP PEAK  7(4Q12) WILD-TYPE                            16                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  7(4Q12) MUTATED                               102
  AMP PEAK  7(4Q12) WILD-TYPE                             423
D7V5, multiclass
                                 clus
vv                                AMP PEAK  7(4Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           1
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                       102
                                 clus
vv                                AMP PEAK  7(4Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            16
  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"
D7V6, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    67  38
  AMP PEAK  7(4Q12) WILD-TYPE 315 140
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     67   38
  AMP PEAK  7(4Q12) WILD-TYPE  315  140
     clus
vv    AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  NO                         67                         315
  YES                        38                         140
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q12) MUTATED       1                         8    93
  AMP PEAK  7(4Q12) WILD-TYPE    12                        31   392
D7V7, multiclass
                           clus
vv                          AMP PEAK  7(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         8
  WHITE                                            93
                           clus
vv                          AMP PEAK  7(4Q12) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          31
  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  87
  AMP PEAK  7(4Q12) WILD-TYPE  10 375
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      2   87
  AMP PEAK  7(4Q12) WILD-TYPE   10  375
                        clus
vv                       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                        87                         375
[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    78 414
  AMP PEAK  8(7P11.2) WILD-TYPE  20  48
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          492                            68 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          414                            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 
        9.17         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 
       55.86        77.65        20.12        42.74        10.36         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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         2.20        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       12.79         8.65         3.19         5.46         9.44         2.56 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.88         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00         2.01        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26        70.52         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 
        3.58        26.79         8.65         7.89        13.61        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.95         6.81         4.37        11.24         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         3.95         5.39         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        3.12         2.56        22.68        34.75         3.91         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        4.34        13.78        10.39         7.59         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
        0.56         3.52         8.52         1.28        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       11.74        13.12         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-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        1.35         5.39         2.89        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-14-1795 
        0.92        40.96         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
        3.42         9.86        19.10         5.52         3.91         9.93 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 
        4.31        29.03         0.82         9.90         3.65        18.28 
TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       13.97        11.77        21.90         0.43        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 
        3.48         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        7.96         1.78         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03        13.87         9.73         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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        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        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-28-2509 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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        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-32-2638 TCGA-32-4210 
       15.02        15.95         7.36         8.84        21.17         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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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        10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

$`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         0.23 
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        32.52        20.09        11.80        10.65        53.98 
TCGA-06-0221 TCGA-06-0410 TCGA-06-1805 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       18.02         4.70        33.90         5.98         0.43        31.50 
TCGA-06-5416 TCGA-06-6389 TCGA-06-6391 TCGA-06-6701 TCGA-08-0344 TCGA-08-0350 
        6.71         7.79         1.48         4.96       108.82         3.42 
TCGA-08-0351 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       53.82        11.77        18.44        58.19         4.80         6.54 
TCGA-12-0818 TCGA-12-0827 TCGA-14-0740 TCGA-14-0865 TCGA-14-1821 TCGA-14-3477 
       91.76        38.76        11.97        16.50        17.79         3.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1460 
       50.53        53.19        26.07        16.31        13.35         6.41 
TCGA-19-0960 TCGA-19-2625 TCGA-19-5956 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        8.61         4.08         6.51        31.33        14.86         5.49 
TCGA-27-2521 TCGA-28-1756 TCGA-28-5216 TCGA-32-1973 TCGA-32-2634 TCGA-32-4208 
       10.39         2.83        13.64        21.07        22.78        21.14 
TCGA-41-4097 TCGA-76-6193 
        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                        108.82 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                        9.485                        15.090 
[1] "0.1 - 127.6 (9.5)"  "0.2 - 108.8 (15.1)"
[1] "hr=" "2.2"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED   190 302
  AMP PEAK  8(7P11.2) WILD-TYPE  30  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED    190  302
  AMP PEAK  8(7P11.2) WILD-TYPE   30   38
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                         190                            30
  MALE                           302                            38
[1] 2 2
[1] FALSE
D8V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  8(7P11.2) MUTATED                              14
  AMP PEAK  8(7P11.2) WILD-TYPE                             3
                               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
D8V5, multiclass
                                 clus
vv                                AMP PEAK  8(7P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            14
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         465
                                 clus
vv                                AMP PEAK  8(7P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               3
  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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED   329 163
  AMP PEAK  8(7P11.2) WILD-TYPE  53  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED    329  163
  AMP PEAK  8(7P11.2) WILD-TYPE   53   15
     clus
vv    AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  NO                          329                            53
  YES                         163                            15
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P11.2) MUTATED      10                        35   425
  AMP PEAK  8(7P11.2) WILD-TYPE     3                         4    60
D8V7, multiclass
                           clus
vv                          AMP PEAK  8(7P11.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          35
  WHITE                                             425
                           clus
vv                          AMP PEAK  8(7P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             4
  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     8 404
  AMP PEAK  8(7P11.2) WILD-TYPE   4  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      8  404
  AMP PEAK  8(7P11.2) WILD-TYPE    4   58
                        clus
vv                       AMP PEAK  8(7P11.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         404
                        clus
vv                       AMP PEAK  8(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            58
[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    74 376
  AMP PEAK  9(7Q11.21) WILD-TYPE  24  86
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           450                            110 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           376                             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 
        9.17         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 
       55.86        77.65        20.12        42.74        10.36         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         0.16 
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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       22.72        10.52        18.74        14.07        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.20         9.21        11.74         2.33        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        46.59        11.80         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        5.46         9.44        56.88         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
       19.00         2.53        40.37        73.84        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
       12.43        22.49        10.36        11.80        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        5.52         0.26        70.52         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.40        22.32        19.56         5.39         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 
        4.93         9.27         2.83        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         3.95         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-08-0244 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        1.87         2.56        22.68         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       10.39         7.59         1.28        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 
        3.19        10.59         0.30         0.56         3.52         1.28 
TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
       10.75        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       14.27        18.48        10.62        23.51        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 
       43.23        25.78        11.54        10.95        11.77        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       13.12         3.22         2.04        15.12         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-14-0866 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-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15        30.18         0.92         6.15        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         9.86        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91         9.93         4.31        29.03         0.82         9.90 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       18.28        13.97        11.77        21.90         8.61         0.43 
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-19-1791 TCGA-19-2619 
       25.38         3.48         7.17        12.66         0.13         9.67 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       11.28        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.73         7.13         9.40         8.88         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 
       33.14        21.30        11.51        24.76        10.39         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-28-1757 
        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-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
        9.04        15.58        11.77        31.27        14.20         7.79 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
        4.21        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-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 
       14.86        16.93        12.23        20.78        15.95         7.36 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 
        8.84        21.17         3.72        12.59        10.62         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-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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        10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

$`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         0.23        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 
        3.58        32.52        23.08         2.20        20.09        12.79 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0178 TCGA-06-0187 TCGA-06-0219 
       11.80         2.56        10.65        53.98        26.33         0.36 
TCGA-06-0221 TCGA-06-0240 TCGA-06-0410 TCGA-06-0747 TCGA-06-1805 TCGA-06-2565 
       18.02        20.42         4.70         2.70        33.90         6.81 
TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 TCGA-06-6389 
        5.98         0.43        31.50        11.24         6.71         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0245 TCGA-08-0246 
        1.48         0.49         4.96         3.12        34.75         3.91 
TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0512 TCGA-08-0514 
      108.82         3.42        53.82         6.41        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0688 TCGA-12-0818 
       18.44        58.19         4.80         6.54        24.13        91.76 
TCGA-12-0819 TCGA-12-0827 TCGA-12-3652 TCGA-14-0740 TCGA-14-0817 TCGA-14-0862 
       24.79        38.76        34.52        11.97         5.39         2.89 
TCGA-14-0865 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 
       16.50        40.96        17.79         3.78        50.53        53.19 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 TCGA-16-1460 TCGA-19-0964 
       26.07        16.31        13.35         3.65         6.41         3.39 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 
        3.25         4.87         1.08         4.08         8.02         6.51 
TCGA-26-1442 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-1837 
       31.33         9.37        14.86         5.49        30.05        14.04 
TCGA-27-2521 TCGA-27-2523 TCGA-28-1756 TCGA-28-5209 TCGA-28-5216 TCGA-32-1973 
       10.39        16.08         2.83        14.53        13.64        21.07 
TCGA-32-2495 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 
       15.02        22.78        21.14        19.86        10.85         0.20 
TCGA-76-4926 TCGA-76-6193 
        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                         108.82 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                          9.44                          13.84 
[1] "0.1 - 127.6 (9.4)"  "0.2 - 108.8 (13.8)"
[1] "hr=" "1.6"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED   172 278
  AMP PEAK  9(7Q11.21) WILD-TYPE  48  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED    172  278
  AMP PEAK  9(7Q11.21) WILD-TYPE   48   62
        clus
vv       AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  FEMALE                          172                             48
  MALE                            278                             62
[1] 2 2
[1] FALSE
D9V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  9(7Q11.21) MUTATED                              11
  AMP PEAK  9(7Q11.21) WILD-TYPE                             6
                                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
D9V5, multiclass
                                 clus
vv                                AMP PEAK  9(7Q11.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             11
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          429
                                 clus
vv                                AMP PEAK  9(7Q11.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                6
  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"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED   300 150
  AMP PEAK  9(7Q11.21) WILD-TYPE  82  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED    300  150
  AMP PEAK  9(7Q11.21) WILD-TYPE   82   28
     clus
vv    AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  NO                           300                             82
  YES                          150                             28
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7Q11.21) MUTATED       8                        32   388
  AMP PEAK  9(7Q11.21) WILD-TYPE     5                         7    97
D9V7, multiclass
                           clus
vv                          AMP PEAK  9(7Q11.21) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           32
  WHITE                                              388
                           clus
vv                          AMP PEAK  9(7Q11.21) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              7
  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     7 368
  AMP PEAK  9(7Q11.21) WILD-TYPE   5  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED      7  368
  AMP PEAK  9(7Q11.21) WILD-TYPE    5   94
                        clus
vv                       AMP PEAK  9(7Q11.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          368
                        clus
vv                       AMP PEAK  9(7Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             94
[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    75 390
  AMP PEAK 10(7Q21.2) WILD-TYPE  23  72
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          465                            95 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          390                            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 
        9.17         4.73        18.35        10.59        20.61        55.86 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       77.65        20.12        42.74        10.36         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         0.16        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        16.21         2.70         4.04        47.31 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        0.10        22.72        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       22.16        10.75         0.20         9.21        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       12.79         8.65         3.19         5.46         9.44         2.56 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.88         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00         2.01        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
       22.49        18.02        10.36        11.80        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        5.52         0.26        70.52         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65         7.89        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.24         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 
        3.95         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-08-0244 
        1.55         4.77         1.87         3.12         2.56        22.68 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
        0.56         3.52         8.52         1.28        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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-12-1092 
        8.94        20.58       127.59         5.82         6.25        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
        3.42         9.44        25.28        13.61        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
       25.78        11.54        10.95        11.77        11.74        13.12 
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-14-0866 
       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-14-1396 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-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
        3.42         9.86        50.53        19.10         5.52         3.91 
TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1062 
        9.93         4.31        29.03         0.82         9.90        18.28 
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         0.43        14.27 
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 
        3.48         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       11.28        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
        9.73        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        33.14        21.30        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
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-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30         3.91         9.04        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.49        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-32-2638 TCGA-32-4210 TCGA-32-4211 
       15.95         7.36         8.84        21.17         3.72        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44        11.84        11.54         7.76         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        10.78        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

$`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         0.23        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         0.26         3.58 
TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0160 TCGA-06-0165 TCGA-06-0178 
       32.52         2.20        20.09        11.80        10.65        53.98 
TCGA-06-0219 TCGA-06-0240 TCGA-06-0410 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 
        0.36        20.42         4.70        33.90         6.81         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         0.49 
TCGA-06-6701 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
        4.96        34.75         3.91       108.82         3.42        53.82 
TCGA-08-0353 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
        6.41        11.77        18.44        58.19         4.80         6.54 
TCGA-12-0827 TCGA-12-1091 TCGA-12-1602 TCGA-12-3652 TCGA-14-0736 TCGA-14-0740 
       38.76        30.54         6.41        34.52        15.12        11.97 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1452 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 
        2.89        16.50         7.10        40.96        17.79         3.78 
TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 TCGA-19-0960 
       53.19        26.07        16.31        13.35         3.65         8.61 
TCGA-19-0964 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 
        3.39         4.87         1.08         4.08         8.02         6.51 
TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 TCGA-27-2528 TCGA-28-1756 
       14.86         5.49        30.05        14.40        15.78         2.83 
TCGA-28-2514 TCGA-28-5208 TCGA-28-5216 TCGA-32-1973 TCGA-32-1977 TCGA-32-2634 
        5.26        15.58        13.64        21.07         0.10        22.78 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 
       21.14        19.86        10.85         0.20         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                        108.82 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                         9.73                         12.39 
[1] "0.1 - 127.6 (9.7)"  "0.1 - 108.8 (12.4)"
[1] "hr=" "1.6"
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED   180 285
  AMP PEAK 10(7Q21.2) WILD-TYPE  40  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED    180  285
  AMP PEAK 10(7Q21.2) WILD-TYPE   40   55
        clus
vv       AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  FEMALE                         180                            40
  MALE                           285                            55
[1] 2 2
[1] FALSE
D10V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 10(7Q21.2) MUTATED                              13
  AMP PEAK 10(7Q21.2) WILD-TYPE                             4
                               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
D10V5, multiclass
                                 clus
vv                                AMP PEAK 10(7Q21.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            13
  TREATED PRIMARY GBM                                      12
  UNTREATED PRIMARY (DE NOVO) GBM                         440
                                 clus
vv                                AMP PEAK 10(7Q21.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               4
  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"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED   311 154
  AMP PEAK 10(7Q21.2) WILD-TYPE  71  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED    311  154
  AMP PEAK 10(7Q21.2) WILD-TYPE   71   24
     clus
vv    AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  NO                          311                            71
  YES                         154                            24
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q21.2) MUTATED       7                        33   403
  AMP PEAK 10(7Q21.2) WILD-TYPE     6                         6    82
D10V7, multiclass
                           clus
vv                          AMP PEAK 10(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          33
  WHITE                                             403
                           clus
vv                          AMP PEAK 10(7Q21.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             6
  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     7 383
  AMP PEAK 10(7Q21.2) WILD-TYPE   5  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED      7  383
  AMP PEAK 10(7Q21.2) WILD-TYPE    5   79
                        clus
vv                       AMP PEAK 10(7Q21.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         383
                        clus
vv                       AMP PEAK 10(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            79
[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    77 381
  AMP PEAK 11(7Q31.2) WILD-TYPE  21  81
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          458                           102 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          381                            81 
$`AMP PEAK 11(7Q31.2) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0015 
        9.17         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 
       55.86        77.65        20.12        53.10        42.74        10.36 
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         0.16        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        16.21         2.70         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
       47.31         0.10        22.72        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       23.08        22.16        10.75         0.20         9.21        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0164 
       11.80        12.79         8.65         3.19         9.44        56.88 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        2.73        91.00         2.01        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       18.02        10.36        11.80        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        70.52         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65         7.89        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        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        11.24         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         3.95         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-08-0244 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        2.56        22.68         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        7.59         1.28        15.06        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
        0.30         0.56         3.52         1.28        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33         5.52        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
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-12-1092 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82         6.25        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       15.85         9.11        14.53         3.98         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.28        13.61        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        11.74        13.12         3.22         2.04 
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-14-0866 TCGA-14-0867 TCGA-14-0871 
        3.25         1.35         5.39        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-14-1450 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       58.78        23.11        30.18         0.92        40.96         6.15 
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         9.86        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        5.52         3.91         9.93         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.90        18.28        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.43        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         3.48         7.17        12.66         0.13 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       11.28        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
        9.73        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        33.14        21.30        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
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-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30         3.91         9.04        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 
       14.20         7.79        13.64         4.21        22.68         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.49        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-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 
        7.36         8.84        21.17         3.72        12.59        10.62 
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-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       11.84        11.54         7.76         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        10.78        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 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

$`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         0.23        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         0.26         3.58        32.52 
TCGA-06-0142 TCGA-06-0146 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        2.20        20.09         5.46        11.80         2.56        10.65 
TCGA-06-0178 TCGA-06-0219 TCGA-06-0240 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 
       53.98         0.36        20.42        33.90         6.81         5.98 
TCGA-06-2570 TCGA-06-5416 TCGA-06-6389 TCGA-06-6693 TCGA-06-6701 TCGA-08-0245 
       31.50         6.71         7.79         0.49         4.96        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 
        3.91       108.82         3.42        53.82         6.41        22.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       11.77         8.52        18.44        58.19         4.80         6.54 
TCGA-12-0615 TCGA-12-0691 TCGA-12-0827 TCGA-12-1091 TCGA-12-1602 TCGA-12-3652 
       14.01         6.12        38.76        30.54         6.41        34.52 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1402 TCGA-14-1452 
       15.12        11.97         2.89        16.50        32.05         7.10 
TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 
        1.15        17.79         3.78        50.53        53.19        26.07 
TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 TCGA-19-0960 TCGA-19-0964 TCGA-19-1789 
       16.31        13.35         3.65         8.61         3.39         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 
        9.67         4.87         1.08         4.08         8.02         6.51 
TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 TCGA-27-2528 TCGA-28-1756 
       14.86         5.49        30.05        14.40        15.78         2.83 
TCGA-28-2514 TCGA-28-5208 TCGA-28-5220 TCGA-32-1973 TCGA-32-1977 TCGA-32-2615 
        5.26        15.58        10.49        21.07         0.10        15.95 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 
       22.78        21.14        19.86        10.85         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                        108.82 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                        9.830                        11.785 
[1] "0.1 - 127.6 (9.8)"  "0.1 - 108.8 (11.8)"
[1] "hr=" "1.4"
D11V2, continuous
D11V3, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   176 282
  AMP PEAK 11(7Q31.2) WILD-TYPE  44  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    176  282
  AMP PEAK 11(7Q31.2) WILD-TYPE   44   58
        clus
vv       AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  FEMALE                         176                            44
  MALE                           282                            58
[1] 2 2
[1] FALSE
D11V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 11(7Q31.2) MUTATED                              12
  AMP PEAK 11(7Q31.2) WILD-TYPE                             5
                               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
D11V5, multiclass
                                 clus
vv                                AMP PEAK 11(7Q31.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            12
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         433
                                 clus
vv                                AMP PEAK 11(7Q31.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               5
  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"
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   304 154
  AMP PEAK 11(7Q31.2) WILD-TYPE  78  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    304  154
  AMP PEAK 11(7Q31.2) WILD-TYPE   78   24
     clus
vv    AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  NO                          304                            78
  YES                         154                            24
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q31.2) MUTATED       7                        33   397
  AMP PEAK 11(7Q31.2) WILD-TYPE     6                         6    88
D11V7, multiclass
                           clus
vv                          AMP PEAK 11(7Q31.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          33
  WHITE                                             397
                           clus
vv                          AMP PEAK 11(7Q31.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             6
  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     7 378
  AMP PEAK 11(7Q31.2) WILD-TYPE   5  84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED      7  378
  AMP PEAK 11(7Q31.2) WILD-TYPE    5   84
                        clus
vv                       AMP PEAK 11(7Q31.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         378
                        clus
vv                       AMP PEAK 11(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            84
[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  85 405
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            70                            490 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            57                            405 
$`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         0.23        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         2.01        28.47        18.31         3.91        11.84 
TCGA-06-0409 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-2557 TCGA-06-2569 
       70.52        35.01         2.04         9.40         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         0.49         7.36         4.96         3.42 
TCGA-08-0351 TCGA-08-0516 TCGA-12-0616 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 
       53.82        18.44        14.43        91.76        24.79        38.76 
TCGA-12-1092 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       21.63         3.42         9.44         6.41        43.23        11.74 
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         3.48         9.67         3.98 
TCGA-19-A6J5 TCGA-26-5133 TCGA-27-1834 TCGA-27-2521 TCGA-28-1746 TCGA-28-5204 
       16.57        14.86        33.14        10.39         0.20         3.91 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1976 TCGA-32-1978 TCGA-32-2632 
        7.79         4.21        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        11.54 

$`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 
        9.17         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        55.86        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 
       10.36        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       26.33        14.93        10.29         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        0.39         6.48         5.49         4.96         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       22.49         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         5.52         0.26         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
        0.16        12.33         3.22         4.47         9.67        23.57 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
        8.65         7.89        13.61        33.90        15.32         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.24         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         3.95         5.39         1.48         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        4.34        13.78        10.39         7.59         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
        9.11        14.86        14.27        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         6.25 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       30.54        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        3.98        25.28        13.61        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         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-14-0862 TCGA-14-0866 
       11.24        13.78         3.25         1.35         2.89        26.33 
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-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.15        12.43         0.99         1.97        17.79        17.85 
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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64        25.38         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.39         5.29         5.42        10.03        13.87         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-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        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        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         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-28-5207 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 
       11.77        31.27        14.20        13.64        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39        21.07         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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.95         7.36        22.78        21.17        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       19.86        10.85        10.62         0.85        13.35         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        0.99         4.44        11.84         7.76         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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  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 
                         91.76                         127.59 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          9.93                          10.16 
[1] "0.2 - 91.8 (9.9)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    30  40
  AMP PEAK 12(8Q24.21) WILD-TYPE 190 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     30   40
  AMP PEAK 12(8Q24.21) WILD-TYPE  190  300
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           30                            190
  MALE                             40                            300
[1] 2 2
[1] FALSE
D12V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 12(8Q24.21) MUTATED                               2
  AMP PEAK 12(8Q24.21) WILD-TYPE                            15
                                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
D12V5, 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)                               15
  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"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    46  24
  AMP PEAK 12(8Q24.21) WILD-TYPE 336 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     46   24
  AMP PEAK 12(8Q24.21) WILD-TYPE  336  154
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            46                            336
  YES                           24                            154
[1] 2 2
[1] FALSE
                                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                        29   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                             29
  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  11 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      1   59
  AMP PEAK 12(8Q24.21) WILD-TYPE   11  403
                        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                            403
[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     2  27
  AMP PEAK 13(11P13) WILD-TYPE  96 435
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          29                          531 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          27                          435 
$`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        10.52        11.80        18.02        22.32 
TCGA-06-1087 TCGA-06-2557 TCGA-08-0386 TCGA-08-0517 TCGA-12-0616 TCGA-12-0670 
        3.58         1.08        15.72        58.19        14.43        25.97 
TCGA-12-0826 TCGA-12-1093 TCGA-12-1598 TCGA-14-0871 TCGA-19-1388 TCGA-19-4065 
       27.78        11.97         9.44        28.93        12.95         7.04 
TCGA-19-5958 TCGA-27-1838 TCGA-27-2521 TCGA-27-2526 TCGA-28-5207 
        5.39        11.51        10.39         2.86         9.04 

$`AMP PEAK 13(11P13) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23 
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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       32.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       12.79         8.65         3.19         5.46         9.44         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.20        12.43        22.49         0.36        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       10.85         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.77         8.52        18.44         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 
        6.54        15.98        17.33         5.52        14.01         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54 
TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       21.63        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.42        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0817 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-14-1453 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         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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         3.48         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-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        16.47         7.00         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.64         4.73         7.96         1.78         6.51         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        21.30        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       14.04        24.76        10.39        16.08         7.59        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-28-5208 
        6.74         4.77         7.30         5.26         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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        21.17        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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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        10.78        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  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 
                       58.19                       127.59 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       11.80                         9.86 
[1] "1.1 - 58.2 (11.8)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED    12  17
  AMP PEAK 13(11P13) WILD-TYPE 208 323
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED     12   17
  AMP PEAK 13(11P13) WILD-TYPE  208  323
        clus
vv       AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  FEMALE                         12                          208
  MALE                           17                          323
[1] 2 2
[1] FALSE
D13V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 13(11P13) MUTATED                               1
  AMP PEAK 13(11P13) WILD-TYPE                            16
                              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
D13V5, multiclass
                                 clus
vv                                AMP PEAK 13(11P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            1
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 13(11P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             16
  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"
D13V6, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED    20   9
  AMP PEAK 13(11P13) WILD-TYPE 362 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED     20    9
  AMP PEAK 13(11P13) WILD-TYPE  362  169
     clus
vv    AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  NO                          20                          362
  YES                          9                          169
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11P13) MUTATED       1                         1    27
  AMP PEAK 13(11P13) WILD-TYPE    12                        38   458
D13V7, multiclass
                           clus
vv                          AMP PEAK 13(11P13) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             27
                           clus
vv                          AMP PEAK 13(11P13) WILD-TYPE
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                           38
  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  26
  AMP PEAK 13(11P13) WILD-TYPE  11 436
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      1   26
  AMP PEAK 13(11P13) WILD-TYPE   11  436
                        clus
vv                       AMP PEAK 13(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         26
                        clus
vv                       AMP PEAK 13(11P13) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          436
[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    15  67
  AMP PEAK 14(12P13.32) WILD-TYPE  83 395
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             82                             478 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             67                             395 
$`AMP PEAK 14(12P13.32) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0051 TCGA-02-0054 TCGA-02-0070 TCGA-02-0074 
        9.17        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 
        0.23        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 
       32.52        20.09        46.59         3.19         2.56        56.88 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0192 TCGA-06-0216 
        2.01        40.37        26.33        28.47        18.31        22.49 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0649 TCGA-06-0743 TCGA-06-0877 
       18.02        11.80        70.52         2.04        22.32         5.65 
TCGA-06-1086 TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-5856 TCGA-06-5859 
        6.35         3.58         9.27         8.55         3.75         4.57 
TCGA-06-6389 TCGA-06-6694 TCGA-06-6699 TCGA-08-0245 TCGA-08-0246 TCGA-08-0352 
        7.79         7.36         1.55        34.75         3.91         1.28 
TCGA-08-0392 TCGA-08-0516 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 
        0.30        18.44         6.12         9.11        14.86        18.48 
TCGA-12-1090 TCGA-12-1098 TCGA-12-1602 TCGA-12-3653 TCGA-14-0740 TCGA-14-0790 
        6.25         3.98         6.41        11.74        11.97        13.78 
TCGA-14-1396 TCGA-14-1453 TCGA-14-1458 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 
        1.12         1.15         6.15        17.79        17.85        17.49 
TCGA-15-1449 TCGA-16-0850 TCGA-16-1460 TCGA-19-1786 TCGA-19-1787 TCGA-19-5954 
        5.52        16.31         6.41         7.17        12.66         7.96 
TCGA-26-1438 TCGA-26-1442 TCGA-26-5132 TCGA-27-1838 TCGA-28-1756 TCGA-28-2506 
       10.03        31.33         9.40        11.51         2.83         6.74 
TCGA-28-5207 TCGA-28-5218 TCGA-32-1979 TCGA-32-1991 TCGA-32-2615 TCGA-32-4208 
        9.04         4.21        19.50        16.93        15.95        21.14 
TCGA-32-4210 TCGA-32-5222 TCGA-74-6577 TCGA-76-4928 
        3.72        10.62         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        55.86        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        10.36        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         2.20        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 
        2.33        16.70         9.80         7.86        19.46        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 
       12.79         8.65         5.46         9.44        11.80        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        2.73        91.00        53.98        19.00         2.53        73.84 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       12.43         0.36        10.36        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        5.52         0.26         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       12.33         3.22         4.47         9.67        23.57         9.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        7.43        26.79         8.65         7.89        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         0.76         4.93         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95         5.39         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        0.49         8.32        12.85         4.77         4.77         4.96 
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       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       65.92         0.10        38.17        25.97        24.13         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.27        91.76        24.79        10.62        23.51        27.78 
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        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
        3.42         9.44        25.28        13.61        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         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-14-1450 TCGA-14-1451 
        0.79         1.38         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 
        7.10        30.18         0.92        40.96        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         9.86        50.53        19.10        53.19         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        9.93        26.07         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       13.35         3.65        18.28        13.97        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 
        5.95        12.95         4.64        25.38         3.48         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
        8.02        18.64         4.73         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 
        5.29         5.42         3.98        16.57        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37        14.86         5.49         8.88         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 
       18.25        33.14        21.30        30.05        14.04        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        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-28-1757 TCGA-28-2502 TCGA-28-2509 
        8.48         1.22         1.55         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79        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-32-1980 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-32-4211 
       15.02         7.36         8.84        22.78        21.17        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85         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        11.54         7.76 
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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                           0.23                            0.10 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                          70.52                          127.59 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                          9.715                          10.305 
[1] "0.2 - 70.5 (9.7)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED    32  50
  AMP PEAK 14(12P13.32) WILD-TYPE 188 290
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED     32   50
  AMP PEAK 14(12P13.32) WILD-TYPE  188  290
        clus
vv       AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  FEMALE                            32                             188
  MALE                              50                             290
[1] 2 2
[1] FALSE
D14V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 14(12P13.32) MUTATED                               1
  AMP PEAK 14(12P13.32) WILD-TYPE                            16
                                 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
D14V5, multiclass
                                 clus
vv                                AMP PEAK 14(12P13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               1
  TREATED PRIMARY GBM                                         2
  UNTREATED PRIMARY (DE NOVO) GBM                            79
                                 clus
vv                                AMP PEAK 14(12P13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                16
  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"
D14V6, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED    59  23
  AMP PEAK 14(12P13.32) WILD-TYPE 323 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED     59   23
  AMP PEAK 14(12P13.32) WILD-TYPE  323  155
     clus
vv    AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  NO                             59                             323
  YES                            23                             155
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12P13.32) MUTATED       3                         4    71
  AMP PEAK 14(12P13.32) WILD-TYPE    10                        35   414
D14V7, multiclass
                           clus
vv                          AMP PEAK 14(12P13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                71
                           clus
vv                          AMP PEAK 14(12P13.32) WILD-TYPE
  ASIAN                                                  10
  BLACK OR AFRICAN AMERICAN                              35
  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  66
  AMP PEAK 14(12P13.32) WILD-TYPE  10 396
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED      2   66
  AMP PEAK 14(12P13.32) WILD-TYPE   10  396
                        clus
vv                       AMP PEAK 14(12P13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            66
                        clus
vv                       AMP PEAK 14(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             396
[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    21 110
  AMP PEAK 15(12Q14.1) WILD-TYPE  77 352
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           131                            429 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           110                            352 
$`AMP PEAK 15(12Q14.1) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0024 TCGA-02-0046 TCGA-02-0051 
        9.17         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 
       16.21        22.72        32.52        22.16         2.33        46.59 
TCGA-06-0152 TCGA-06-0157 TCGA-06-0162 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
       11.80         3.19         2.56        56.88         0.23         2.20 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 
        2.01         2.53        28.47        18.31         3.91        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0402 TCGA-06-0409 
       22.49         0.36        18.02        11.80         0.26        70.52 
TCGA-06-0412 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0875 TCGA-06-0877 
        8.05         2.04         9.40        22.32        43.46         5.65 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
        6.35         3.58        33.90         0.76         4.93         9.27 
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-08-0245 TCGA-08-0246 TCGA-08-0352 
        1.48         7.36         8.32        34.75         3.91         1.28 
TCGA-08-0380 TCGA-08-0518 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0657 
       10.85         1.28        14.43         1.64         5.95         0.10 
TCGA-12-0670 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-0826 
       25.97         6.12         9.11        14.86        18.48        27.78 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1098 TCGA-12-1598 TCGA-12-1602 TCGA-12-3653 
        5.82         6.25         3.98         9.44         6.41        11.74 
TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 TCGA-14-1451 TCGA-14-1821 TCGA-14-1823 
       13.78         1.12        58.78        23.11        17.79        17.85 
TCGA-14-2554 TCGA-15-1444 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 
       17.49        50.53         5.52         3.91         9.93        16.31 
TCGA-16-1056 TCGA-19-0957 TCGA-19-0960 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 
       13.35        21.90         8.61         7.17        12.66         0.13 
TCGA-19-2624 TCGA-19-5950 TCGA-19-5960 TCGA-26-1438 TCGA-26-5135 TCGA-27-1833 
        0.16        11.28         5.42        10.03         8.88        18.25 
TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2526 TCGA-28-1746 TCGA-28-2506 
       21.30        11.51        24.76         2.86         0.20         6.74 
TCGA-28-5207 TCGA-28-5209 TCGA-28-5214 TCGA-28-5218 TCGA-32-1979 TCGA-32-2615 
        9.04        14.53        14.20         4.21        19.50        15.95 
TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-4097 
       21.14        12.59        10.62         0.85         8.94         0.20 
TCGA-41-5651 TCGA-74-6577 TCGA-76-4928 TCGA-76-4935 TCGA-76-6193 
       11.54         4.34         3.09        10.78         2.70 

$`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 
       55.86        77.65        20.12        42.74        24.59        10.36 
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         0.23        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         0.16        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         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       10.52        18.74        14.07        23.08        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        9.21         2.20        11.74        20.09        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 
        7.86        19.46        12.79         8.65         5.46         9.44 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       11.80        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 
        2.73        91.00        53.98        19.00        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       26.33        14.93        10.29         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         5.49         4.96        11.84         0.20 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0410 
       10.36        20.42        14.96        10.32         5.52         4.70 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       23.57        19.56         5.39         2.70         2.17         0.92 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 
        7.43        26.79         8.65         7.89        13.61        15.32 
TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        1.08         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.24         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         3.95         7.79 
TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        0.49        12.85         4.77         1.55         4.77         4.96 
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       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0619 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0688 
       14.01        10.39         7.17        65.92        38.17        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
        5.49        14.27        91.76        24.79        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1091 TCGA-12-1092 
       38.76         8.94        20.58       127.59        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       11.97        11.38        15.85         9.11        14.53         3.42 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.28        13.61        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         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-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       11.24         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-14-1452 TCGA-14-1453 TCGA-14-1454 
        1.38         3.75        32.05         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         6.15        12.43         0.99         1.97 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        7.63         5.88         7.17         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
        9.86        19.10        53.19        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        0.82         9.90         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       11.77         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 
        5.95        12.95         4.64        25.38         3.48         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         7.53         4.08        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         7.04         6.64         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 
        7.96         1.78         6.51         5.39         5.29         3.98 
TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.40        14.86         5.49         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1836 
        2.33         4.80        16.60         9.86        33.14        30.05 
TCGA-27-1837 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       14.04        10.39        10.39        16.08         7.59        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         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-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 
        7.30         5.26         3.91        15.58        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64        22.68        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 
       21.07         0.49         0.10        15.85         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-32-4210 TCGA-32-4213 
        7.36         8.84        22.78        21.17         3.72        19.86 
TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       10.85        13.35         9.53         0.99         4.44        11.84 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76         3.45        20.91        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-6191 
        4.80         4.54         3.65         9.17         2.53        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  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 
                         70.52                         127.59 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                          9.40                          10.36 
[1] "0.1 - 70.5 (9.4)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    56  75
  AMP PEAK 15(12Q14.1) WILD-TYPE 164 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     56   75
  AMP PEAK 15(12Q14.1) WILD-TYPE  164  265
        clus
vv       AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  FEMALE                           56                            164
  MALE                             75                            265
[1] 2 2
[1] FALSE
D15V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 15(12Q14.1) MUTATED                               2
  AMP PEAK 15(12Q14.1) WILD-TYPE                            15
                                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
D15V5, multiclass
                                 clus
vv                                AMP PEAK 15(12Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          126
                                 clus
vv                                AMP PEAK 15(12Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               15
  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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    91  40
  AMP PEAK 15(12Q14.1) WILD-TYPE 291 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     91   40
  AMP PEAK 15(12Q14.1) WILD-TYPE  291  138
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  NO                            91                            291
  YES                           40                            138
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q14.1) MUTATED       4                         9   112
  AMP PEAK 15(12Q14.1) WILD-TYPE     9                        30   373
D15V7, multiclass
                           clus
vv                          AMP PEAK 15(12Q14.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              112
                           clus
vv                          AMP PEAK 15(12Q14.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             30
  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     1 111
  AMP PEAK 15(12Q14.1) WILD-TYPE  11 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED      1  111
  AMP PEAK 15(12Q14.1) WILD-TYPE   11  351
                        clus
vv                       AMP PEAK 15(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       AMP PEAK 15(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            351
[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  78
  AMP PEAK 16(12Q15) WILD-TYPE  85 384
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          91                          469 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          78                          384 
$`AMP PEAK 16(12Q15) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0024 TCGA-02-0039 TCGA-02-0051 TCGA-02-0052 
        9.17        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 
       22.16         0.20        46.59        11.80         2.56        56.88 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 TCGA-06-0188 
        0.23         2.20         2.01         2.53        26.33        28.47 
TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 TCGA-06-0409 TCGA-06-0648 
       18.31         3.91        12.43        22.49        70.52         9.67 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0877 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 
        9.40        22.32         5.65        20.94         6.35         3.58 
TCGA-06-2561 TCGA-06-2569 TCGA-06-5415 TCGA-06-5856 TCGA-06-6390 TCGA-06-6391 
        9.27         0.43         8.55         3.75         5.39         1.48 
TCGA-06-6695 TCGA-06-6700 TCGA-08-0246 TCGA-12-0616 TCGA-12-0670 TCGA-12-0691 
        8.32         4.77         3.91        14.43        25.97         6.12 
TCGA-12-0772 TCGA-12-0778 TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 TCGA-12-1602 
       53.10        14.86        27.78         6.25         3.98         6.41 
TCGA-12-3653 TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 TCGA-14-1451 TCGA-14-1821 
       11.74        13.78         1.12        58.78        23.11        17.79 
TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 TCGA-19-0957 TCGA-19-1786 TCGA-19-1787 
       17.85        17.49         5.52        21.90         7.17        12.66 
TCGA-19-2624 TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-27-2518 TCGA-27-2526 
        0.16        10.03         9.40         8.88        24.76         2.86 
TCGA-28-2506 TCGA-28-5207 TCGA-28-5214 TCGA-28-5218 TCGA-32-1978 TCGA-32-1979 
        6.74         9.04        14.20         4.21        15.85        19.50 
TCGA-32-2615 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-74-6577 
       15.95        21.14        12.59        10.62         0.85         4.34 
TCGA-74-6584 
        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        55.86        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 
       10.36        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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       23.08        10.75         9.21         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        16.70         9.80         7.86        19.46        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 
        8.65         3.19         5.46         9.44        11.80        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 
        5.29        19.04         3.12        13.02         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 
       53.98        19.00        40.37        73.84        14.93        10.29 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        4.96        11.84         0.20         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        4.47         2.04        23.57        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        43.46        46.19         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        5.85         5.42         7.43        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.24         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         3.95 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        7.79         0.49         7.36        12.85         4.77         1.55 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       38.17        24.13         2.63        18.12        28.41        12.43 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.10         5.49         9.11        14.27        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-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       15.85         9.11        14.53         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       13.61        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-0812 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-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
        3.75        32.05         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         6.15        12.43         0.99         1.97         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17         7.96         3.78         3.42         9.86 
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         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 
        3.65        18.28        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 
        0.43        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64        25.38         3.48         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         7.53         4.08        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        5.42         3.98        16.57        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5136 TCGA-26-5139 
        7.13         9.37        14.86         5.49         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 
       33.14        21.30        30.05        14.04        11.51        10.39 
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-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 
        1.55         2.83         0.13         0.66         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26         3.91        15.58        14.53        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64        22.68        10.49         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       21.07         0.49         0.10         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-32-4210 TCGA-32-4213 TCGA-32-4719 
        8.84        22.78        21.17         3.72        19.86        10.85 
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-74-6573 TCGA-74-6575 TCGA-74-6578 
        0.20        11.54         7.76         3.45        20.91        14.33 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  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 
                       70.52                       127.59 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       10.03                        10.29 
[1] "0.2 - 70.5 (10.0)"  "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D16V2, continuous
D16V3, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    32  59
  AMP PEAK 16(12Q15) WILD-TYPE 188 281
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     32   59
  AMP PEAK 16(12Q15) WILD-TYPE  188  281
        clus
vv       AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  FEMALE                         32                          188
  MALE                           59                          281
[1] 2 2
[1] FALSE
D16V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 16(12Q15) MUTATED                               2
  AMP PEAK 16(12Q15) WILD-TYPE                            15
                              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
D16V5, multiclass
                                 clus
vv                                AMP PEAK 16(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         87
                                 clus
vv                                AMP PEAK 16(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             15
  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"
D16V6, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    59  32
  AMP PEAK 16(12Q15) WILD-TYPE 323 146
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     59   32
  AMP PEAK 16(12Q15) WILD-TYPE  323  146
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  NO                          59                          323
  YES                         32                          146
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q15) MUTATED       3                         5    79
  AMP PEAK 16(12Q15) WILD-TYPE    10                        34   406
D16V7, multiclass
                           clus
vv                          AMP PEAK 16(12Q15) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             79
                           clus
vv                          AMP PEAK 16(12Q15) WILD-TYPE
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           34
  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  77
  AMP PEAK 16(12Q15) WILD-TYPE  12 385
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED      0   77
  AMP PEAK 16(12Q15) WILD-TYPE   12  385
                        clus
vv                       AMP PEAK 16(12Q15) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         77
                        clus
vv                       AMP PEAK 16(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          385
[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  95 433
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          528 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          29                          433 
$`AMP PEAK 17(13Q34) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0025 TCGA-02-0114 TCGA-02-0281 TCGA-02-0289 
        9.17        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         4.96        18.02         3.58         3.75 
TCGA-08-0386 TCGA-12-0769 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-0817 
       15.72        12.43        21.63         6.41        11.74         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         9.04        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        55.86        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       10.36        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         0.23 
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 
        0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         2.20        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.20        12.43        22.49         0.36        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       70.52         4.70         8.05         0.16        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         6.35        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        7.89        13.61        33.90        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 
        6.12         2.63        18.12        28.41        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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-12-1093 
       20.58       127.59         5.82         6.25        30.54        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        9.44        25.28        13.61        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0862 
        2.24        11.24        13.78         3.25         1.35         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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.15        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-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.78         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 
       19.10        53.19         5.52         3.91         9.93        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       18.28         6.41        11.77        21.90         8.61         0.43 
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 
        3.48         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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        10.39        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-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        7.63         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-28-5208 
        6.74         4.77         7.30         5.26         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68        10.49         5.42        21.07         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        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        11.54         7.76 
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 
       10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  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 
                      12.545                        9.900 
[1] "1.0 - 100.0 (12.5)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1"  
D17V2, continuous
D17V3, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED    10  22
  AMP PEAK 17(13Q34) WILD-TYPE 210 318
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED     10   22
  AMP PEAK 17(13Q34) WILD-TYPE  210  318
        clus
vv       AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  FEMALE                         10                          210
  MALE                           22                          318
[1] 2 2
[1] FALSE
D17V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 17(13Q34) MUTATED                               1
  AMP PEAK 17(13Q34) WILD-TYPE                            16
                              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
D17V5, 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)                             16
  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"
D17V6, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED    23   9
  AMP PEAK 17(13Q34) WILD-TYPE 359 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED     23    9
  AMP PEAK 17(13Q34) WILD-TYPE  359  169
     clus
vv    AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  NO                          23                          359
  YES                          9                          169
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(13Q34) MUTATED       0                         3    29
  AMP PEAK 17(13Q34) WILD-TYPE    13                        36   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                           36
  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  12 436
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED      0   26
  AMP PEAK 17(13Q34) WILD-TYPE   12  436
                        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                          436
[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     2  27
  AMP PEAK 18(13Q34) WILD-TYPE  96 435
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          29                          531 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          27                          435 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0114 TCGA-02-0281 TCGA-02-0289 TCGA-02-0338 
        9.17        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 
       18.02         3.58        15.06        15.72         3.19        14.43 
TCGA-12-0769 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-0817 TCGA-14-0871 
       12.43        21.63         6.41        11.74         5.39        28.93 
TCGA-14-1453 TCGA-14-4157 TCGA-19-1388 TCGA-19-1390 TCGA-19-1787 TCGA-19-A6J4 
        1.15         3.42        12.95        25.38        12.66         3.98 
TCGA-28-1752 TCGA-28-5207 TCGA-32-1970 TCGA-32-2615 TCGA-41-3392 
        8.48         9.04        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        55.86        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        10.36        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 
        0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.73        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 
        7.59         3.42        53.82         1.28         6.41        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 
       15.98        17.33         5.52        14.01         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 
       24.13         6.12         2.63        18.12        28.41        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
        3.42         9.44        25.28        13.61        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-0862 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        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         3.48         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.39         5.29         5.42        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        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        10.39        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-28-1757 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-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26         3.91        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        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-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        21.17 
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        10.62 
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-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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        10.78        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  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 
                       12.43                         9.90 
[1] "1.0 - 100.0 (12.4)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    10  19
  AMP PEAK 18(13Q34) WILD-TYPE 210 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     10   19
  AMP PEAK 18(13Q34) WILD-TYPE  210  321
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         10                          210
  MALE                           19                          321
[1] 2 2
[1] FALSE
D18V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 18(13Q34) MUTATED                               1
  AMP PEAK 18(13Q34) WILD-TYPE                            16
                              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
D18V5, multiclass
                                 clus
vv                                AMP PEAK 18(13Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            1
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 18(13Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             16
  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"
D18V6, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    21   8
  AMP PEAK 18(13Q34) WILD-TYPE 361 170
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     21    8
  AMP PEAK 18(13Q34) WILD-TYPE  361  170
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                          21                          361
  YES                          8                          170
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       0                         3    25
  AMP PEAK 18(13Q34) WILD-TYPE    13                        36   460
D18V7, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             25
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           36
  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  23
  AMP PEAK 18(13Q34) WILD-TYPE  12 439
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      0   23
  AMP PEAK 18(13Q34) WILD-TYPE   12  439
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         23
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          439
[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  95 429
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             524 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             33                             429 
$`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         9.80        46.59         9.44 
TCGA-06-0177 TCGA-06-0195 TCGA-06-0237 TCGA-06-0397 TCGA-06-0414 TCGA-06-0747 
        2.01         7.04        10.36         5.52        35.01         2.70 
TCGA-06-1087 TCGA-06-2563 TCGA-06-2569 TCGA-06-5415 TCGA-08-0244 TCGA-08-0246 
        3.58        30.64         0.43         8.55        22.68         3.91 
TCGA-08-0351 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-1600 
       53.82        15.72         3.52         8.52        10.39        13.61 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0867 TCGA-16-0846 TCGA-19-0962 
       43.23        11.74        11.97         2.04         3.91         0.43 
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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         7.86        19.46        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        2.73        91.00        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 
       18.02        11.80        20.42        14.96        10.32         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       70.52         4.70         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       19.56         5.39         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
        2.83         5.95         6.81         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        3.12         2.56        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 
       13.78        10.39         7.59         3.42         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.77        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        6.25        30.54        21.63        11.97        11.38        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         3.42         9.44        25.28 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.41        59.41        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       34.52        13.12         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-14-0817 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         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       53.19         5.52         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 
       13.97         6.41        11.77        21.90         8.61        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         3.48         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         1.08         7.53         0.16         4.08        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
        5.42         3.98        16.57        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-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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        10.39        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-28-1752 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-28-2514 
        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        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-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.95         7.36        22.78        21.17 
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        10.62 
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-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38        17.06         8.35         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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 
                          53.82                          127.59 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                          9.685                          10.240 
[1] "0.4 - 53.8 (9.7)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED    12  24
  AMP PEAK 19(14Q32.33) WILD-TYPE 208 316
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED     12   24
  AMP PEAK 19(14Q32.33) WILD-TYPE  208  316
        clus
vv       AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  FEMALE                            12                             208
  MALE                              24                             316
[1] 2 2
[1] FALSE
D19V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 19(14Q32.33) MUTATED                               2
  AMP PEAK 19(14Q32.33) WILD-TYPE                            15
                                 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
D19V5, 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)                                15
  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"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED    25  11
  AMP PEAK 19(14Q32.33) WILD-TYPE 357 167
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED     25   11
  AMP PEAK 19(14Q32.33) WILD-TYPE  357  167
     clus
vv    AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  NO                             25                             357
  YES                            11                             167
[1] 2 2
[1] FALSE
                                 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                        37   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                              37
  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  12 428
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED      0   34
  AMP PEAK 19(14Q32.33) WILD-TYPE   12  428
                        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                             428
[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  45
  AMP PEAK 20(17P13.2) WILD-TYPE  93 417
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            50                            510 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            45                            417 
$`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         5.29 
TCGA-06-0173 TCGA-06-0195 TCGA-06-0216 TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 
        0.23         7.04        22.49        70.52        35.01         9.40 
TCGA-06-0743 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-A5U1 TCGA-08-0347 
       22.32         3.58         8.65         1.08         1.87        13.78 
TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
       10.39         3.42        53.82         6.41        22.52        14.70 
TCGA-08-0375 TCGA-08-0389 TCGA-08-0392 TCGA-08-0510 TCGA-12-0821 TCGA-12-0822 
        9.17         3.19         0.30         3.52        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        13.61         6.41         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         9.04         4.21        15.95         3.72 
TCGA-41-2575 TCGA-41-4097 
        9.53         0.20 

$`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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 
       10.65        19.04         3.12        13.02         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        4.96        11.84         0.20        12.43         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 
        4.47         9.67         2.04        23.57        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        6.35        26.79         7.89        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 
        4.34         7.59         1.28        15.06        35.64        19.53 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 
        0.95        10.85        15.72        10.59         0.56        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 
       14.86        14.27        91.76        24.79        18.48        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 
       21.63        11.97        11.38        15.85        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        3.42         9.44        25.28        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-0817 
       23.05         2.24        11.24        13.78         3.25         5.39 
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-14-1455 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-14-1823 
        6.15        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         9.86        50.53        19.10         5.52         3.91 
TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        9.93        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64         3.48         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-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 
        6.51         5.39         5.29         5.42        16.57        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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        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-28-1756 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-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        3.91        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64        22.68        10.49         5.42        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-32-1991 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-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02         7.36         8.84        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 
        8.94         0.99         4.44        11.84        11.54         7.76 
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 
       10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  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 
                         70.52                         127.59 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                         9.465                         10.240 
[1] "0.2 - 70.5 (9.5)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    15  35
  AMP PEAK 20(17P13.2) WILD-TYPE 205 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     15   35
  AMP PEAK 20(17P13.2) WILD-TYPE  205  305
        clus
vv       AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  FEMALE                           15                            205
  MALE                             35                            305
[1] 2 2
[1] FALSE
D20V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 20(17P13.2) MUTATED                               3
  AMP PEAK 20(17P13.2) WILD-TYPE                            14
                                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
D20V5, multiclass
                                 clus
vv                                AMP PEAK 20(17P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           46
                                 clus
vv                                AMP PEAK 20(17P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    32  18
  AMP PEAK 20(17P13.2) WILD-TYPE 350 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     32   18
  AMP PEAK 20(17P13.2) WILD-TYPE  350  160
     clus
vv    AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  NO                            32                            350
  YES                           18                            160
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17P13.2) MUTATED       0                         4    42
  AMP PEAK 20(17P13.2) WILD-TYPE    13                        35   443
D20V7, multiclass
                           clus
vv                          AMP PEAK 20(17P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               42
                           clus
vv                          AMP PEAK 20(17P13.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             35
  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  42
  AMP PEAK 20(17P13.2) WILD-TYPE  11 420
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED      1   42
  AMP PEAK 20(17P13.2) WILD-TYPE   11  420
                        clus
vv                       AMP PEAK 20(17P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       AMP PEAK 20(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            420
[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     7  74
  AMP PEAK 21(17Q25.1) WILD-TYPE  91 388
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            81                            479 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            74                            388 
$`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        11.80 
TCGA-06-0166 TCGA-06-0173 TCGA-06-0188 TCGA-06-0195 TCGA-06-0216 TCGA-06-0237 
        5.29         0.23        28.47         7.04        22.49        10.36 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 
       70.52         4.70        35.01         2.04         9.40        22.32 
TCGA-06-0744 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 
       19.56         7.43         3.58         8.65         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         4.34         3.42         6.41         3.52 
TCGA-08-0514 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0818 TCGA-12-0821 
        8.52         5.52        10.39        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         6.25        21.63         9.11         3.98        13.61 
TCGA-12-1602 TCGA-12-5301 TCGA-14-0813 TCGA-14-0865 TCGA-14-1453 TCGA-14-1794 
        6.41         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         5.52         3.91        13.97 
TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-A6J4 TCGA-27-1835 TCGA-27-2521 
       12.95        25.38         3.48         3.98        21.30        10.39 
TCGA-28-1746 TCGA-28-1757 TCGA-28-2506 TCGA-28-5207 TCGA-28-5215 TCGA-28-5218 
        0.20         0.13         6.74         9.04         7.79         4.21 
TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-41-2575 TCGA-41-3915 
       16.93        15.02        15.95         7.36         9.53        11.84 
TCGA-41-4097 TCGA-74-6573 TCGA-76-6280 
        0.20         3.45        11.38 

$`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 
        9.17        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        55.86        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        10.36        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         0.23 
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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        9.80         7.86        19.46        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12        13.02         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       26.33        14.93        10.29        18.31         4.67         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.20        12.43         0.36        18.02        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       14.96        10.32         5.52         0.26         8.05         0.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0745 
       12.33         3.22         4.47         9.67        23.57         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         6.35 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
       26.79         7.89        13.61        33.90        15.32         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         0.49         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        1.55         4.96         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91       108.82         1.74        13.78        10.39         7.59 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       10.59         0.30         0.56        11.77        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        0.10        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 
       14.86        14.27        24.79        18.48        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 
        8.94        20.58       127.59         5.82        30.54        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       11.38        15.85        14.53         3.42         9.44        25.28 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 
       34.52        11.74        13.12         3.22        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-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        3.25         5.39         2.89        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-14-1454 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         6.15        12.43         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.63        17.49         7.96         3.42         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10        53.19         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 
        3.39        10.75         9.07         5.95         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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         5.42        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       33.14        30.05        14.04        11.51        24.76        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-28-1756 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.66         4.77         7.30         5.26         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        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-32-1979 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-32-2632 TCGA-32-2634 TCGA-32-2638 
       14.86        12.23        20.78         8.84        22.78        21.17 
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        10.62 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 
        0.85        13.35         8.94         0.99         4.44        11.54 
TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76        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-76-6282 TCGA-76-6285 
       10.78        16.70         3.29         2.70        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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  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 
                          7.79                          10.49 
[1] "0.1 - 91.8 (7.8)"   "0.1 - 127.6 (10.5)"
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    26  55
  AMP PEAK 21(17Q25.1) WILD-TYPE 194 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     26   55
  AMP PEAK 21(17Q25.1) WILD-TYPE  194  285
        clus
vv       AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  FEMALE                           26                            194
  MALE                             55                            285
[1] 2 2
[1] FALSE
D21V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 21(17Q25.1) MUTATED                               3
  AMP PEAK 21(17Q25.1) WILD-TYPE                            14
                                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
D21V5, multiclass
                                 clus
vv                                AMP PEAK 21(17Q25.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           76
                                 clus
vv                                AMP PEAK 21(17Q25.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    53  28
  AMP PEAK 21(17Q25.1) WILD-TYPE 329 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     53   28
  AMP PEAK 21(17Q25.1) WILD-TYPE  329  150
     clus
vv    AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  NO                            53                            329
  YES                           28                            150
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(17Q25.1) MUTATED       0                         8    69
  AMP PEAK 21(17Q25.1) WILD-TYPE    13                        31   416
D21V7, multiclass
                           clus
vv                          AMP PEAK 21(17Q25.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               69
                           clus
vv                          AMP PEAK 21(17Q25.1) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             31
  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  67
  AMP PEAK 21(17Q25.1) WILD-TYPE  10 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED      2   67
  AMP PEAK 21(17Q25.1) WILD-TYPE   10  395
                        clus
vv                       AMP PEAK 21(17Q25.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 21(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            395
[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    41 195
  AMP PEAK 22(19P13.3) WILD-TYPE  57 267
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           236                            324 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           195                            267 
$`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        55.86        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         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0137 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        3.58        32.52        23.08         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        9.80        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
        3.19         5.46         9.44        56.88         0.23         2.20 
TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 
        2.73         2.01        19.00        73.84        10.29        18.31 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 
        0.39         6.48         5.49         3.91        11.84        22.49 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       18.02        10.36        10.32         0.26        70.52         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.01         3.22        23.57        22.32        19.56         2.70 
TCGA-06-0877 TCGA-06-0879 TCGA-06-1086 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
        5.65        22.98         6.35         7.89        15.32        30.64 
TCGA-06-2565 TCGA-06-2570 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
        6.81        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 
        3.95         0.49         8.32         1.55         3.12         3.91 
TCGA-08-0347 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       13.78         1.28         6.41        22.52        14.70        35.64 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
        9.17        15.72        10.59         0.30         0.56         3.52 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 
        8.52         1.28        17.33         5.52        65.92         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       25.97        24.13        18.12        28.41        12.43        53.10 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 
       14.86        14.27        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 
       11.38         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
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         9.93         4.31         9.90        13.35        18.28 
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         3.48         7.17 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2629 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 
        3.25         4.87        16.47        11.28         8.02         4.73 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1799 TCGA-26-5139 
        1.78         5.39         5.29        16.57         9.37         1.58 
TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 
       18.25        24.76        10.39        16.08         7.59        15.78 
TCGA-28-1746 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 
        0.20         9.21         7.63         8.48         1.22         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 
        6.74         7.30         5.26        15.58        14.53        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 
        7.79        13.64         4.21         5.42        15.39         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 TCGA-32-2495 TCGA-32-2632 
       15.85        19.50         4.67        14.86        15.02         8.84 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 
       21.17        21.14        12.59        10.62        13.35         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-74-6578 TCGA-76-4925 TCGA-76-4934 
        4.44        11.84        11.54        14.33         4.80         2.53 
TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
       11.38         4.83         0.23         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`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 
        9.17         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        10.36         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 
        0.23        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         0.16        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        16.21 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       22.72        10.52        18.74        14.07        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0149 TCGA-06-0160 
        0.20         9.21         2.20        11.74         7.86        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        2.56        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 
       91.00        53.98         2.53        40.37        26.33        28.47 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 
       14.93         4.67         7.04         2.60         4.96         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
       12.43         0.36        11.80        20.42        14.96         5.52 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        8.05         0.16        12.33         4.47         9.67         2.04 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        9.40         5.39         2.17         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         5.85         5.42        20.94         7.43         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.79         8.65        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93         9.27         2.83         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        11.24         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-A5U1 
        7.36        12.85         4.77         4.77         4.96         1.87 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 TCGA-08-0358 
       10.39         7.59         3.42        53.82        15.06        19.53 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
        0.95        10.85         3.19        11.77        18.44        58.19 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 
       10.75         4.80         6.54        15.98        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 
        1.64        10.39         5.95         7.17        38.17         6.12 
TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0821 
        2.63        43.10         5.49         9.11        91.76        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       23.51        38.76         8.94       127.59         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       30.54        21.63        11.97        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
        3.98        59.41        43.23        13.12         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 
       15.12        11.97         0.95         2.24         3.25         1.35 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.89        16.50        28.93        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
        1.12         3.75        23.11         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.15        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 
        5.88         3.78         9.86        50.53        53.19         5.52 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 
       26.07        16.31        29.03         0.82         3.65        13.97 
TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        21.90         8.61         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
       10.75         5.95         4.64        12.66         0.13         9.67 
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-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 
        6.64        18.64         7.96         6.51         5.42         3.98 
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         1.22         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60         9.86        33.14        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2526 TCGA-27-2527 TCGA-28-1747 
       14.04        11.51        10.39         2.86        14.40         2.53 
TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2509 TCGA-28-5204 
        8.35         1.55         2.83         0.13         4.77         3.91 
TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 TCGA-28-5219 TCGA-28-5220 TCGA-32-1973 
        9.04        11.77        31.27        22.68        10.49        21.07 
TCGA-32-1976 TCGA-32-1980 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        0.49         1.18        12.69        16.93        12.23        20.78 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 
       15.95         7.36        22.78         3.72        19.86        10.85 
TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 
        0.85         8.94         0.99         0.20         7.76         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        10.78        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         9.27         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 
                         92.65                         127.59 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                         11.46                           9.14 
[1] "0.1 - 92.7 (11.5)" "0.1 - 127.6 (9.1)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED    93 143
  AMP PEAK 22(19P13.3) WILD-TYPE 127 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED     93  143
  AMP PEAK 22(19P13.3) WILD-TYPE  127  197
        clus
vv       AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  FEMALE                           93                            127
  MALE                            143                            197
[1] 2 2
[1] FALSE
D22V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 22(19P13.3) MUTATED                               7
  AMP PEAK 22(19P13.3) WILD-TYPE                            10
                                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
D22V5, multiclass
                                 clus
vv                                AMP PEAK 22(19P13.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              7
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          219
                                 clus
vv                                AMP PEAK 22(19P13.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               10
  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"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED   162  74
  AMP PEAK 22(19P13.3) WILD-TYPE 220 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED    162   74
  AMP PEAK 22(19P13.3) WILD-TYPE  220  104
     clus
vv    AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  NO                           162                            220
  YES                           74                            104
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(19P13.3) MUTATED       8                        16   206
  AMP PEAK 22(19P13.3) WILD-TYPE     5                        23   279
D22V7, multiclass
                           clus
vv                          AMP PEAK 22(19P13.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              206
                           clus
vv                          AMP PEAK 22(19P13.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             23
  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     6 194
  AMP PEAK 22(19P13.3) WILD-TYPE   6 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED      6  194
  AMP PEAK 22(19P13.3) WILD-TYPE    6  268
                        clus
vv                       AMP PEAK 22(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          194
                        clus
vv                       AMP PEAK 22(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            268
[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    43 198
  AMP PEAK 23(19P13.2) WILD-TYPE  55 264
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           241                            319 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                           198                            264 
$`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        55.86        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         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.10         3.58        23.08         2.33        16.70         9.80 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 
       19.46        46.59        11.80        12.79         8.65         5.46 
TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
        9.44        56.88         0.23         2.20         2.73         2.01 
TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 
       19.00        73.84        10.29        18.31         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 
        5.49         3.91        11.84        22.49        18.02        10.36 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 
       10.32         0.26        70.52         4.70        35.01         3.22 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0875 TCGA-06-0877 
       23.57        22.32        19.56         2.70        43.46         5.65 
TCGA-06-0879 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
       22.98         6.35        26.79         7.89        15.32        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 
        5.95         6.81         8.98         8.55         6.71         3.95 
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         3.91        13.78 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 
        1.28         6.41        22.52        14.70        35.64         9.17 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       15.72        10.59         0.30         0.56         3.52         8.52 
TCGA-08-0518 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0656 
        1.28        15.98        17.33         5.52        14.43        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
        0.10        25.97        24.13        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 
       53.10        14.27        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 
       11.38         3.42         9.44        25.28        13.61        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5299 TCGA-14-0783 
       11.54        10.95        34.52        11.74         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         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
        3.91         9.93         9.90        13.35        18.28        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         3.48 
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        16.47        11.28 
TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-26-1799 
        8.02         4.73         1.78         5.39         5.29         9.37 
TCGA-26-5139 TCGA-27-1831 TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 
        1.58        16.60        18.25        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 TCGA-28-1751 
        7.59         2.86        15.78         0.20         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-28-5219 
       15.58        14.53        14.20        13.64         4.21        22.68 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 
        5.42        15.39         0.10        15.85        19.50         4.67 
TCGA-32-1987 TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       14.86        15.02         8.84        21.17        21.14         3.72 
TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       12.59        10.62        13.35         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-74-6578 TCGA-76-4925 TCGA-76-4934 TCGA-76-6280 
       11.84        11.54        14.33         4.80         2.53        11.38 
TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        4.83         0.23         7.73         7.79         1.61        17.72 
TCGA-87-5896 
       26.30 

$`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 
        9.17         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        10.36         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         0.23        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         0.16        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        16.21        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       32.52        10.52        18.74        14.07        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 
        0.20         9.21         2.20        11.74        20.09         7.86 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
        3.19        11.80         2.56        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 
        3.12        13.02        91.00        53.98         2.53        40.37 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       26.33        28.47        14.93         4.67         7.04         2.60 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 
        4.96         0.20        12.43         0.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       14.96         5.52         8.05         0.16        12.33         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.67         2.04         9.40         5.39         2.17         0.92 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17         5.85         5.42        20.94         7.43 
TCGA-06-1087 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        3.58         8.65        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
        4.93         9.27         2.83         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        11.24         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         0.49         7.36        12.85         4.77         4.96 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        1.87         2.56        22.68        34.75       108.82         1.74 
TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 
        4.34        10.39         7.59         3.42        53.82        15.06 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0512 TCGA-08-0516 
       19.53         0.95        10.85         3.19        11.77        18.44 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-12-0615 TCGA-12-0618 
       58.19        10.75         4.80         6.54        14.01         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 
       10.39         5.95         7.17        38.17         6.12         2.63 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0821 
       43.10         5.49         9.11        14.86        91.76        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       23.51        38.76         8.94       127.59         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       30.54        21.63        11.97        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-5295 
        3.98         6.41        59.41        43.23        11.77        13.12 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0787 TCGA-14-0812 
        2.04        15.12        11.97         0.95         2.24         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        16.50        28.93        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 
        1.38         1.12         3.75        23.11         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.15        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 
        7.63         5.88         3.78         9.86        50.53        53.19 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 
       26.07        16.31         4.31        29.03         0.82         3.65 
TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        21.90         8.61         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1389 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 
       10.75         4.64        12.66         0.13         9.67         1.08 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        7.53         4.08         7.00         7.04         6.64        18.64 
TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        7.96         6.51         5.42         3.98        16.57        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        5.49         8.88         1.22         7.92         2.33         4.80 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        33.14        21.30        30.05        14.04        11.51 
TCGA-27-2519 TCGA-27-2527 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 
       10.39        14.40         2.53         8.35         1.55         2.83 
TCGA-28-1757 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 
        0.13         4.77         3.91         9.04        11.77        31.27 
TCGA-28-5215 TCGA-28-5220 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 TCGA-32-1986 
        7.79        10.49        21.07         0.49         1.18        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.95         7.36        22.78 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-4097 TCGA-41-6646 
       19.86        10.85         0.85         8.94         0.20         7.76 
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-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 
        2.70        17.06         8.35        20.98         5.03         9.27 
TCGA-OX-A56R 
        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 
                         11.38                           9.17 
[1] "0.1 - 100.0 (11.4)" "0.1 - 127.6 (9.2)" 
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.2) MUTATED    94 147
  AMP PEAK 23(19P13.2) WILD-TYPE 126 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED     94  147
  AMP PEAK 23(19P13.2) WILD-TYPE  126  193
        clus
vv       AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  FEMALE                           94                            126
  MALE                            147                            193
[1] 2 2
[1] FALSE
D23V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 23(19P13.2) MUTATED                               6
  AMP PEAK 23(19P13.2) WILD-TYPE                            11
                                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
D23V5, multiclass
                                 clus
vv                                AMP PEAK 23(19P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          225
                                 clus
vv                                AMP PEAK 23(19P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               11
  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"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(19P13.2) MUTATED   164  77
  AMP PEAK 23(19P13.2) WILD-TYPE 218 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED    164   77
  AMP PEAK 23(19P13.2) WILD-TYPE  218  101
     clus
vv    AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  NO                           164                            218
  YES                           77                            101
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(19P13.2) MUTATED       7                        16   210
  AMP PEAK 23(19P13.2) WILD-TYPE     6                        23   275
D23V7, multiclass
                           clus
vv                          AMP PEAK 23(19P13.2) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              210
                           clus
vv                          AMP PEAK 23(19P13.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             23
  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     6 198
  AMP PEAK 23(19P13.2) WILD-TYPE   6 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED      6  198
  AMP PEAK 23(19P13.2) WILD-TYPE    6  264
                        clus
vv                       AMP PEAK 23(19P13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       AMP PEAK 23(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            264
[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    37 172
  AMP PEAK 24(19Q12) WILD-TYPE  61 290
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         209                          351 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                         172                          290 
$`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         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 
       47.31         0.10         3.58        23.08         2.33        16.70 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 
        9.80        19.46        46.59        11.80         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
        5.46         9.44        56.88         0.23         2.20         2.01 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 
       19.00         2.53        73.84        10.29        18.31         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 
        6.48         5.49         3.91        11.84        22.49        10.36 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 
       10.32         0.26        70.52         4.70        35.01         3.22 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 
       23.57        22.32        19.56         2.70         5.65        22.98 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 TCGA-06-2565 
        6.35         3.58         7.89        15.32        30.64         6.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 TCGA-06-6695 TCGA-06-6699 
        8.98         8.55         6.71         3.95         8.32         1.55 
TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0352 TCGA-08-0355 
        3.12         3.91        13.78         7.59         1.28        22.52 
TCGA-08-0356 TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       14.70         9.17        15.72        10.59         0.56         3.52 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
        8.52         1.28         6.54        15.98        17.33         5.52 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       25.97        24.13        18.12        28.41        12.43        53.10 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 
       14.86        14.27        24.79        27.78        20.58        11.38 
TCGA-12-1095 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.85         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
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         5.52         3.91         9.93 
TCGA-16-1055 TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1392 TCGA-19-1786 
        9.90        18.28        11.77         9.07         3.48         7.17 
TCGA-19-1789 TCGA-19-2620 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 
        3.25         4.87        11.28         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        16.57         9.37         1.58        18.25        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 
       10.39        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 
       15.58        14.53        14.20        13.64         4.21        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        21.17        21.14        10.62        13.35         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-74-6578 TCGA-76-4934 TCGA-76-6280 
       11.84         0.20        11.54        14.33         2.53        11.38 
TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 TCGA-81-5911 TCGA-87-5896 
        4.83         0.23         7.73        17.72        26.30 

$`AMP PEAK 24(19Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        9.17         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 
       55.86        53.10        24.59        10.36        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         0.23        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 
        0.16        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        16.21        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       10.52        18.74        14.07        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 TCGA-06-0154 
        9.21         2.20        11.74        20.09         7.86        12.79 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 
       13.02         2.73        91.00        53.98        40.37        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 
       28.47        14.93         4.67         7.04         2.60         4.96 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.20        12.43         0.36        18.02        11.80        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       14.96         5.52         8.05         0.16        12.33         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.67         2.04         9.40         5.39         2.17         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         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
        7.43        26.79         8.65        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 
        0.76         4.93         9.27         2.83         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        11.24         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         0.49         7.36        12.85 
TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.77         4.96         1.87         2.56        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 
       34.75       108.82         1.74         4.34        10.39         3.42 
TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       53.82         6.41        15.06        35.64        19.53         0.95 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       10.85         3.19         0.30        11.77        18.44        58.19 
TCGA-08-0520 TCGA-08-0521 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       10.75         4.80        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 
        5.95         7.17        65.92         0.10        38.17         6.12 
TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0820 
        2.63        43.10         5.49         9.11        91.76        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 
       10.62        23.51        38.76         8.94       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1096 TCGA-12-1097 
        6.25        30.54        21.63        11.97         9.11        14.53 
TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
        3.98        59.41        43.23        13.12         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-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-1037 TCGA-14-1043 
        3.25         1.35         2.89        16.50        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        1.38         1.12         3.75        23.11         7.10         1.15 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
       17.79         7.63         5.88         3.78         3.42         9.86 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       50.53        53.19        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 
        0.82        13.35         3.65        13.97         6.41        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 
        8.61         0.43        14.27         3.39        10.75         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
       12.95         4.64        25.38        12.66         0.13         9.67 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 
        7.04         6.64        18.64         7.96         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        5.29         5.42        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         1.22 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
        7.92         2.33         4.80        16.60         9.86        33.14 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2523 TCGA-27-2526 
       21.30        30.05        14.04        11.51        16.08         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 
       14.40         0.20         2.53         8.35         1.55         2.83 
TCGA-28-1757 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 
        0.13         4.77         3.91         9.04        11.77        31.27 
TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 
        7.79        22.68        10.49         5.42        21.07         0.49 
TCGA-32-1980 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 
        1.18        12.69        16.93        12.23        20.78        15.95 
TCGA-32-2616 TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        7.36        22.78         3.72        12.59        19.86        10.85 
TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-6646 TCGA-74-6573 
        0.85         8.94         9.53         0.99         7.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34         8.22         7.50         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        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 
        2.70        17.06         8.35        20.98         5.03         9.27 
TCGA-76-6664 TCGA-81-5910 TCGA-OX-A56R 
        7.79         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 
                       11.28                         9.21 
[1] "0.1 - 92.7 (11.3)" "0.1 - 127.6 (9.2)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                              cls
clus                             0   1
  AMP PEAK 24(19Q12) MUTATED    85 124
  AMP PEAK 24(19Q12) WILD-TYPE 135 216
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED     85  124
  AMP PEAK 24(19Q12) WILD-TYPE  135  216
        clus
vv       AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  FEMALE                         85                          135
  MALE                          124                          216
[1] 2 2
[1] FALSE
D24V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 24(19Q12) MUTATED                               8
  AMP PEAK 24(19Q12) WILD-TYPE                             9
                              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
D24V5, multiclass
                                 clus
vv                                AMP PEAK 24(19Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            8
  TREATED PRIMARY GBM                                      8
  UNTREATED PRIMARY (DE NOVO) GBM                        193
                                 clus
vv                                AMP PEAK 24(19Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              9
  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"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(19Q12) MUTATED   144  65
  AMP PEAK 24(19Q12) WILD-TYPE 238 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED    144   65
  AMP PEAK 24(19Q12) WILD-TYPE  238  113
     clus
vv    AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  NO                         144                          238
  YES                         65                          113
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19Q12) MUTATED       6                        15   180
  AMP PEAK 24(19Q12) WILD-TYPE     7                        24   305
D24V7, multiclass
                           clus
vv                          AMP PEAK 24(19Q12) MUTATED
  ASIAN                                              6
  BLACK OR AFRICAN AMERICAN                         15
  WHITE                                            180
                           clus
vv                          AMP PEAK 24(19Q12) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           24
  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     6 174
  AMP PEAK 24(19Q12) WILD-TYPE   6 288
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED      6  174
  AMP PEAK 24(19Q12) WILD-TYPE    6  288
                        clus
vv                       AMP PEAK 24(19Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        174
                        clus
vv                       AMP PEAK 24(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          288
[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     8  60
  AMP PEAK 25(21Q21.1) WILD-TYPE  90 402
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            68                            492 
  AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE 
                            60                            402 
$`AMP PEAK 25(21Q21.1) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0025 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
        9.17        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 
       10.52         0.20         7.86        46.59         9.44        56.88 
TCGA-06-0168 TCGA-06-0176 TCGA-06-0177 TCGA-06-0188 TCGA-06-0189 TCGA-06-0197 
       19.04        91.00         2.01        28.47        14.93         2.60 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0644 TCGA-06-0743 TCGA-06-1086 TCGA-06-1087 
       22.49        10.36        12.33        22.32         6.35         3.58 
TCGA-06-1806 TCGA-06-2565 TCGA-06-2567 TCGA-06-5856 TCGA-06-6698 TCGA-08-0246 
       15.32         6.81         4.37         3.75         4.77         3.91 
TCGA-08-0386 TCGA-08-0510 TCGA-12-0619 TCGA-12-0822 TCGA-12-1095 TCGA-12-1602 
       15.72         3.52        10.39        23.51        15.85         6.41 
TCGA-12-3646 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1454 TCGA-16-0846 
       43.23         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 
        3.48        12.66         7.96         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         9.04         7.79        13.64 
TCGA-28-5218 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-41-2575 
        4.21        15.95         8.84        22.78         3.72         9.53 
TCGA-41-3915 TCGA-76-6657 
       11.84         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        55.86        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 
       10.36        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         0.23 
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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        32.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       22.16        10.75         9.21         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        16.70         9.80        19.46        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        8.65         3.19         5.46        11.80         2.56        10.65 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
        5.29         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         4.67         7.04         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       35.01         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        5.42        20.94         7.43        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
        2.83        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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 
       12.85         1.55         4.77         4.96         1.87         3.12 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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-12-1093 TCGA-12-1094 
        5.82         6.25        30.54        21.63        11.97        11.38 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       13.61        59.41        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       26.33        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-14-1455 
       32.05        58.78        23.11         7.10         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        5.52         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
       25.38         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         5.42        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 
        7.92         2.33         4.80        16.60        18.25        33.14 
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        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       10.39        16.08         7.59        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-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         0.66         7.30         5.26         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 
       15.58        14.53        11.77        31.27        14.20        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-32-2616 TCGA-32-2638 
       16.93        12.23        20.78        15.02         7.36        21.17 
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        10.62         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 
       13.35         8.94         0.99         4.44         0.20        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 
       17.06         8.35        20.98         4.83         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  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 
                         10.11                          10.11 
[1] "0.2 - 92.7 (10.1)"  "0.1 - 127.6 (10.1)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                                cls
clus                               0   1
  AMP PEAK 25(21Q21.1) MUTATED    27  41
  AMP PEAK 25(21Q21.1) WILD-TYPE 193 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED     27   41
  AMP PEAK 25(21Q21.1) WILD-TYPE  193  299
        clus
vv       AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE
  FEMALE                           27                            193
  MALE                             41                            299
[1] 2 2
[1] FALSE
D25V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 25(21Q21.1) MUTATED                               5
  AMP PEAK 25(21Q21.1) WILD-TYPE                            12
                                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
D25V5, multiclass
                                 clus
vv                                AMP PEAK 25(21Q21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           62
                                 clus
vv                                AMP PEAK 25(21Q21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               12
  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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(21Q21.1) MUTATED    43  25
  AMP PEAK 25(21Q21.1) WILD-TYPE 339 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED     43   25
  AMP PEAK 25(21Q21.1) WILD-TYPE  339  153
     clus
vv    AMP PEAK 25(21Q21.1) MUTATED AMP PEAK 25(21Q21.1) WILD-TYPE
  NO                            43                            339
  YES                           25                            153
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(21Q21.1) MUTATED       4                         3    60
  AMP PEAK 25(21Q21.1) WILD-TYPE     9                        36   425
D25V7, multiclass
                           clus
vv                          AMP PEAK 25(21Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               60
                           clus
vv                          AMP PEAK 25(21Q21.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             36
  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  60
  AMP PEAK 25(21Q21.1) WILD-TYPE  12 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(21Q21.1) MUTATED      0   60
  AMP PEAK 25(21Q21.1) WILD-TYPE   12  402
                        clus
vv                       AMP PEAK 25(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       AMP PEAK 25(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            402
[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  81 383
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            464 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            79                            383 
$`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         0.10         2.56        56.88         5.29 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 TCGA-06-0195 TCGA-06-0208 TCGA-06-0402 
       13.02         2.73        40.37         7.04         5.49         0.26 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 TCGA-06-0879 TCGA-06-1084 
       22.32         5.39         2.70         7.17        22.98         7.43 
TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-2562 TCGA-06-5411 TCGA-06-5859 
        3.58         8.65         7.89         2.83         8.35         4.57 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.49        22.68       108.82         3.19        10.59         0.30 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0517 TCGA-08-0520 TCGA-08-0531 TCGA-12-0688 
        3.52         8.52        58.19        10.75         5.52        24.13 
TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-3649 TCGA-12-3651 
       18.48        11.97        11.38        15.85        11.54        11.77 
TCGA-12-3653 TCGA-14-0786 TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
       11.74        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         6.15        17.79         5.52         4.31        13.35 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1387 TCGA-19-2619 TCGA-19-2629 TCGA-19-5947 
        0.43        14.27         5.95         9.67        16.47         6.64 
TCGA-19-5950 TCGA-19-5958 TCGA-27-1833 TCGA-27-2521 TCGA-27-2524 TCGA-28-1747 
       11.28         5.39        18.25        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        21.17        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 
        9.17         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        55.86        77.65        10.36         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         0.23 
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 
        0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        0.26         4.04        47.31         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       10.65        19.04         3.12         0.23         2.20        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
        2.01        53.98        19.00         2.53        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       28.47        14.93        10.29        18.31         4.67         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 
       20.42        14.96        10.32         5.52        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 
        9.67         2.04        23.57         9.40        19.56         2.17 
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         5.85         5.42 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       20.94         6.35        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         0.76         4.93         9.27        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0245 
        4.77         4.96         1.87         3.12         2.56        34.75 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 
       15.72         0.56        11.77        18.44         1.28         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        6.54        15.98        17.33        14.01        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54 
TCGA-12-1092 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       21.63         9.11        14.53         3.98         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       10.95        34.52        13.12         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        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-14-1401 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-14-1823 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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         3.91         9.93        26.07        16.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         0.82         9.90         3.65        18.28        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0964 TCGA-19-1385 
        6.41        11.77        21.90         8.61         3.39        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07        12.95         4.64        25.38         3.48         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-19-5951 TCGA-19-5952 
        0.16         4.08         7.00         7.04         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
        4.73         7.96         1.78         6.51         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        33.14        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        10.39        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        0.20         9.21         7.63         1.22         1.55         0.13 
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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       15.58        14.53        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68        10.49        15.39        21.07         0.49 
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-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        22.78         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       10.62         0.85        13.35         8.94         0.99         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 
       11.84        11.54         7.76         3.45         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-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
       17.06         4.83         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 
        1.61        17.72 

  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 
                        108.82                         127.59 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          9.22                          10.34 
[1] "0.1 - 108.8 (9.2)"  "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    28  68
  DEL PEAK  1(1P36.32) WILD-TYPE 192 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     28   68
  DEL PEAK  1(1P36.32) WILD-TYPE  192  272
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           28                            192
  MALE                             68                            272
[1] 2 2
[1] FALSE
D26V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  1(1P36.32) MUTATED                               1
  DEL PEAK  1(1P36.32) WILD-TYPE                            16
                                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
D26V5, 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)                               16
  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"
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    66  30
  DEL PEAK  1(1P36.32) WILD-TYPE 316 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     66   30
  DEL PEAK  1(1P36.32) WILD-TYPE  316  148
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            66                            316
  YES                           30                            148
[1] 2 2
[1] FALSE
                                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                        33   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                             33
  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  11 381
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      1   81
  DEL PEAK  1(1P36.32) WILD-TYPE   11  381
                        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                            381
[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    21 109
  DEL PEAK  2(1P36.23) WILD-TYPE  77 353
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           130                            430 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           109                            353 
$`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         4.04        23.08 
TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        5.46         2.56        56.88         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 
       13.02         2.73        40.37        10.29        18.31         7.04 
TCGA-06-0208 TCGA-06-0219 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 
        5.49         0.36        22.32         5.39         2.70         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       22.98         5.42         7.43         3.58         8.65         7.89 
TCGA-06-1804 TCGA-06-2562 TCGA-06-2565 TCGA-06-5411 TCGA-06-5414 TCGA-06-5415 
       13.61         2.83         6.81         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         0.49        22.68       108.82         1.74         9.17 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 TCGA-08-0514 
       15.72         3.19        10.59         0.30         3.52         8.52 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 
        1.28        10.75         5.52        65.92        25.97        24.13 
TCGA-12-0769 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 
       12.43         9.11        14.86        18.48        11.97        11.38 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1599 TCGA-12-3649 TCGA-12-3652 TCGA-14-0736 
       15.85        14.53        25.28        11.54        34.52        15.12 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
       23.05         2.24        11.24         2.89        16.50         1.12 
TCGA-14-1458 TCGA-14-1827 TCGA-14-1829 TCGA-16-0861 TCGA-16-1045 TCGA-16-1056 
        6.15         5.88         7.17         4.31        29.03        13.35 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1386 TCGA-19-1387 TCGA-19-2619 TCGA-19-2620 
        0.43        14.27         9.07         5.95         9.67         4.87 
TCGA-19-2629 TCGA-19-5947 TCGA-19-5950 TCGA-19-5959 TCGA-26-1439 TCGA-26-6173 
       16.47         6.64        11.28         5.29        13.87         7.92 
TCGA-27-1833 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 
       18.25        10.39         7.59         8.35         8.48         0.66 
TCGA-28-5211 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-2634 TCGA-32-2638 
       11.77         5.42         0.10        15.85        22.78        21.17 
TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-74-6575 
       10.62        13.35         9.53         4.44         0.20        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 
        0.23         1.61        26.30         5.92 

$`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 
        9.17         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        55.86        77.65        24.59        10.36 
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         0.23 
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         0.16        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        16.21         2.70         0.26        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        0.10         3.58        22.72        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.07        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         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         0.23         2.20        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
        2.01        53.98        19.00         2.53        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       28.47        14.93         4.67         2.60         0.39         6.48 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       23.57         9.40        19.56         2.17         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         5.85        20.94         6.35        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         0.76         4.93         9.27 
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 
       11.24         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         3.95         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0246 
        4.96         1.87         3.12         2.56        34.75         3.91 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 
       19.53         0.95        10.85         0.56        11.77        18.44 
TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
       58.19         4.80         6.54        15.98        17.33        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 
       14.43         1.64        10.39         5.95         7.17         0.10 
TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 
       38.17         6.12         2.63        18.12        28.41        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
       43.10         5.49        14.27        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-12-1098 
        5.82         6.25        30.54        21.63         9.11         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.42         9.44        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       25.78        10.95        11.77        11.74        13.12         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0790 TCGA-14-0812 
        2.04        11.97         0.95         6.21        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-14-1401 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-14-1456 
       23.11         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-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       16.31         0.82         9.90         3.65        18.28        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0964 TCGA-19-1385 
        6.41        11.77        21.90         8.61         3.39        10.75 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.48         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        3.25         0.13         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.00         7.04         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78         6.51         5.39         5.42         3.98        16.57 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03         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-26-6174 
       14.86         5.49         8.88         1.22         1.58         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60         9.86        33.14        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        10.39        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         3.91         9.04        15.58        14.53 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        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-74-6573 TCGA-74-6577 TCGA-74-6578 
       11.84        11.54         7.76         3.45         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4934 
        8.22         7.50         4.80         4.54         3.65         2.53 
TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 
       10.78         3.29         2.70        11.38        17.06         4.83 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 
        9.27         7.73         7.79        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 
                        108.82                         127.59 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                         9.600                         10.255 
[1] "0.1 - 108.8 (9.6)"  "0.1 - 127.6 (10.3)"
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    38  92
  DEL PEAK  2(1P36.23) WILD-TYPE 182 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     38   92
  DEL PEAK  2(1P36.23) WILD-TYPE  182  248
        clus
vv       DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  FEMALE                           38                            182
  MALE                             92                            248
[1] 2 2
[1] FALSE
D27V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  2(1P36.23) MUTATED                               1
  DEL PEAK  2(1P36.23) WILD-TYPE                            16
                                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                               126
  DEL PEAK  2(1P36.23) WILD-TYPE                             399
D27V5, multiclass
                                 clus
vv                                DEL PEAK  2(1P36.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          126
                                 clus
vv                                DEL PEAK  2(1P36.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               16
  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"
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    93  37
  DEL PEAK  2(1P36.23) WILD-TYPE 289 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     93   37
  DEL PEAK  2(1P36.23) WILD-TYPE  289  141
     clus
vv    DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  NO                            93                            289
  YES                           37                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.23) MUTATED       6                         8   112
  DEL PEAK  2(1P36.23) WILD-TYPE     7                        31   373
D27V7, multiclass
                           clus
vv                          DEL PEAK  2(1P36.23) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              112
                           clus
vv                          DEL PEAK  2(1P36.23) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             31
  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"
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED     1 108
  DEL PEAK  2(1P36.23) WILD-TYPE  11 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED      1  108
  DEL PEAK  2(1P36.23) WILD-TYPE   11  354
                        clus
vv                       DEL PEAK  2(1P36.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          108
                        clus
vv                       DEL PEAK  2(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            354
[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    10  50
  DEL PEAK  3(1P32.3) WILD-TYPE  88 412
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           60                           500 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           50                           412 
$`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        16.21        28.47         4.67 
TCGA-06-0241 TCGA-06-0410 TCGA-06-0646 TCGA-06-0649 TCGA-06-0743 TCGA-06-0749 
       14.96         4.70         4.47         2.04        22.32         2.17 
TCGA-06-0750 TCGA-06-1802 TCGA-06-2561 TCGA-06-2567 TCGA-06-5411 TCGA-08-0244 
        0.92         7.89         9.27         4.37         8.35        22.68 
TCGA-08-0344 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 TCGA-08-0529 TCGA-12-0654 
      108.82        10.59         0.30         3.52        17.33         7.17 
TCGA-12-0773 TCGA-12-0776 TCGA-12-1092 TCGA-12-3649 TCGA-14-0813 TCGA-14-1452 
       43.10         9.11        21.63        11.54         1.35         7.10 
TCGA-14-1455 TCGA-14-1458 TCGA-14-1795 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 
        0.92         6.15         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        16.47         5.39         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         7.79        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 
        9.17         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        55.86        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        10.36         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         0.23 
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 
        0.16        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         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       22.49         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26        70.52         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.01        12.33         3.22         9.67        23.57         9.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
       19.56         5.39         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        6.35         3.58        26.79         8.65        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         0.76         4.93         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         0.43        31.50        11.24 
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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         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-A6S1 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        2.56        34.75         3.91         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 TCGA-08-0512 
        9.17        10.85        15.72         3.19         0.56        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        6.54        15.98         5.52        14.01        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.39         5.95        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       53.10         5.49        14.86        14.27        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-12-1093 
       20.58       127.59         5.82         6.25        30.54        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       25.78        10.95        11.77        34.52        11.74        13.12 
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-14-0817 
       23.05         2.24        11.24        13.78         3.25         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-14-1396 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-14-1454 TCGA-14-1456 TCGA-14-1459 
       58.78        23.11         1.15        30.18        40.96        12.43 
TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       16.31         4.31         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         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-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        7.96         1.78         6.51         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 
       16.57        10.03        13.87        31.33         7.13         9.40 
TCGA-26-5133 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       14.86         8.88         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        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        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 
        9.04        15.58        14.53        11.77        14.20         4.21 
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-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        21.17        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        10.62         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        11.54         7.76 
TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
        3.45         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        11.38         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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  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 
                       108.82                        127.59 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                        9.320                        10.375 
[1] "0.2 - 108.8 (9.3)"  "0.1 - 127.6 (10.4)"
[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 202 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     18   42
  DEL PEAK  3(1P32.3) WILD-TYPE  202  298
        clus
vv       DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  FEMALE                          18                           202
  MALE                            42                           298
[1] 2 2
[1] FALSE
D28V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  3(1P32.3) MUTATED                               1
  DEL PEAK  3(1P32.3) WILD-TYPE                            16
                               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
D28V5, 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)                              16
  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"
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED    35  25
  DEL PEAK  3(1P32.3) WILD-TYPE 347 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     35   25
  DEL PEAK  3(1P32.3) WILD-TYPE  347  153
     clus
vv    DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  NO                           35                           347
  YES                          25                           153
[1] 2 2
[1] FALSE
                               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                        35   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                            35
  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  11 414
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED      1   48
  DEL PEAK  3(1P32.3) WILD-TYPE   11  414
                        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                           414
[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  91 422
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           47                           513 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           40                           422 
$`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        10.36        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         0.26        14.07         3.12         2.73 
TCGA-06-1802 TCGA-06-2565 TCGA-06-5411 TCGA-06-A5U1 TCGA-08-0244 TCGA-08-0344 
        7.89         6.81         8.35         1.87        22.68       108.82 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0392 TCGA-08-0510 TCGA-12-0615 TCGA-12-0691 
       13.78        10.39         0.30         3.52        14.01         6.12 
TCGA-12-0819 TCGA-12-0827 TCGA-12-3652 TCGA-14-1452 TCGA-16-1047 TCGA-16-1055 
       24.79        38.76        34.52         7.10         0.82         9.90 
TCGA-16-1062 TCGA-19-0964 TCGA-19-1387 TCGA-19-1390 TCGA-19-2619 TCGA-19-2629 
       18.28         3.39         5.95        25.38         9.67        16.47 
TCGA-19-5953 TCGA-19-5959 TCGA-26-1440 TCGA-27-1837 TCGA-28-2502 TCGA-28-5208 
        4.73         5.29         9.73        14.04         0.66        15.58 
TCGA-28-5213 TCGA-32-4719 TCGA-41-5651 TCGA-74-6575 TCGA-76-6285 
       31.27        10.85        11.54        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 
        9.17         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        55.86        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         0.23        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         0.16 
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        16.21         2.70 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       10.52        18.74        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 
       56.88        10.65         5.29        19.04        13.02         0.23 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.20        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       22.49         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
        7.43         6.35         3.58        26.79         8.65        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
        2.83        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        11.24         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 
        3.95         7.79         5.39         1.48         0.49         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-A6S0 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
        3.12         2.56        34.75         3.91         1.74         4.34 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 
       10.85        15.72         3.19        10.59         0.56        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        6.54        15.98        17.33         5.52        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        24.13         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       91.76        18.48        10.62        23.51        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 
       43.23        25.78        11.54        10.95        11.77        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0817 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-14-1034 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-14-1453 TCGA-14-1454 
        3.75        32.05        58.78        23.11         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         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1056 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 
        4.31        29.03        13.35         3.65        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 
       11.77        21.90         8.61         0.43        14.27        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07        12.95         4.64         3.48         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-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 
       18.64         7.96         1.78         6.51         5.39         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 
        3.98        16.57        10.03        13.87        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1838 TCGA-27-2518 
       18.25        33.14        21.30        30.05        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        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-28-2506 
        8.48         1.22         1.55         2.83         0.13         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 
        4.77         7.30         5.26         3.91         9.04        14.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        14.20         7.79        13.64         4.21        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        21.17        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.62         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 
        0.99         4.44        11.84         0.20         7.76         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        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-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                         0.26                          0.10 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                       108.82                        127.59 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                        10.72                          9.90 
[1] "0.3 - 108.8 (10.7)" "0.1 - 127.6 (9.9)" 
[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 202 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED     18   29
  DEL PEAK  4(1P22.1) WILD-TYPE  202  311
        clus
vv       DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  FEMALE                          18                           202
  MALE                            29                           311
[1] 2 2
[1] FALSE
D29V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  4(1P22.1) MUTATED                               1
  DEL PEAK  4(1P22.1) WILD-TYPE                            16
                               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
D29V5, 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)                              16
  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"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED    34  13
  DEL PEAK  4(1P22.1) WILD-TYPE 348 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED     34   13
  DEL PEAK  4(1P22.1) WILD-TYPE  348  165
     clus
vv    DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  NO                           34                           348
  YES                          13                           165
[1] 2 2
[1] FALSE
                               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                        35   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                            35
  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  11 422
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED      1   40
  DEL PEAK  4(1P22.1) WILD-TYPE   11  422
                        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                           422
[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  39
  DEL PEAK  5(1Q42.11) WILD-TYPE  89 423
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            48                            512 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            39                            423 
$`DEL PEAK  5(1Q42.11) MUTATED`
TCGA-02-0084 TCGA-02-0099 TCGA-02-0106 TCGA-02-0281 TCGA-02-0333 TCGA-02-0446 
        0.23         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         0.10        10.29        11.80         0.26         7.43 
TCGA-06-1802 TCGA-06-1806 TCGA-06-2558 TCGA-06-5411 TCGA-06-6390 TCGA-08-0246 
        7.89        15.32         0.76         8.35         5.39         3.91 
TCGA-08-0392 TCGA-08-0510 TCGA-12-0620 TCGA-12-0656 TCGA-12-0776 TCGA-12-1599 
        0.30         3.52         5.95        65.92         9.11        25.28 
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         0.43         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        16.47        16.57        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 

$`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 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 
        2.70         0.26         4.04        47.31         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        28.47        14.93        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       10.36        20.42        14.96        10.32         5.52        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
       20.94         6.35         3.58        26.79         8.65        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         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        7.79         1.48         0.49         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-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 TCGA-12-0657 
       14.01        14.43         1.64        10.39         7.17         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        12.43        53.10        43.10         5.49        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        6.25        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 
        9.11        14.53         3.98         3.42         9.44        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       15.12         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        1.35         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 
       19.30         0.79         1.12         3.75        32.05        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         6.15 
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 
        9.86        50.53        19.10        53.19         5.52         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       11.77         8.61        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         3.48         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-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        3.98        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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        10.39        16.08         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-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
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-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1991 TCGA-32-2491 
       15.85        19.50         1.18         4.67        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       20.78        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         3.45 
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        10.78        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 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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 
                         65.92                         127.59 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                         8.120                         10.375 
[1] "0.1 - 65.9 (8.1)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED    18  30
  DEL PEAK  5(1Q42.11) WILD-TYPE 202 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED     18   30
  DEL PEAK  5(1Q42.11) WILD-TYPE  202  310
        clus
vv       DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  FEMALE                           18                            202
  MALE                             30                            310
[1] 2 2
[1] FALSE
D30V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  5(1Q42.11) MUTATED                               2
  DEL PEAK  5(1Q42.11) WILD-TYPE                            15
                                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
D30V5, multiclass
                                 clus
vv                                DEL PEAK  5(1Q42.11) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           45
                                 clus
vv                                DEL PEAK  5(1Q42.11) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               15
  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"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED    28  20
  DEL PEAK  5(1Q42.11) WILD-TYPE 354 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED     28   20
  DEL PEAK  5(1Q42.11) WILD-TYPE  354  158
     clus
vv    DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  NO                            28                            354
  YES                           20                            158
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(1Q42.11) MUTATED       0                         5    39
  DEL PEAK  5(1Q42.11) WILD-TYPE    13                        34   446
D30V7, multiclass
                           clus
vv                          DEL PEAK  5(1Q42.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               39
                           clus
vv                          DEL PEAK  5(1Q42.11) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             34
  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  36
  DEL PEAK  5(1Q42.11) WILD-TYPE  10 426
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED      2   36
  DEL PEAK  5(1Q42.11) WILD-TYPE   10  426
                        clus
vv                       DEL PEAK  5(1Q42.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK  5(1Q42.11) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            426
[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  90 436
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         34                         526 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         26                         436 
$`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         0.23         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 
        7.86        15.32         0.76         8.35        15.72         0.30 
TCGA-08-0510 TCGA-12-0776 TCGA-12-0780 TCGA-12-3648 TCGA-14-0740 TCGA-14-0812 
        3.52         9.11        14.27        25.78        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         0.43         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        16.57        14.86         7.79        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 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        0.10         3.58        22.72        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 
        2.20        11.74        20.09        16.70         9.80        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        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         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       10.59         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
       43.10         5.49        14.86        91.76        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-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33         2.04        28.93        19.30         0.79 
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-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18         0.92         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 
        8.61        14.27         3.39        10.75         9.07         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        3.48         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        3.98        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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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 
       10.39        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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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-32-1987 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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
        7.36         8.84        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       11.54         7.76         3.45        14.33         8.22         7.50 
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        10.78 
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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                       0.23                        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 
                       9.39                       10.24 
[1] "0.2 - 41.0 (9.4)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.1"
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED    13  21
  DEL PEAK  6(1Q44) WILD-TYPE 207 319
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED     13   21
  DEL PEAK  6(1Q44) WILD-TYPE  207  319
        clus
vv       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  FEMALE                        13                         207
  MALE                          21                         319
[1] 2 2
[1] FALSE
D31V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK  6(1Q44) MUTATED                               2                   1
  DEL PEAK  6(1Q44) WILD-TYPE                            15                  17
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  6(1Q44) MUTATED                                31
  DEL PEAK  6(1Q44) WILD-TYPE                             494
D31V5, 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)                            15
  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"
D31V6, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED    22  12
  DEL PEAK  6(1Q44) WILD-TYPE 360 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED     22   12
  DEL PEAK  6(1Q44) WILD-TYPE  360  166
     clus
vv    DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  NO                         22                         360
  YES                        12                         166
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(1Q44) MUTATED       0                         3    27
  DEL PEAK  6(1Q44) WILD-TYPE    13                        36   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                          36
  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  11 438
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED      1   24
  DEL PEAK  6(1Q44) WILD-TYPE   11  438
                        clus
vv                       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        24                         438
[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     3  42
  DEL PEAK  7(2Q22.1) WILD-TYPE  95 420
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           45                           515 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           42                           420 
$`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        11.80         2.53        28.47        35.01         2.04 
TCGA-06-0749 TCGA-06-1087 TCGA-06-5416 TCGA-06-5856 TCGA-06-6390 TCGA-06-6694 
        2.17         3.58         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        14.01        10.62        27.78         3.42 
TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 TCGA-14-0812 
        9.44        13.61        43.23        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        16.31        12.95        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-28-2509 TCGA-28-5215 TCGA-32-1978 
        3.48         4.08         6.51         4.77         7.79        15.85 
TCGA-32-2615 TCGA-76-4934 TCGA-76-6191 
       15.95         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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        2.01        53.98        19.00        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.20        12.43        22.49         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       70.52         4.70         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        5.39         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        7.79         1.48         0.49         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        1.55         4.77         4.96         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
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 
        6.25        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 
        9.11        14.53         3.98        25.28         6.41        59.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
       13.12         3.22         2.04        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         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         6.15 
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-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
        9.86        19.10         5.52         3.91         9.93        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        7.96         1.78         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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        10.39        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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         7.30         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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-32-2616 
       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        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 
       10.78         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         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  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 
                        10.19                         10.03 
[1] "1.9 - 53.2 (10.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    21  24
  DEL PEAK  7(2Q22.1) WILD-TYPE 199 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     21   24
  DEL PEAK  7(2Q22.1) WILD-TYPE  199  316
        clus
vv       DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  FEMALE                          21                           199
  MALE                            24                           316
[1] 2 2
[1] FALSE
D32V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  7(2Q22.1) MUTATED                               3
  DEL PEAK  7(2Q22.1) WILD-TYPE                            14
                               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
D32V5, multiclass
                                 clus
vv                                DEL PEAK  7(2Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          40
                                 clus
vv                                DEL PEAK  7(2Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              14
  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"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    25  20
  DEL PEAK  7(2Q22.1) WILD-TYPE 357 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     25   20
  DEL PEAK  7(2Q22.1) WILD-TYPE  357  158
     clus
vv    DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  NO                           25                           357
  YES                          20                           158
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(2Q22.1) MUTATED       0                         5    40
  DEL PEAK  7(2Q22.1) WILD-TYPE    13                        34   445
D32V7, multiclass
                           clus
vv                          DEL PEAK  7(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              40
                           clus
vv                          DEL PEAK  7(2Q22.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            34
  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  37
  DEL PEAK  7(2Q22.1) WILD-TYPE  12 425
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED      0   37
  DEL PEAK  7(2Q22.1) WILD-TYPE   12  425
                        clus
vv                       DEL PEAK  7(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK  7(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           425
[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     6  48
  DEL PEAK  8(2Q37.1) WILD-TYPE  92 414
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           54                           506 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           48                           414 
$`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         0.23 
TCGA-02-0104 TCGA-02-0338 TCGA-06-0152 TCGA-06-0182 TCGA-06-0188 TCGA-06-0221 
       65.00        10.59        11.80         2.53        28.47        18.02 
TCGA-06-0414 TCGA-06-0649 TCGA-06-2562 TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 
       35.01         2.04         2.83         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        53.82        22.52        11.77        18.12        27.78 
TCGA-12-1099 TCGA-12-1600 TCGA-12-3646 TCGA-12-5301 TCGA-14-0783 TCGA-14-0812 
        3.42        13.61        43.23         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        16.31 
TCGA-16-1047 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 
        0.82        12.95        25.38         3.48         4.08         6.51 
TCGA-27-2521 TCGA-28-1750 TCGA-28-2509 TCGA-28-5215 TCGA-32-1978 TCGA-32-2495 
       10.39         8.35         4.77         7.79        15.85        15.02 
TCGA-32-2615 TCGA-41-3393 TCGA-41-6646 TCGA-76-4934 TCGA-76-6280 TCGA-76-6657 
       15.95         4.44         7.76         2.53        11.38         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 
        9.17         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        55.86        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        10.36        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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       53.98        19.00        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       12.43        22.49         0.36        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        8.05         0.16        12.33         3.22         4.47         9.67 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         0.49         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 
        1.55         4.77         4.96         1.87         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       10.39         7.59         3.42         1.28         6.41        15.06 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 
       38.17        25.97        24.13         6.12         2.63        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 
       14.53         3.98         9.44        25.28         6.41        59.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
       13.12         3.22        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         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         6.15 
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-14-3477 TCGA-15-0742 TCGA-15-1446 
        7.17        17.49         7.96         3.78         9.86        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
        5.52         3.91         9.93        26.07         4.31        29.03 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        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        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-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         7.63         8.48         1.22         1.55         2.83 
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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        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-32-2616 
       12.69        14.86        16.93        12.23        20.78         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-74-6573 
        9.53         0.99        11.84         0.20        11.54         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        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                         0.23                          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 
                        10.29                          9.98 
[1] "0.2 - 89.7 (10.3)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    26  28
  DEL PEAK  8(2Q37.1) WILD-TYPE 194 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     26   28
  DEL PEAK  8(2Q37.1) WILD-TYPE  194  312
        clus
vv       DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  FEMALE                          26                           194
  MALE                            28                           312
[1] 2 2
[1] FALSE
D33V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  8(2Q37.1) MUTATED                               2
  DEL PEAK  8(2Q37.1) WILD-TYPE                            15
                               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
D33V5, multiclass
                                 clus
vv                                DEL PEAK  8(2Q37.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          51
                                 clus
vv                                DEL PEAK  8(2Q37.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              15
  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"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    33  21
  DEL PEAK  8(2Q37.1) WILD-TYPE 349 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     33   21
  DEL PEAK  8(2Q37.1) WILD-TYPE  349  157
     clus
vv    DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  NO                           33                           349
  YES                          21                           157
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(2Q37.1) MUTATED       0                         3    50
  DEL PEAK  8(2Q37.1) WILD-TYPE    13                        36   435
D33V7, multiclass
                           clus
vv                          DEL PEAK  8(2Q37.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              50
                           clus
vv                          DEL PEAK  8(2Q37.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            36
  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  45
  DEL PEAK  8(2Q37.1) WILD-TYPE  11 417
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED      1   45
  DEL PEAK  8(2Q37.1) WILD-TYPE   11  417
                        clus
vv                       DEL PEAK  8(2Q37.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK  8(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           417
[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    11  41
  DEL PEAK  9(3P21.1) WILD-TYPE  87 421
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           52                           508 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           41                           421 
$`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         0.23        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 
       16.21        22.72        11.80        12.43        22.49        18.02 
TCGA-06-0409 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-5416 TCGA-06-5859 
       70.52         5.39         7.17         3.58         6.71         4.57 
TCGA-06-6390 TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 
        5.39        34.75         3.91        15.72        10.59        18.44 
TCGA-08-0517 TCGA-12-0776 TCGA-12-0826 TCGA-12-3653 TCGA-14-0862 TCGA-14-1458 
       58.19         9.11        27.78        11.74         2.89         6.15 
TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-1047 
       17.85         3.78        53.19         5.52        26.07         0.82 
TCGA-19-0964 TCGA-19-1388 TCGA-19-2625 TCGA-26-1439 TCGA-26-1440 TCGA-28-1752 
        3.39        12.95         4.08        13.87         9.73         8.48 
TCGA-28-1756 TCGA-32-1991 TCGA-32-2615 TCGA-76-4929 
        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 
        9.17         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        55.86        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        10.36        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         0.16        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         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.20         0.36        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         5.52         0.26         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        2.04        23.57         9.40        22.32        19.56         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.17         0.92        43.46        46.19         5.65        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
        5.85         5.42        20.94         7.43         6.35        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95         7.79         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
        3.19         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.10         5.49        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        5.39        16.50        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-14-1451 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-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
       40.96        12.43         0.99         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 
       50.53        19.10         3.91         9.93        16.31         4.31 
TCGA-16-1045 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         9.90        13.35         3.65        18.28        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         0.43        14.27 
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         3.48 
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-19-2629 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       16.57        10.03        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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        10.39 
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-28-1757 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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        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-32-2491 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 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         9.17         2.53        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                         0.23                          0.10 
  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 
                        12.69                          9.86 
[1] "0.2 - 100.0 (12.7)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.5"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED    21  31
  DEL PEAK  9(3P21.1) WILD-TYPE 199 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED     21   31
  DEL PEAK  9(3P21.1) WILD-TYPE  199  309
        clus
vv       DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  FEMALE                          21                           199
  MALE                            31                           309
[1] 2 2
[1] FALSE
D34V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  9(3P21.1) MUTATED                               0
  DEL PEAK  9(3P21.1) WILD-TYPE                            17
                               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
D34V5, multiclass
                                 clus
vv                                DEL PEAK  9(3P21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             0
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          49
                                 clus
vv                                DEL PEAK  9(3P21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              17
  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"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED    42  10
  DEL PEAK  9(3P21.1) WILD-TYPE 340 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED     42   10
  DEL PEAK  9(3P21.1) WILD-TYPE  340  168
     clus
vv    DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  NO                           42                           340
  YES                          10                           168
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P21.1) MUTATED       0                         5    45
  DEL PEAK  9(3P21.1) WILD-TYPE    13                        34   440
D34V7, multiclass
                           clus
vv                          DEL PEAK  9(3P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              45
                           clus
vv                          DEL PEAK  9(3P21.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            34
  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  45
  DEL PEAK  9(3P21.1) WILD-TYPE  10 417
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED      2   45
  DEL PEAK  9(3P21.1) WILD-TYPE   10  417
                        clus
vv                       DEL PEAK  9(3P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK  9(3P21.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           417
[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     8  50
  DEL PEAK 10(3Q13.31) WILD-TYPE  90 412
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            58                            502 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            50                            412 
$`DEL PEAK 10(3Q13.31) MUTATED`
TCGA-02-0001 TCGA-02-0021 TCGA-02-0054 TCGA-02-0055 TCGA-02-0060 TCGA-02-0069 
        9.17        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 
        0.23        92.65        15.91        25.71        16.80        22.72 
TCGA-06-0152 TCGA-06-0166 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.80         5.29        12.43        22.49         0.36        18.02 
TCGA-06-0397 TCGA-06-0409 TCGA-06-1806 TCGA-06-2569 TCGA-06-5859 TCGA-06-6389 
        5.52        70.52        15.32         0.43         4.57         7.79 
TCGA-06-6390 TCGA-06-A5U1 TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 
        5.39         1.87        34.75         3.91        15.72        10.59 
TCGA-08-0516 TCGA-12-0691 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0826 
       18.44         6.12        43.10         5.49         9.11        27.78 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1600 TCGA-12-3651 TCGA-12-3653 TCGA-14-0812 
        5.82        30.54        13.61        11.77        11.74         3.25 
TCGA-14-0871 TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 
       28.93         6.15        17.85        53.19         5.52        12.95 
TCGA-19-2621 TCGA-19-A6J4 TCGA-26-1439 TCGA-28-1752 TCGA-28-1757 TCGA-28-5220 
        1.08         3.98        13.87         8.48         0.13        10.49 
TCGA-32-1973 TCGA-32-2615 TCGA-76-4929 TCGA-76-6280 
       21.07        15.95         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        55.86        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        10.36        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         0.16         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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        4.96        11.84         0.20        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       14.96        10.32         0.26         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         4.37        31.50        11.24 
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-06-6388 TCGA-06-6391 
        6.71         2.73         3.75         6.15         3.95         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 
        4.77         4.96         3.12         2.56        22.68       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
        0.30         0.56         3.52        11.77         8.52        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0778 
        2.63        18.12        28.41        12.43        53.10        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1092 
       38.76         8.94        20.58       127.59         6.25        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.42         9.44        25.28         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       25.78        11.54        10.95        34.52        13.12         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-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24        13.78         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-14-1459 
        7.10         1.15        30.18         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         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         9.86        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.48         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         7.53         0.16         4.08        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.42        16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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        10.39        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-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 
        7.63         1.22         1.55         2.83         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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
        4.21        22.68         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-32-2616 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        21.17        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        10.62         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        11.54         7.76 
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        10.78 
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-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  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 
                         11.56                           9.90 
[1] "0.1 - 92.7 (11.6)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED    26  32
  DEL PEAK 10(3Q13.31) WILD-TYPE 194 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED     26   32
  DEL PEAK 10(3Q13.31) WILD-TYPE  194  308
        clus
vv       DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  FEMALE                           26                            194
  MALE                             32                            308
[1] 2 2
[1] FALSE
D35V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 10(3Q13.31) MUTATED                               3
  DEL PEAK 10(3Q13.31) WILD-TYPE                            14
                                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                                53
  DEL PEAK 10(3Q13.31) WILD-TYPE                             472
D35V5, multiclass
                                 clus
vv                                DEL PEAK 10(3Q13.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           53
                                 clus
vv                                DEL PEAK 10(3Q13.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D35V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED    43  15
  DEL PEAK 10(3Q13.31) WILD-TYPE 339 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED     43   15
  DEL PEAK 10(3Q13.31) WILD-TYPE  339  163
     clus
vv    DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  NO                            43                            339
  YES                           15                            163
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q13.31) MUTATED       2                         7    49
  DEL PEAK 10(3Q13.31) WILD-TYPE    11                        32   436
D35V7, multiclass
                           clus
vv                          DEL PEAK 10(3Q13.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               49
                           clus
vv                          DEL PEAK 10(3Q13.31) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             32
  WHITE                                                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"
D35V8, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED     2  49
  DEL PEAK 10(3Q13.31) WILD-TYPE  10 413
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED      2   49
  DEL PEAK 10(3Q13.31) WILD-TYPE   10  413
                        clus
vv                       DEL PEAK 10(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       DEL PEAK 10(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            413
[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  89 413
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           58                           502 
  DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE 
                           49                           413 
$`DEL PEAK 11(3Q22.1) MUTATED`
TCGA-02-0001 TCGA-02-0026 TCGA-02-0039 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 
        9.17        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         0.23        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        23.08        11.80         2.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0409 TCGA-06-1806 TCGA-06-2569 
       12.43        22.49        18.02        70.52        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 
        3.91        15.72        10.59        18.44         6.12        43.10 
TCGA-12-0776 TCGA-12-0826 TCGA-12-1089 TCGA-12-1600 TCGA-12-3651 TCGA-12-3653 
        9.11        27.78         5.82        13.61        11.77        11.74 
TCGA-14-0812 TCGA-14-0871 TCGA-14-1453 TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 
        3.25        28.93         1.15         6.15        17.85        53.19 
TCGA-15-1449 TCGA-19-1388 TCGA-19-2621 TCGA-19-A6J4 TCGA-26-1439 TCGA-28-1752 
        5.52        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        55.86        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        10.36        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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
        0.26         4.04        47.31         0.10         3.58        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       10.52        18.74        14.07        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 
        5.49         3.91         4.96        11.84         0.20         0.36 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26         4.70         8.05         0.16        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.24         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         3.95         1.48         0.49         7.36         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-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        2.56        34.75       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
        9.17        10.85         3.19         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.77         8.52        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       12.43        53.10         5.49        14.86        14.27        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-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        9.44        25.28         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.54        10.95        34.52        13.12         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-14-1454 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-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 
        3.78         3.42         9.86        50.53        19.10         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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         3.48 
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-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         5.42        16.57 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03         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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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        10.39 
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-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        1.55         2.83         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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
       10.49         5.42        15.39         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-32-2632 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 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         9.17         2.53        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  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 
                       11.755                         9.900 
[1] "0.1 - 92.7 (11.8)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q22.1) MUTATED    23  35
  DEL PEAK 11(3Q22.1) WILD-TYPE 197 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED     23   35
  DEL PEAK 11(3Q22.1) WILD-TYPE  197  305
        clus
vv       DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE
  FEMALE                          23                           197
  MALE                            35                           305
[1] 2 2
[1] FALSE
D36V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 11(3Q22.1) MUTATED                               3
  DEL PEAK 11(3Q22.1) WILD-TYPE                            14
                               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
D36V5, 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)                              14
  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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q22.1) MUTATED    41  17
  DEL PEAK 11(3Q22.1) WILD-TYPE 341 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED     41   17
  DEL PEAK 11(3Q22.1) WILD-TYPE  341  161
     clus
vv    DEL PEAK 11(3Q22.1) MUTATED DEL PEAK 11(3Q22.1) WILD-TYPE
  NO                           41                           341
  YES                          17                           161
[1] 2 2
[1] FALSE
                               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                        34   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                            34
  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  10 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q22.1) MUTATED      2   49
  DEL PEAK 11(3Q22.1) WILD-TYPE   10  413
                        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                           413
[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     9  56
  DEL PEAK 12(3Q29) WILD-TYPE  89 406
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         65                         495 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                         56                         406 
$`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         0.23        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        11.80         5.46 
TCGA-06-0159 TCGA-06-0175 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        9.44         2.73        12.43        22.49         0.36        18.02 
TCGA-06-0409 TCGA-06-0745 TCGA-06-1806 TCGA-06-2563 TCGA-06-2565 TCGA-06-5415 
       70.52         5.39        15.32        30.64         6.81         8.55 
TCGA-06-5859 TCGA-06-6390 TCGA-06-6693 TCGA-08-0246 TCGA-08-0351 TCGA-08-0386 
        4.57         5.39         0.49         3.91        53.82        15.72 
TCGA-08-0392 TCGA-08-0516 TCGA-08-0531 TCGA-12-0662 TCGA-12-0776 TCGA-12-0826 
        0.30        18.44         5.52        38.17         9.11        27.78 
TCGA-12-0829 TCGA-12-1091 TCGA-12-1098 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       20.58        30.54         3.98        34.52        11.74        13.12 
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 
        5.52        12.95        25.38         7.00         6.51         3.98 
TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-27-2523 TCGA-27-2528 TCGA-28-5220 
       13.87         4.80        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 
        9.17         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        55.86        20.12        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       10.36        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 
        0.16         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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 
        0.26         4.04        47.31         0.10         3.58        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 
        0.20         9.21         2.20        11.74        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       19.04         3.12        13.02         0.23         2.20        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        4.96        11.84         0.20        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         5.52         0.26         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        2.04        23.57         9.40        22.32        19.56         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 
        1.08         0.76         4.93         9.27         2.83         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        11.24         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         3.95         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        1.87         3.12         2.56        22.68        34.75       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       19.53         0.95         9.17        10.85         3.19        10.59 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
       10.75         4.80         6.54        15.98        17.33        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        0.10        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        12.43        53.10        43.10         5.49        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
       38.76         8.94       127.59         5.82         6.25        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       11.97        11.38        15.85         9.11        14.53         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 
       25.78        11.54        10.95        11.77         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-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.15        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-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 
        7.96         3.78         9.86        50.53        19.10         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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         3.48         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-19-4065 TCGA-19-5947 
        7.53         0.16         4.08        16.47         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        5.39         5.29         5.42        16.57        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-27-1831 
        8.88         1.22         1.58         7.92         2.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       11.51        24.76        10.39         7.59         2.86        14.40 
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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        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        21.17        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        10.62         0.85        13.35         8.94 
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        11.54         7.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 TCGA-76-4926 
        3.45        20.91         4.34        14.33         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        10.78        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                       0.23                        0.10 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                      92.65                      127.59 
  DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE 
                       11.8                         9.9 
[1] "0.2 - 92.7 (11.8)" "0.1 - 127.6 (9.9)"
[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 195 300
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED     25   40
  DEL PEAK 12(3Q29) WILD-TYPE  195  300
        clus
vv       DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  FEMALE                        25                         195
  MALE                          40                         300
[1] 2 2
[1] FALSE
D37V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 12(3Q29) MUTATED                               3                   2
  DEL PEAK 12(3Q29) WILD-TYPE                            14                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 12(3Q29) MUTATED                                60
  DEL PEAK 12(3Q29) WILD-TYPE                             465
D37V5, 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)                            14
  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"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(3Q29) MUTATED    48  17
  DEL PEAK 12(3Q29) WILD-TYPE 334 161
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED     48   17
  DEL PEAK 12(3Q29) WILD-TYPE  334  161
     clus
vv    DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  NO                         48                         334
  YES                        17                         161
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(3Q29) MUTATED       1                         5    57
  DEL PEAK 12(3Q29) WILD-TYPE    12                        34   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                          34
  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  11 408
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(3Q29) MUTATED      1   54
  DEL PEAK 12(3Q29) WILD-TYPE   11  408
                        clus
vv                       DEL PEAK 12(3Q29) MUTATED DEL PEAK 12(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        54                         408
[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     9  67
  DEL PEAK 13(4P16.3) WILD-TYPE  89 395
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           76                           484 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                           67                           395 
$`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        55.86        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 
       22.16        11.80         5.29         0.23         2.20         2.73 
TCGA-06-0177 TCGA-06-0192 TCGA-06-0216 TCGA-06-0414 TCGA-06-0645 TCGA-06-0744 
        2.01        18.31        22.49        35.01         3.22        19.56 
TCGA-06-1087 TCGA-06-1800 TCGA-06-2557 TCGA-06-5416 TCGA-06-6693 TCGA-06-A6S0 
        3.58        26.79         1.08         6.71         0.49         3.12 
TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 
       34.75         1.74         4.34        10.39         3.42        53.82 
TCGA-08-0355 TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0516 TCGA-08-0525 
       22.52         0.95        10.85        15.72        18.44        15.98 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0662 TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 
       10.39         5.95        38.17        38.76         9.44        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3653 TCGA-14-0867 TCGA-14-1454 TCGA-14-1458 
       43.23        25.78        11.74         2.04        30.18         6.15 
TCGA-14-1821 TCGA-14-1823 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-19-1388 
       17.79        17.85         5.52         9.93        26.07        12.95 
TCGA-19-2629 TCGA-19-4065 TCGA-27-1830 TCGA-27-1837 TCGA-27-1838 TCGA-28-2509 
       16.47         7.04         4.80        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         9.04        11.77        14.20        15.85         8.84 
TCGA-32-4210 TCGA-76-4925 TCGA-76-4928 TCGA-76-4934 
        3.72         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 
        9.17         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        10.36        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         0.23 
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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       23.08        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       13.02        91.00        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        26.33        28.47        14.93        10.29         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        4.96        11.84         0.20        12.43         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        70.52         4.70         8.05         0.16        12.33 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        7.43         6.35         8.65         7.89        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
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-A6S1 
        4.77         1.55         4.77         4.96         1.87         2.56 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 TCGA-08-0349 TCGA-08-0352 
       22.68         3.91       108.82        13.78         7.59         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
        6.41        15.06        14.70        35.64        19.53         9.17 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
        8.52        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 
       17.33         5.52        14.01        14.43         1.64         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       65.92         0.10        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        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         6.25        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       15.85         9.11        14.53         3.98         3.42        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       13.61         6.41        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0817 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-14-1455 
       32.05        58.78        23.11         7.10         1.15         0.92 
TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 
       40.96        12.43         0.99         1.97         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0850 TCGA-16-0861 
       50.53        19.10        53.19         3.91        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.48         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        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1831 TCGA-27-1832 
        1.22         1.58         7.92         2.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2518 TCGA-27-2519 
       18.25        33.14        21.30        30.05        24.76        10.39 
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-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5215 
        7.30         3.91        15.58        14.53        31.27         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.95         7.36        22.78        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        7.50         4.54         3.65         9.17        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                         0.23                          0.10 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                        82.59                        127.59 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                       11.785                         9.765 
[1] "0.2 - 82.6 (11.8)" "0.1 - 127.6 (9.8)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED    25  51
  DEL PEAK 13(4P16.3) WILD-TYPE 195 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED     25   51
  DEL PEAK 13(4P16.3) WILD-TYPE  195  289
        clus
vv       DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  FEMALE                          25                           195
  MALE                            51                           289
[1] 2 2
[1] FALSE
D38V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 13(4P16.3) MUTATED                               1
  DEL PEAK 13(4P16.3) WILD-TYPE                            16
                               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
D38V5, multiclass
                                 clus
vv                                DEL PEAK 13(4P16.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          74
                                 clus
vv                                DEL PEAK 13(4P16.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              16
  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"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED    58  18
  DEL PEAK 13(4P16.3) WILD-TYPE 324 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED     58   18
  DEL PEAK 13(4P16.3) WILD-TYPE  324  160
     clus
vv    DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  NO                           58                           324
  YES                          18                           160
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4P16.3) MUTATED       3                         5    63
  DEL PEAK 13(4P16.3) WILD-TYPE    10                        34   422
D38V7, multiclass
                           clus
vv                          DEL PEAK 13(4P16.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              63
                           clus
vv                          DEL PEAK 13(4P16.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            34
  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  60
  DEL PEAK 13(4P16.3) WILD-TYPE  10 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      2   60
  DEL PEAK 13(4P16.3) WILD-TYPE   10  402
                        clus
vv                       DEL PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           402
[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    17  72
  DEL PEAK 14(4Q34.3) WILD-TYPE  81 390
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           89                           471 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                           72                           390 
$`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        32.52        22.16        11.80 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0192 TCGA-06-0216 
        5.29         2.20         2.73         2.01        18.31        22.49 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 
       35.01        12.33         3.22        19.56         3.58        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-08-0246 TCGA-08-0350 TCGA-08-0351 
        4.57         7.79         5.39         3.91         3.42        53.82 
TCGA-08-0354 TCGA-08-0356 TCGA-08-0358 TCGA-08-0386 TCGA-12-0619 TCGA-12-0691 
       15.06        14.70        19.53        15.72        10.39         6.12 
TCGA-12-0769 TCGA-12-0827 TCGA-12-1098 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 
       12.43        38.76         3.98         9.44        59.41        43.23 
TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-0787 TCGA-14-0813 TCGA-14-0862 
       11.74        15.12        11.97         2.24         1.35         2.89 
TCGA-14-0867 TCGA-14-1453 TCGA-14-1454 TCGA-14-1458 TCGA-14-1821 TCGA-14-1823 
        2.04         1.15        30.18         6.15        17.79        17.85 
TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 TCGA-19-1387 
        9.86        53.19         5.52         9.93        29.03         5.95 
TCGA-19-1388 TCGA-19-1390 TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-1442 
       12.95        25.38        16.47         7.04        16.57        31.33 
TCGA-27-1838 TCGA-27-2518 TCGA-28-1749 TCGA-28-1756 TCGA-28-2514 TCGA-28-5214 
       11.51        24.76         9.21         2.83         5.26        14.20 
TCGA-28-5220 TCGA-32-1973 TCGA-32-2491 TCGA-32-2632 TCGA-32-2634 TCGA-32-4208 
       10.49        21.07        12.23         8.84        22.78        21.14 
TCGA-41-5651 TCGA-76-4934 TCGA-76-6285 TCGA-76-6286 TCGA-OX-A56R 
       11.54         2.53         8.35        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 
        9.17         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        55.86        77.65        20.12 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
        4.04        47.31         0.10         3.58        22.72        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       18.74        14.07        23.08        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        46.59        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0176 TCGA-06-0178 
       19.04         3.12        13.02         0.23        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       12.43         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        8.05         0.16         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        22.32         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 
        5.42        20.94         7.43         6.35         8.65         7.89 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         4.37        31.50        11.24 
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         3.95         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0344 
        1.87         3.12         2.56        22.68        34.75       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
        6.41        22.52        35.64         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 
       25.97        24.13         2.63        18.12        28.41        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       11.97        11.38        15.85         9.11        14.53         3.42 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61         6.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       11.77        34.52        13.12         3.22         2.04         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 
        6.21        23.05        11.24        13.78         3.25         5.39 
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-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        7.10         0.92        40.96        12.43         0.99         1.97 
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-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
        3.42        50.53        19.10         3.91        26.07        16.31 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 
       14.27         3.39        10.75         9.07         4.64         3.48 
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-19-2631 TCGA-19-5947 
        1.08         7.53         0.16         4.08         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 
        6.51         5.39         5.29         5.42         3.98        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
       13.87         9.73         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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       30.05        14.04        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 
        2.86        14.40        15.78         0.20         2.53         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 
        7.63         8.48         1.22         1.55         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         4.77         7.30         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
       22.68         5.42        15.39         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-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2638 TCGA-32-4210 
       20.78        15.02        15.95         7.36        21.17         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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  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 
                        59.41                        127.59 
  DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE 
                        12.23                          9.67 
[1] "0.4 - 59.4 (12.2)" "0.1 - 127.6 (9.7)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q34.3) MUTATED    26  63
  DEL PEAK 14(4Q34.3) WILD-TYPE 194 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED     26   63
  DEL PEAK 14(4Q34.3) WILD-TYPE  194  277
        clus
vv       DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE
  FEMALE                          26                           194
  MALE                            63                           277
[1] 2 2
[1] FALSE
D39V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 14(4Q34.3) MUTATED                               2
  DEL PEAK 14(4Q34.3) WILD-TYPE                            15
                               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
D39V5, multiclass
                                 clus
vv                                DEL PEAK 14(4Q34.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          85
                                 clus
vv                                DEL PEAK 14(4Q34.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              15
  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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q34.3) MUTATED    67  22
  DEL PEAK 14(4Q34.3) WILD-TYPE 315 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED     67   22
  DEL PEAK 14(4Q34.3) WILD-TYPE  315  156
     clus
vv    DEL PEAK 14(4Q34.3) MUTATED DEL PEAK 14(4Q34.3) WILD-TYPE
  NO                           67                           315
  YES                          22                           156
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q34.3) MUTATED       4                         8    77
  DEL PEAK 14(4Q34.3) WILD-TYPE     9                        31   408
D39V7, multiclass
                           clus
vv                          DEL PEAK 14(4Q34.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              77
                           clus
vv                          DEL PEAK 14(4Q34.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            31
  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  71
  DEL PEAK 14(4Q34.3) WILD-TYPE  10 391
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q34.3) MUTATED      2   71
  DEL PEAK 14(4Q34.3) WILD-TYPE   10  391
                        clus
vv                       DEL PEAK 14(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK 14(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           391
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 15(5Q35.3) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q35.3) MUTATED    12  40
  DEL PEAK 15(5Q35.3) WILD-TYPE  86 422
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                           52                           508 
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                           40                           422 
$`DEL PEAK 15(5Q35.3) MUTATED`
TCGA-02-0010 TCGA-02-0011 TCGA-02-0025 TCGA-02-0026 TCGA-02-0052 TCGA-02-0070 
       35.41        20.71        42.74        24.59        12.59        25.05 
TCGA-02-0084 TCGA-02-0099 TCGA-02-0104 TCGA-02-2483 TCGA-06-0128 TCGA-06-0188 
        0.23         3.48        65.00        15.32        22.72        28.47 
TCGA-06-0237 TCGA-06-0414 TCGA-06-0644 TCGA-06-0649 TCGA-06-0686 TCGA-06-0744 
       10.36        35.01        12.33         2.04         9.40        19.56 
TCGA-06-1087 TCGA-06-2569 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 TCGA-08-0386 
        3.58         0.43         7.79       108.82         3.42        15.72 
TCGA-08-0516 TCGA-08-0517 TCGA-12-0818 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 
       18.44        58.19        91.76        11.74        11.97         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-1395 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 
       16.50         2.04         1.38         1.15        17.79         3.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-0960 TCGA-19-1387 TCGA-19-4065 
       50.53        53.19        16.31         8.61         5.95         7.04 
TCGA-26-5133 TCGA-27-1834 TCGA-27-2521 TCGA-28-1756 TCGA-28-5215 TCGA-41-3392 
       14.86        33.14        10.39         2.83         7.79         0.99 
TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 TCGA-76-4929 
        0.20        11.54         4.80         3.65 

$`DEL PEAK 15(5Q35.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0014 
        9.17         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-02-0027 
       20.61        55.86        77.65        20.12        53.10        10.36 
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-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 
       18.31         6.87        14.73         3.22        15.09         6.54 
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-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       26.43        28.70         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-02-0106 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-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         0.16        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-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.45        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.31         0.10         3.58        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        2.53        40.37        73.84        26.33        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 
        0.16         3.22         4.47         9.67        23.57        22.32 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.24         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-06-6694 
        4.57         3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 
        1.87         3.12         2.56        22.68        34.75         3.91 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 
        1.74         4.34        13.78        10.39         7.59        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       19.53         0.95         9.17        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 
        0.30         0.56         3.52        11.77         8.52         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        5.49         9.11        14.86        14.27        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-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         0.95         6.21        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-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1396 
       26.33        28.93        15.95        19.30         0.79         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         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
        3.42         9.86        19.10         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
        0.43        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.48         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-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        16.47         7.00         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 
        9.73        31.33         7.13         9.37         9.40         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        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        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-28-1757 TCGA-28-2502 
        7.63         8.48         1.22         1.55         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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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        21.17        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        10.62         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 
       13.35         8.94         9.53         4.44        11.84         7.76 
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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         9.17         2.53        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                          0.2                           0.1 
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                       108.82                        127.59 
  DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE 
                       11.855                         9.880 
[1] "0.2 - 108.8 (11.9)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q35.3) MUTATED    20  32
  DEL PEAK 15(5Q35.3) WILD-TYPE 200 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q35.3) MUTATED     20   32
  DEL PEAK 15(5Q35.3) WILD-TYPE  200  308
        clus
vv       DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE
  FEMALE                          20                           200
  MALE                            32                           308
[1] 2 2
[1] FALSE
D40V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 15(5Q35.3) MUTATED                               1
  DEL PEAK 15(5Q35.3) WILD-TYPE                            16
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 15(5Q35.3) MUTATED                     1
  DEL PEAK 15(5Q35.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 15(5Q35.3) MUTATED                                50
  DEL PEAK 15(5Q35.3) WILD-TYPE                             475
D40V5, multiclass
                                 clus
vv                                DEL PEAK 15(5Q35.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          50
                                 clus
vv                                DEL PEAK 15(5Q35.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              16
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           475
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q35.3) MUTATED    39  13
  DEL PEAK 15(5Q35.3) WILD-TYPE 343 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q35.3) MUTATED     39   13
  DEL PEAK 15(5Q35.3) WILD-TYPE  343  165
     clus
vv    DEL PEAK 15(5Q35.3) MUTATED DEL PEAK 15(5Q35.3) WILD-TYPE
  NO                           39                           343
  YES                          13                           165
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q35.3) MUTATED       1                         5    46
  DEL PEAK 15(5Q35.3) WILD-TYPE    12                        34   439
D40V7, multiclass
                           clus
vv                          DEL PEAK 15(5Q35.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              46
                           clus
vv                          DEL PEAK 15(5Q35.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            34
  WHITE                                               439
[1] 3 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(5Q35.3) MUTATED     3  40
  DEL PEAK 15(5Q35.3) WILD-TYPE   9 422
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q35.3) MUTATED      3   40
  DEL PEAK 15(5Q35.3) WILD-TYPE    9  422
                        clus
vv                       DEL PEAK 15(5Q35.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       DEL PEAK 15(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           422
[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    22 134
  DEL PEAK 16(6Q22.31) WILD-TYPE  76 328
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           156                            404 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                           134                            328 
$`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 
        0.26        10.52        22.16         9.21        12.79         2.56 
TCGA-06-0166 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0192 TCGA-06-0201 
        5.29        40.37        73.84        26.33        18.31         0.39 
TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0402 TCGA-06-0644 
        3.91        12.43        22.49         0.36         0.26        12.33 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
        4.47         2.04         0.92        15.32         1.08         9.27 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
       11.24         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         3.91 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0392 
        6.41        22.52        19.53         9.17        10.85         0.30 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 
        3.52        11.77        58.19        15.98        14.01        14.43 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0691 TCGA-12-0692 TCGA-12-0772 TCGA-12-0780 
        7.17        65.92         6.12         2.63        53.10        14.27 
TCGA-12-0822 TCGA-12-1093 TCGA-12-1095 TCGA-12-1098 TCGA-12-1099 TCGA-12-1602 
       23.51        11.97        15.85         3.98         3.42         6.41 
TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0787 TCGA-14-0817 
       43.23        11.74         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 
        9.86         3.91         4.31        29.03         3.65        13.97 
TCGA-19-0962 TCGA-19-1392 TCGA-19-2619 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 
        0.43         3.48         9.67        16.47         7.04         6.64 
TCGA-19-5952 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1443 
       18.64         5.42         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        18.25         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         3.91         9.04        14.53        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-74-6573 TCGA-74-6575 TCGA-76-4925 
        0.99         0.20        11.54         3.45        20.91         4.80 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-6282 TCGA-76-6285 TCGA-OX-A56R 
        3.09         3.65         9.17        17.06         8.35         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 
        9.17        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 
       55.86        77.65        53.10        42.74        10.36        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         0.23        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 
        0.16        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 
       16.21         2.70         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
       22.72        32.52        18.74        14.07        23.08        10.75 
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        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
        9.80         7.86        19.46        46.59        11.80         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46         9.44        11.80        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0188 
       91.00         2.01        53.98        19.00         2.53        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 
       14.93        10.29         4.67         7.04         2.60         6.48 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0221 TCGA-06-0237 
        5.49         4.96        11.84         0.20        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       11.80        20.42        14.96        10.32         5.52        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 
        4.70         8.05         0.16        35.01         3.22         9.67 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17        43.46        46.19         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79         8.65         7.89        13.61        33.90         0.76 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93         2.83        30.64         5.95         6.81         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         3.95         7.79         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        0.49         8.32        12.85         4.77         4.77         4.96 
TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        3.12        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 
       15.06        14.70        35.64         0.95        15.72         3.19 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 
       10.59         0.56         8.52        18.44         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 
        4.80         6.54        17.33         5.52         1.64        10.39 
TCGA-12-0620 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 
        5.95         0.10        38.17        25.97        24.13        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        12.43        43.10         5.49         9.11        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 TCGA-12-1599 
       21.63        11.38         9.11        14.53         9.44        25.28 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       13.61        59.41        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       34.52        13.12         2.04        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
       23.05        11.24        13.78         3.25         1.35         2.89 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        28.93        15.95         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-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        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-14-3477 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
        3.78        50.53        19.10        53.19         5.52         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 
       26.07        16.31         0.82         9.90        13.35        18.28 
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-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 
        7.17        12.66         3.25         0.13         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 
        7.53         0.16         4.08         7.00        11.28         8.02 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
       16.57         9.73        31.33         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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        4.80        16.60        33.14        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 
       11.51        24.76        10.39        10.39        16.08        14.40 
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-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        1.22         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 
       15.58        11.77        14.20         7.79        13.64         4.21 
TCGA-28-5219 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
       22.68        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
       19.50         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 
       20.78         7.36         8.84        21.17        19.86        10.62 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6577 
        8.94         9.53         4.44        11.84         7.76         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4934 TCGA-76-4935 
       14.33         8.22         7.50         4.54         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29         2.70        11.38        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  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 
                         92.65                         127.59 
  DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE 
                          9.24                          10.39 
[1] "0.2 - 92.7 (9.2)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
                                cls
clus                               0   1
  DEL PEAK 16(6Q22.31) MUTATED    70  86
  DEL PEAK 16(6Q22.31) WILD-TYPE 150 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED     70   86
  DEL PEAK 16(6Q22.31) WILD-TYPE  150  254
        clus
vv       DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE
  FEMALE                           70                            150
  MALE                             86                            254
[1] 2 2
[1] FALSE
D41V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 16(6Q22.31) MUTATED                               5
  DEL PEAK 16(6Q22.31) WILD-TYPE                            12
                                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
D41V5, multiclass
                                 clus
vv                                DEL PEAK 16(6Q22.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                          144
                                 clus
vv                                DEL PEAK 16(6Q22.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               12
  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"
D41V6, binary
                                cls
clus                               0   1
  DEL PEAK 16(6Q22.31) MUTATED   106  50
  DEL PEAK 16(6Q22.31) WILD-TYPE 276 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED    106   50
  DEL PEAK 16(6Q22.31) WILD-TYPE  276  128
     clus
vv    DEL PEAK 16(6Q22.31) MUTATED DEL PEAK 16(6Q22.31) WILD-TYPE
  NO                           106                            276
  YES                           50                            128
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q22.31) MUTATED       5                        14   130
  DEL PEAK 16(6Q22.31) WILD-TYPE     8                        25   355
D41V7, multiclass
                           clus
vv                          DEL PEAK 16(6Q22.31) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              130
                           clus
vv                          DEL PEAK 16(6Q22.31) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             25
  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     1 132
  DEL PEAK 16(6Q22.31) WILD-TYPE  11 330
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(6Q22.31) MUTATED      1  132
  DEL PEAK 16(6Q22.31) WILD-TYPE   11  330
                        clus
vv                       DEL PEAK 16(6Q22.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          132
                        clus
vv                       DEL PEAK 16(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            330
[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    26 151
  DEL PEAK 17(6Q26) WILD-TYPE  72 311
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        177                         383 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        151                         311 
$`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 
       10.36        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         4.04        47.31 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0142 TCGA-06-0155 TCGA-06-0162 
       10.52        22.16         9.21         2.20         8.65         2.56 
TCGA-06-0166 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0209 TCGA-06-0214 
        5.29        40.37        73.84        26.33         3.91        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 
       22.49         0.36        12.33         4.47         2.04         0.92 
TCGA-06-0878 TCGA-06-0882 TCGA-06-1084 TCGA-06-1087 TCGA-06-1806 TCGA-06-2557 
        7.17         5.42         7.43         3.58        15.32         1.08 
TCGA-06-2561 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 TCGA-06-5416 
        9.27        11.24         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         3.91         6.41        22.52        14.70        19.53 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 
        9.17        10.85         0.30         3.52        11.77        58.19 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       15.98        14.01        14.43         7.17        65.92         0.10 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0780 
        6.12         2.63        28.41        12.43        53.10        14.27 
TCGA-12-0822 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1095 TCGA-12-1099 
       23.51         5.82        30.54        11.97        15.85         3.42 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0817 
        6.41        43.23        11.74         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         9.86        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         0.82         3.65        13.97         0.43         9.07 
TCGA-19-1392 TCGA-19-1789 TCGA-19-2619 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        3.48         3.25         9.67        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 
        6.64        18.64         6.51         5.42         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        18.25        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         3.91         9.04        14.53        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-74-6573 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-6282 
       11.54         3.45         3.09         3.65         9.17        17.06 
TCGA-76-6285 TCGA-81-5911 TCGA-OX-A56R 
        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 
        9.17        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 
       55.86        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         0.23        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         0.16        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        16.21         2.70         0.26         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        32.52        18.74        14.07        23.08 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.75         0.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46         9.44        11.80        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0188 
       91.00         2.01        53.98        19.00         2.53        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         5.49         4.96        11.84         0.20 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
       35.01         3.22         9.67        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 
       19.56         5.39         2.70         2.17        43.46        46.19 
TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 
        5.65        22.98         5.85        20.94         6.35        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
        8.65         7.89        13.61        33.90         0.76         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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         3.95         7.79         1.48         0.49         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0244 
       12.85         4.77         4.77         4.96         3.12        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       34.75       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0357 
        7.59         3.42        53.82         1.28        15.06        35.64 
TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 
        0.95        15.72         3.19        10.59         0.56         8.52 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       18.44         1.28        10.75         4.80         6.54        17.33 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 
        5.52         1.64        10.39         5.95        38.17        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       24.13        18.12        43.10         5.49         9.11        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-12-1090 TCGA-12-1092 TCGA-12-1094 
        8.94        20.58       127.59         6.25        21.63        11.38 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98         9.44        25.28        13.61 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
       13.12         2.04        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0866 
        2.24        11.24        13.78         3.25         1.35        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1043 TCGA-14-1396 TCGA-14-1401 
        2.04        28.93        15.95         0.79         1.12         3.75 
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-14-1825 
        6.15        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-15-1444 
        5.88         7.17        17.49         7.96         3.78        50.53 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1055 
       53.19         5.52         9.93        26.07        16.31         9.90 
TCGA-16-1056 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       13.35        18.28         6.41        11.77        21.90         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
       14.27         3.39        10.75         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 
       25.38         7.17        12.66         0.13         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 
        7.53         0.16         4.08        11.28         8.02         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1438 
        7.96         1.78         5.39         5.29        16.57        10.03 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
        9.73        31.33         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.22         1.58         2.33         4.80        16.60 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 
       33.14        21.30        30.05        14.04        11.51        10.39 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 
       16.08         2.86        14.40        15.78         0.20         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        7.63         8.48         1.55         2.83         0.13         0.66 
TCGA-28-2513 TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
        7.30        15.58        11.77        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        0.10        19.50        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4213 
       20.78         7.36         8.84        22.78        21.17        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 
       10.62         0.85         8.94         9.53         4.44        11.84 
TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        4.80         4.54         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        11.38        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        9.27         7.73         7.79         1.61        26.30 

  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 
                      92.65                      127.59 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       9.27                       10.39 
[1] "0.1 - 92.7 (9.3)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    76 101
  DEL PEAK 17(6Q26) WILD-TYPE 144 239
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     76  101
  DEL PEAK 17(6Q26) WILD-TYPE  144  239
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        76                         144
  MALE                         101                         239
[1] 2 2
[1] FALSE
D42V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 17(6Q26) MUTATED                               6                   9
  DEL PEAK 17(6Q26) WILD-TYPE                            11                   9
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 17(6Q26) MUTATED                               162
  DEL PEAK 17(6Q26) WILD-TYPE                             363
D42V5, multiclass
                                 clus
vv                                DEL PEAK 17(6Q26) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           6
  TREATED PRIMARY GBM                                     9
  UNTREATED PRIMARY (DE NOVO) GBM                       162
                                 clus
vv                                DEL PEAK 17(6Q26) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            11
  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"
D42V6, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED   122  55
  DEL PEAK 17(6Q26) WILD-TYPE 260 123
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED    122   55
  DEL PEAK 17(6Q26) WILD-TYPE  260  123
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                        122                         260
  YES                        55                         123
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED       4                        15   151
  DEL PEAK 17(6Q26) WILD-TYPE     9                        24   334
D42V7, multiclass
                           clus
vv                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        15
  WHITE                                           151
                           clus
vv                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          24
  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     2 150
  DEL PEAK 17(6Q26) WILD-TYPE  10 312
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      2  150
  DEL PEAK 17(6Q26) WILD-TYPE   10  312
                        clus
vv                       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                       150                         312
[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  52
  DEL PEAK 18(8P23.2) WILD-TYPE  85 410
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           65                           495 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           52                           410 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-02-0001 TCGA-02-0009 TCGA-02-0025 TCGA-02-0051 TCGA-02-0059 TCGA-02-0060 
        9.17        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        16.21         9.44         3.12        13.02         7.04 
TCGA-06-0216 TCGA-06-0410 TCGA-06-0743 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 
       22.49         4.70        22.32        11.24         8.35         8.81 
TCGA-06-6693 TCGA-06-A5U1 TCGA-08-0246 TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 
        0.49         1.87         3.91         0.30         3.52        15.98 
TCGA-12-0691 TCGA-12-0776 TCGA-12-0826 TCGA-12-0827 TCGA-12-1093 TCGA-12-1098 
        6.12         9.11        27.78        38.76        11.97         3.98 
TCGA-12-1598 TCGA-12-3651 TCGA-14-0736 TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 
        9.44        11.77        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        13.35        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         1.22        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-76-4934 
        3.91        21.14         3.72        10.85         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        55.86        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 
       10.36        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         0.23        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 
        0.16        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 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       11.80        12.79         8.65         3.19         5.46        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 
        2.56        56.88        10.65         5.29        19.04         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         4.67         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26        70.52         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       23.57         9.40        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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         3.95         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-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.77         4.96         3.12         2.56        22.68        34.75 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       15.72         3.19        10.59         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.10         5.49        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        10.62        23.51         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         6.25        30.54        21.63        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        9.11        14.53         3.42        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.41        43.23        25.78        11.54        10.95        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       11.74        13.12         3.22         2.04        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-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        1.35         5.39        16.50        26.33         2.04        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-14-1451 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-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
        6.15        12.43         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 
        4.31        29.03         0.82         9.90         3.65        18.28 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         0.43        14.27         3.39 
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         3.48 
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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03         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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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        10.39 
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-28-1755 TCGA-28-1756 
        9.21         7.63         8.48         1.22         1.55         2.83 
TCGA-28-2506 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        6.74         7.30         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        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-32-4211 TCGA-32-4213 TCGA-32-5222 
        8.84        22.78        21.17        12.59        19.86        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        10.78        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         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  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 
                        58.78                        127.59 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         9.17                         10.36 
[1] "0.1 - 58.8 (9.2)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D43V2, continuous
D43V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    29  36
  DEL PEAK 18(8P23.2) WILD-TYPE 191 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     29   36
  DEL PEAK 18(8P23.2) WILD-TYPE  191  304
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                          29                           191
  MALE                            36                           304
[1] 2 2
[1] FALSE
D43V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 18(8P23.2) MUTATED                               2
  DEL PEAK 18(8P23.2) WILD-TYPE                            15
                               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
D43V5, multiclass
                                 clus
vv                                DEL PEAK 18(8P23.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          62
                                 clus
vv                                DEL PEAK 18(8P23.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              15
  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"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    46  19
  DEL PEAK 18(8P23.2) WILD-TYPE 336 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     46   19
  DEL PEAK 18(8P23.2) WILD-TYPE  336  159
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                           46                           336
  YES                          19                           159
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED       5                         3    53
  DEL PEAK 18(8P23.2) WILD-TYPE     8                        36   432
D43V7, multiclass
                           clus
vv                          DEL PEAK 18(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              53
                           clus
vv                          DEL PEAK 18(8P23.2) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            36
  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  56
  DEL PEAK 18(8P23.2) WILD-TYPE  12 406
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      0   56
  DEL PEAK 18(8P23.2) WILD-TYPE   12  406
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           406
[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    67 342
  DEL PEAK 19(9P21.3) WILD-TYPE  31 120
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          409                           151 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                          342                           120 
$`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        55.86 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0027 TCGA-02-0037 TCGA-02-0038 
       77.65        20.12        53.10        10.36         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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 
       18.74        14.07        23.08        10.75         9.21         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       11.74         2.33         9.80        19.46        46.59        12.79 
TCGA-06-0155 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0169 
        8.65         5.46         2.56        56.88         5.29         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 
       13.02         0.23         2.73         2.01        19.00        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0208 
       26.33        28.47        10.29        18.31         0.39         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        3.91         4.96        11.84        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       18.02        10.36        14.96        10.32         5.52        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.67         2.04        23.57        22.32        19.56         5.39 
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 
       22.98         5.42         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
        8.65         7.89        13.61        15.32         1.08         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        0.43        11.24         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         3.95         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0352 
        3.91         1.74         4.34        13.78        10.39         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
        0.95         9.17        10.59         0.30         0.56         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
        8.52        18.44        58.19         1.28        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       17.33         5.52        14.01         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 
        0.10        25.97        24.13         6.12         2.63        28.41 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
        5.49        14.86        14.27        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-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1602 TCGA-12-3648 
       14.53         3.98         3.42        25.28         6.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-0813 TCGA-14-0817 
       23.05         2.24        11.24        13.78         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
        2.89        16.50        26.33        28.93        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 
        1.38         1.12         3.75        32.05         7.10         1.15 
TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        0.92         6.15        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-15-1447 TCGA-15-1449 TCGA-16-0846 
        9.86        50.53        19.10        53.19         5.52         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       18.28        13.97        11.77         8.61         0.43        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-19-1789 TCGA-19-1791 TCGA-19-2619 
       25.38         3.48         7.17         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        4.87         4.08        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 
        6.51         5.39         5.29         3.98        16.57        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5134 TCGA-26-5139 
        9.73        31.33         7.13         9.37         5.49         1.58 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       30.05        14.04        10.39        16.08         7.59         2.86 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 
       15.78         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         3.91        15.58        14.53        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        7.79        13.64        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 
       16.93        20.78        15.02        15.95        21.17        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 
        3.72        12.59        19.86        10.85        10.62        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 
        8.94         9.53         0.99         4.44         0.20         7.76 
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 
       10.78        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         0.23         7.79         1.61        26.30 
TCGA-OX-A56R 
        5.92 

$`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 
        9.17         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         0.23        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        32.52        10.52        22.16         0.20 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0157 TCGA-06-0159 
       20.09        16.70         7.86        11.80         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        19.04         2.20        91.00        53.98 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
        2.53        40.37        14.93         4.67         7.04         2.60 
TCGA-06-0206 TCGA-06-0213 TCGA-06-0238 TCGA-06-0240 TCGA-06-0402 TCGA-06-0414 
        6.48         0.20        11.80        20.42         0.26        35.01 
TCGA-06-0686 TCGA-06-0749 TCGA-06-0881 TCGA-06-0939 TCGA-06-1805 TCGA-06-2558 
        9.40         2.17         5.85        20.94        33.90         0.76 
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-08-0245 TCGA-08-0344 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.77        34.75       108.82         7.59         3.42        53.82 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0512 TCGA-08-0521 TCGA-08-0524 
       10.85        15.72         3.19        11.77         4.80         6.54 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0662 TCGA-12-0703 TCGA-12-0769 
       14.43         1.64        10.39        38.17        18.12        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 TCGA-12-0820 TCGA-12-1090 TCGA-12-1096 
       53.10        43.10         9.11        18.48         6.25         9.11 
TCGA-12-1598 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-14-0812 TCGA-14-0867 
        9.44        13.61        59.41        43.23         3.25         2.04 
TCGA-14-1034 TCGA-14-1450 TCGA-14-1451 TCGA-14-1454 TCGA-14-1456 TCGA-14-1794 
       15.95        58.78        23.11        30.18        40.96         0.99 
TCGA-14-3477 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1460 TCGA-19-0957 
        3.78         9.93        26.07        16.31         6.41        21.90 
TCGA-19-1787 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-5960 TCGA-26-1438 
       12.66         1.08         7.53         0.16         5.42        10.03 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 TCGA-27-1835 
        9.40        14.86         8.88         1.22         7.92        21.30 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2527 TCGA-28-1746 TCGA-28-1752 
       11.51        24.76        10.39        14.40         0.20         8.48 
TCGA-28-2509 TCGA-28-5207 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-32-1980 
        4.77         9.04        14.20         4.21        22.68         1.18 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-41-2571 
       14.86        12.23         7.36         8.84        22.78         0.85 
TCGA-41-3915 TCGA-41-5651 TCGA-76-6193 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 
       11.84        11.54         2.70        20.98         9.27         7.73 
TCGA-81-5911 
       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                        108.82 
  DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE 
                         9.67                         10.65 
[1] "0.1 - 127.6 (9.7)"  "0.2 - 108.8 (10.7)"
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
                               cls
clus                              0   1
  DEL PEAK 19(9P21.3) MUTATED   164 245
  DEL PEAK 19(9P21.3) WILD-TYPE  56  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED    164  245
  DEL PEAK 19(9P21.3) WILD-TYPE   56   95
        clus
vv       DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE
  FEMALE                         164                            56
  MALE                           245                            95
[1] 2 2
[1] FALSE
D44V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 19(9P21.3) MUTATED                              12
  DEL PEAK 19(9P21.3) WILD-TYPE                             5
                               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
D44V5, multiclass
                                 clus
vv                                DEL PEAK 19(9P21.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            12
  TREATED PRIMARY GBM                                      15
  UNTREATED PRIMARY (DE NOVO) GBM                         382
                                 clus
vv                                DEL PEAK 19(9P21.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               5
  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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(9P21.3) MUTATED   274 135
  DEL PEAK 19(9P21.3) WILD-TYPE 108  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED    274  135
  DEL PEAK 19(9P21.3) WILD-TYPE  108   43
     clus
vv    DEL PEAK 19(9P21.3) MUTATED DEL PEAK 19(9P21.3) WILD-TYPE
  NO                          274                           108
  YES                         135                            43
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9P21.3) MUTATED       9                        31   354
  DEL PEAK 19(9P21.3) WILD-TYPE     4                         8   131
D44V7, multiclass
                           clus
vv                          DEL PEAK 19(9P21.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          31
  WHITE                                             354
                           clus
vv                          DEL PEAK 19(9P21.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  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     8 334
  DEL PEAK 19(9P21.3) WILD-TYPE   4 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9P21.3) MUTATED      8  334
  DEL PEAK 19(9P21.3) WILD-TYPE    4  128
                        clus
vv                       DEL PEAK 19(9P21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         334
                        clus
vv                       DEL PEAK 19(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           128
[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    10  66
  DEL PEAK 20(9Q34.2) WILD-TYPE  88 396
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           76                           484 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                           66                           396 
$`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        55.86        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 
       18.74         9.21         2.56         0.23         2.01         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0237 TCGA-06-0409 TCGA-06-0412 TCGA-06-0743 
        3.91         4.96        10.36        70.52         8.05        22.32 
TCGA-06-0745 TCGA-06-0879 TCGA-06-1086 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
        5.39        22.98         6.35        15.32         1.08         9.27 
TCGA-06-2565 TCGA-06-5412 TCGA-06-6694 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0246 
        6.81         4.54         7.36         1.87         2.56         3.91 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0510 TCGA-12-0707 TCGA-12-0821 TCGA-12-0826 
        6.41        22.52         3.52        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        30.54        11.97         6.41        25.78        34.52 
TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-1395 TCGA-14-1396 TCGA-14-1456 
       11.74        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 
        9.86        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 
        0.82        14.27         7.00         5.39         3.98        13.87 
TCGA-26-5136 TCGA-27-2521 TCGA-27-2528 TCGA-28-1757 TCGA-28-2506 TCGA-28-5220 
        1.22        10.39        15.78         0.13         6.74        10.49 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 
       21.14        19.86        10.85        13.35 

$`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 
        9.17         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 
       10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 
        0.10         3.58        32.52        10.52        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       22.16        10.75         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       11.80        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.02         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        6.48        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       18.02        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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         5.85         5.42        20.94         7.43         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79         8.65         7.89        13.61        33.90         0.76 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93         2.83        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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A6S0 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        3.12        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       15.06        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       18.12        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 
       14.86        14.27        91.76        24.79        18.48        23.51 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
        8.94        20.58       127.59         5.82         6.25        21.63 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 
        9.44        25.28        13.61        59.41        43.23        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       10.95        11.77        13.12         3.22         2.04         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-14-0817 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-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1401 TCGA-14-1402 
       28.93        15.95        19.30         0.79         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 
        6.15        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-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
        3.42        19.10         5.52         9.93        26.07        16.31 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         8.61         0.43         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         3.48 
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        16.47         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 
        1.78         6.51         5.29         5.42        16.57        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-27-1830 
        5.49         8.88         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
        2.86        14.40         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 
        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-28-5207 TCGA-28-5208 
        4.77         7.30         5.26         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        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-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
        7.36         8.84        22.78        21.17         3.72        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       10.62         0.85         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  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 
                        70.52                        127.59 
  DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE 
                        10.80                          9.83 
[1] "0.1 - 70.5 (10.8)" "0.1 - 127.6 (9.8)"
[1] "hr=" "1"  
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 20(9Q34.2) MUTATED    30  46
  DEL PEAK 20(9Q34.2) WILD-TYPE 190 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED     30   46
  DEL PEAK 20(9Q34.2) WILD-TYPE  190  294
        clus
vv       DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE
  FEMALE                          30                           190
  MALE                            46                           294
[1] 2 2
[1] FALSE
D45V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 20(9Q34.2) MUTATED                               5
  DEL PEAK 20(9Q34.2) WILD-TYPE                            12
                               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
D45V5, multiclass
                                 clus
vv                                DEL PEAK 20(9Q34.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             5
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          68
                                 clus
vv                                DEL PEAK 20(9Q34.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              12
  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"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK 20(9Q34.2) MUTATED    50  26
  DEL PEAK 20(9Q34.2) WILD-TYPE 332 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED     50   26
  DEL PEAK 20(9Q34.2) WILD-TYPE  332  152
     clus
vv    DEL PEAK 20(9Q34.2) MUTATED DEL PEAK 20(9Q34.2) WILD-TYPE
  NO                           50                           332
  YES                          26                           152
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(9Q34.2) MUTATED       1                         8    66
  DEL PEAK 20(9Q34.2) WILD-TYPE    12                        31   419
D45V7, multiclass
                           clus
vv                          DEL PEAK 20(9Q34.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              66
                           clus
vv                          DEL PEAK 20(9Q34.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            31
  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  68
  DEL PEAK 20(9Q34.2) WILD-TYPE  12 394
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9Q34.2) MUTATED      0   68
  DEL PEAK 20(9Q34.2) WILD-TYPE   12  394
                        clus
vv                       DEL PEAK 20(9Q34.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 20(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           394
[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    71 383
  DEL PEAK 21(10P15.3) WILD-TYPE  27  79
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           454                            106 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                           383                             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        55.86        77.65        20.12 
TCGA-02-0024 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       53.10        10.36         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         0.23 
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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        4.04         0.10        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       22.16        10.75         0.20         9.21        11.74         2.33 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
       16.70         7.86        19.46        46.59        11.80         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
        3.19         5.46         9.44         2.56        56.88         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
        2.01        19.00        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       14.96        10.32         0.26        70.52         4.70        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
        5.85         5.42        20.94         7.43         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 
        8.65         7.89        13.61         1.08         0.76         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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         3.95         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        4.77         1.87         2.56        22.68        34.75         3.91 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0520 TCGA-08-0521 
        0.56         3.52        11.77         8.52        10.75         4.80 
TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       20.58        30.54        11.97        11.38        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         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-1821 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-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
        7.96         9.86        19.10         5.52         3.91         9.93 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       13.97        11.77        21.90         0.43        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         3.48 
TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        7.17         3.25         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        9.73         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.22         1.58         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 
       18.25        33.14        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 
       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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79        13.64        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39         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-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       15.95        22.78        21.17         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        10.62         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 
        0.99         4.44        11.84         0.20         7.76         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        10.78 
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         0.23         9.27         7.73 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

$`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 
        9.17        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         0.16        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        47.31         3.58        22.72 
TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0154 TCGA-06-0160 
       32.52         2.20        20.09         9.80        12.79        11.80 
TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0213 TCGA-06-0240 
       10.65        91.00        53.98         2.53         0.20        20.42 
TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 TCGA-06-1806 
        5.52         8.05         0.16         6.35        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-08-0344 TCGA-08-0350 TCGA-08-0351 
        1.48         4.96         3.12       108.82         3.42        53.82 
TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 
        0.30        18.44        58.19         1.28         6.54        15.98 
TCGA-08-0531 TCGA-12-0773 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
        5.52        43.10       127.59         5.82         6.25        21.63 
TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-3477 TCGA-14-4157 
        3.42         1.12        40.96         6.15         3.78         3.42 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 
       50.53        53.19        26.07        16.31         4.31         6.41 
TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-5958 
        8.61        25.38        12.66         0.13         9.67         5.39 
TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 TCGA-27-1838 TCGA-27-2521 TCGA-27-2526 
       31.33         7.13         7.92        11.51        10.39         2.86 
TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1991 TCGA-32-2616 
        1.55         2.83         4.21        21.07        16.93         7.36 
TCGA-32-2632 TCGA-32-4208 TCGA-41-5651 TCGA-76-6664 
        8.84        21.14        11.54         7.79 

  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 
                         92.65                         127.59 
  DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE 
                          9.86                          11.67 
[1] "0.1 - 92.7 (9.9)"   "0.1 - 127.6 (11.7)"
[1] "hr=" "1.8"
D46V2, continuous
D46V3, binary
                                cls
clus                               0   1
  DEL PEAK 21(10P15.3) MUTATED   172 282
  DEL PEAK 21(10P15.3) WILD-TYPE  48  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED    172  282
  DEL PEAK 21(10P15.3) WILD-TYPE   48   58
        clus
vv       DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE
  FEMALE                          172                             48
  MALE                            282                             58
[1] 2 2
[1] FALSE
D46V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 21(10P15.3) MUTATED                              10
  DEL PEAK 21(10P15.3) WILD-TYPE                             7
                                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
D46V5, multiclass
                                 clus
vv                                DEL PEAK 21(10P15.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             10
  TREATED PRIMARY GBM                                       11
  UNTREATED PRIMARY (DE NOVO) GBM                          433
                                 clus
vv                                DEL PEAK 21(10P15.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                7
  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"
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(10P15.3) MUTATED   308 146
  DEL PEAK 21(10P15.3) WILD-TYPE  74  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED    308  146
  DEL PEAK 21(10P15.3) WILD-TYPE   74   32
     clus
vv    DEL PEAK 21(10P15.3) MUTATED DEL PEAK 21(10P15.3) WILD-TYPE
  NO                           308                             74
  YES                          146                             32
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10P15.3) MUTATED       8                        30   396
  DEL PEAK 21(10P15.3) WILD-TYPE     5                         9    89
D46V7, multiclass
                           clus
vv                          DEL PEAK 21(10P15.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           30
  WHITE                                              396
                           clus
vv                          DEL PEAK 21(10P15.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  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     8 369
  DEL PEAK 21(10P15.3) WILD-TYPE   4  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10P15.3) MUTATED      8  369
  DEL PEAK 21(10P15.3) WILD-TYPE    4   93
                        clus
vv                       DEL PEAK 21(10P15.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          369
                        clus
vv                       DEL PEAK 21(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             93
[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    72 384
  DEL PEAK 22(10P13) WILD-TYPE  26  78
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         456                          104 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                         384                           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        55.86        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        10.36         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         0.23        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 
        2.70         0.26         4.04         0.10        22.72        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
        9.21        11.74         2.33        16.70         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         2.56        56.88         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.02         0.23         2.20         2.73         2.01        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        5.49         3.91         4.96        11.84        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        10.36        11.80        14.96        10.32 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 
        0.26        70.52         4.70         8.05        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
        7.89        13.61         1.08         0.76         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95         6.81         5.98         4.37        11.24 
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         3.95         5.39         0.49 
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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        1.87         2.56        22.68        34.75         3.91         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        4.34        13.78        10.39         7.59         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
        9.17        10.85        15.72         3.19        10.59         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 
        3.52        11.77         8.52        10.75         4.80        17.33 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        2.63        18.12        28.41        12.43        53.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        9.11        14.86        14.27        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1091 
       23.51        27.78        38.76         8.94        20.58        30.54 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0817 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-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 
       28.93        15.95        19.30         0.79         1.38         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-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        0.92        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-15-0742 
        7.63         5.88         7.17        17.49         7.96         9.86 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       19.10         5.52         9.93        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       13.35         3.65        18.28        13.97        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.43        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-19-2620 
       12.95         4.64         3.48         7.17         3.25         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        7.96         1.78         6.51         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 
       16.57        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         1.22         1.58         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        24.76        10.39        10.39        16.08         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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 
       22.68        10.49         5.42        15.39         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-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 
       20.78        15.02        15.95        22.78        21.17         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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        9.27         7.73         1.61        17.72        26.30         5.92 

$`DEL PEAK 22(10P13) WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0026 
        9.17        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         0.16        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        47.31         3.58        32.52         2.20        20.09 
TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 
        9.80        11.80        10.65        91.00        53.98         2.53 
TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 
        0.20        20.42         5.52         0.16         6.35        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-A6S0 TCGA-08-0344 TCGA-08-0350 
        7.79         1.48         4.96         3.12       108.82         3.42 
TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0524 
       53.82         0.30        18.44        58.19         1.28         6.54 
TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 
       15.98         5.52        43.10        91.76       127.59         5.82 
TCGA-12-1090 TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 
        6.25        21.63         3.42         1.12        40.96         6.15 
TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
        3.78         3.42        50.53        53.19         3.91        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 
       16.31         4.31         6.41         8.61        25.38        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-5958 TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 
        0.13         9.67         5.39        31.33         7.13         7.92 
TCGA-27-1836 TCGA-27-1838 TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 
       30.05        11.51         2.86         1.55         2.83         4.21 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1991 TCGA-32-2616 TCGA-32-2632 TCGA-32-4208 
       21.07         0.49        16.93         7.36         8.84        21.14 
TCGA-41-5651 TCGA-76-6664 
       11.54         7.79 

  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 
                       92.65                       127.59 
  DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE 
                       9.900                       11.525 
[1] "0.1 - 92.7 (9.9)"   "0.1 - 127.6 (11.5)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                              cls
clus                             0   1
  DEL PEAK 22(10P13) MUTATED   171 285
  DEL PEAK 22(10P13) WILD-TYPE  49  55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED    171  285
  DEL PEAK 22(10P13) WILD-TYPE   49   55
        clus
vv       DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE
  FEMALE                        171                           49
  MALE                          285                           55
[1] 2 2
[1] FALSE
D47V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 22(10P13) MUTATED                              10
  DEL PEAK 22(10P13) WILD-TYPE                             7
                              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
D47V5, multiclass
                                 clus
vv                                DEL PEAK 22(10P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           10
  TREATED PRIMARY GBM                                     11
  UNTREATED PRIMARY (DE NOVO) GBM                        435
                                 clus
vv                                DEL PEAK 22(10P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              7
  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"
D47V6, binary
                              cls
clus                             0   1
  DEL PEAK 22(10P13) MUTATED   312 144
  DEL PEAK 22(10P13) WILD-TYPE  70  34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED    312  144
  DEL PEAK 22(10P13) WILD-TYPE   70   34
     clus
vv    DEL PEAK 22(10P13) MUTATED DEL PEAK 22(10P13) WILD-TYPE
  NO                         312                           70
  YES                        144                           34
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P13) MUTATED       8                        30   398
  DEL PEAK 22(10P13) WILD-TYPE     5                         9    87
D47V7, multiclass
                           clus
vv                          DEL PEAK 22(10P13) MUTATED
  ASIAN                                              8
  BLACK OR AFRICAN AMERICAN                         30
  WHITE                                            398
                           clus
vv                          DEL PEAK 22(10P13) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            9
  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     8 371
  DEL PEAK 22(10P13) WILD-TYPE   4  91
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(10P13) MUTATED      8  371
  DEL PEAK 22(10P13) WILD-TYPE    4   91
                        clus
vv                       DEL PEAK 22(10P13) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                        371
                        clus
vv                       DEL PEAK 22(10P13) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           91
[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    73 388
  DEL PEAK 23(10P11.23) WILD-TYPE  25  74
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            461                              99 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                            388                              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        55.86        77.65        20.12 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       10.36         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         0.23        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 
       47.31         0.10         3.58        22.72        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       11.74         2.33        16.70         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        2.56        56.88         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        0.23         2.20         2.73         2.01        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        5.49         3.91         4.96        11.84        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        10.36        11.80        14.96        10.32 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 
        0.26        70.52         4.70         8.05        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
        7.89        13.61         1.08         0.76         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95         6.81         5.98         4.37        11.24 
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         3.95         5.39         0.49 
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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75         3.91         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       13.78        10.39         7.59         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       10.85        15.72         3.19        10.59         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       11.77         8.52         1.28        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       53.10         5.49         9.11        14.86        14.27        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       20.58        30.54        11.97        11.38        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         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
        9.86        19.10         5.52         9.93        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 
        9.90        13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
        9.07         5.95        12.95         4.64         3.48         7.17 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        9.73         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.22         1.58         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 
       18.25        33.14        21.30        30.05        14.04        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       10.39        10.39         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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79        13.64        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39         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-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       15.95        22.78        21.17         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        10.62         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        11.54         7.76 
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 
       10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         1.61        17.72        26.30         5.92 

$`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 
        9.17        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         0.16 
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        32.52         2.20 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 
       20.09         9.80        11.80        10.65        91.00        53.98 
TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 
        0.20        20.42         5.52         0.16         6.35        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-08-0344 
        7.79         1.48         7.36         8.32         4.96       108.82 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 
        3.42        53.82         0.30        18.44        58.19         6.54 
TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
       43.10        91.76       127.59         5.82         6.25        21.63 
TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 TCGA-14-3477 
        3.42         1.12        40.96         6.15        17.79         3.78 
TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
        3.42        50.53        53.19         3.91        26.07        16.31 
TCGA-16-0861 TCGA-16-1460 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-5956 
        4.31         6.41        25.38        12.66         0.13         6.51 
TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 TCGA-27-1838 TCGA-27-2523 TCGA-27-2526 
       31.33         7.13         7.92        11.51        16.08         2.86 
TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1991 TCGA-32-2616 
        1.55         2.83         4.21        21.07        16.93         7.36 
TCGA-32-2632 TCGA-32-4208 TCGA-76-6664 
        8.84        21.14         7.79 

  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 
                          92.65                          127.59 
  DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE 
                           9.73                           12.92 
[1] "0.1 - 92.7 (9.7)"   "0.1 - 127.6 (12.9)"
[1] "hr=" "2"  
D48V2, continuous
D48V3, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10P11.23) MUTATED   175 286
  DEL PEAK 23(10P11.23) WILD-TYPE  45  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED    175  286
  DEL PEAK 23(10P11.23) WILD-TYPE   45   54
        clus
vv       DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE
  FEMALE                           175                              45
  MALE                             286                              54
[1] 2 2
[1] FALSE
D48V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 23(10P11.23) MUTATED                              11
  DEL PEAK 23(10P11.23) WILD-TYPE                             6
                                 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
D48V5, multiclass
                                 clus
vv                                DEL PEAK 23(10P11.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              11
  TREATED PRIMARY GBM                                        10
  UNTREATED PRIMARY (DE NOVO) GBM                           440
                                 clus
vv                                DEL PEAK 23(10P11.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 6
  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"
D48V6, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10P11.23) MUTATED   313 148
  DEL PEAK 23(10P11.23) WILD-TYPE  69  30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED    313  148
  DEL PEAK 23(10P11.23) WILD-TYPE   69   30
     clus
vv    DEL PEAK 23(10P11.23) MUTATED DEL PEAK 23(10P11.23) WILD-TYPE
  NO                            313                              69
  YES                           148                              30
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10P11.23) MUTATED       8                        33   399
  DEL PEAK 23(10P11.23) WILD-TYPE     5                         6    86
D48V7, multiclass
                           clus
vv                          DEL PEAK 23(10P11.23) MUTATED
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            33
  WHITE                                               399
                           clus
vv                          DEL PEAK 23(10P11.23) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                               6
  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     8 377
  DEL PEAK 23(10P11.23) WILD-TYPE   4  85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10P11.23) MUTATED      8  377
  DEL PEAK 23(10P11.23) WILD-TYPE    4   85
                        clus
vv                       DEL PEAK 23(10P11.23) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           377
                        clus
vv                       DEL PEAK 23(10P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              85
[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    81 416
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  46
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            497                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            416                              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        55.86        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       10.36         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         0.23        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       23.08        22.16        10.75         0.20         9.21        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         2.56        56.88         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.02         0.23         2.20         2.73         2.01        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         0.26        70.52         4.70         8.05 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79         8.65         7.89        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 
        0.76         4.93         9.27         2.83         5.95         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        5.98         4.37        11.24         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 
        3.95         5.39         0.49         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         1.55         4.77         1.87         3.12         2.56 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        34.75         3.91         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       10.39         7.59         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       11.77         8.52         1.28        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       53.10         5.49         9.11        14.86        14.27        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        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1401 TCGA-14-1402 
       15.95        19.30         0.79         1.38         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-14-1459 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-14-3477 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.78         9.86        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       19.10         5.52         9.93        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48 
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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78         6.51         5.29         5.42         3.98        16.57 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87         9.73         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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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        10.39 
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-28-2509 
        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-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        14.20         7.79        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-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        21.17        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        10.62         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        11.54         7.76 
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 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
        8.35        20.98         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

$`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 
        9.17        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         0.16        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        53.98        20.42 
TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1806 TCGA-06-2563 TCGA-06-2569 
        5.52         0.16         6.35        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 
      108.82         3.42        53.82        18.44        58.19         6.54 
TCGA-12-0773 TCGA-12-0818 TCGA-12-1090 TCGA-12-1098 TCGA-14-1396 TCGA-14-1456 
       43.10        91.76         6.25         3.98         1.12        40.96 
TCGA-14-1458 TCGA-14-1821 TCGA-14-4157 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
        6.15        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         5.39        31.33         2.83 
TCGA-28-5218 TCGA-32-2616 TCGA-76-6656 
        4.21         7.36         4.83 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.10                            0.16 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         127.59                          108.82 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           9.90                           12.66 
[1] "0.1 - 127.6 (9.9)"  "0.2 - 108.8 (12.7)"
[1] "hr=" "2"  
D49V2, continuous
D49V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   194 303
  DEL PEAK 24(10Q23.31) WILD-TYPE  26  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    194  303
  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                           194                              26
  MALE                             303                              37
[1] 2 2
[1] FALSE
D49V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 24(10Q23.31) MUTATED                              12
  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
D49V5, multiclass
                                 clus
vv                                DEL PEAK 24(10Q23.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              12
  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"
D49V6, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   339 158
  DEL PEAK 24(10Q23.31) WILD-TYPE  43  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    339  158
  DEL PEAK 24(10Q23.31) WILD-TYPE   43   20
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                            339                              43
  YES                           158                              20
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED      10                        34   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                            34
  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    10 409
  DEL PEAK 24(10Q23.31) WILD-TYPE   2  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     10  409
  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                           409
                        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    83 415
  DEL PEAK 25(10Q26.3) WILD-TYPE  15  47
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           498                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           415                             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        55.86        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        10.36         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         0.23        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        9.21        11.74         2.33        20.09        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
        3.19         5.46         9.44         2.56        56.88         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        2.01        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 
       10.36        11.80        14.96        10.32         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         3.58        26.79         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5408 
       30.64         5.95         6.81         5.98         4.37        11.24 
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         3.95         5.39         0.49 
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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        4.34        13.78        10.39         7.59         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       18.12        28.41        12.43        53.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        14.27        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 
       30.54        21.63        11.97        11.38        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         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        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-14-1823 
       30.18         0.92        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-15-1449 TCGA-16-0846 
        3.42         9.86        50.53        19.10         5.52         3.91 
TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        9.93        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       13.35         3.65        18.28        13.97        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 
        8.61         0.43        14.27         3.39         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        10.39         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-28-1757 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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        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-32-1979 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-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        21.17        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        10.62         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        11.54         7.76 
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 
       10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

$`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 
        9.17        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 
        0.16        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        53.98        20.42         5.52         0.16 
TCGA-06-1086 TCGA-06-1806 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 
        6.35        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        34.75         3.42 
TCGA-08-0351 TCGA-08-0516 TCGA-08-0524 TCGA-12-0773 TCGA-12-0818 TCGA-12-1090 
       53.82        18.44         6.54        43.10        91.76         6.25 
TCGA-12-1099 TCGA-14-0871 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 
        3.42        28.93         1.12        40.96         6.15        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         4.21 
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                           0.16 
  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 
                         9.860                         12.525 
[1] "0.1 - 127.6 (9.9)"  "0.2 - 100.0 (12.5)"
[1] "hr=" "1.7"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED   194 304
  DEL PEAK 25(10Q26.3) WILD-TYPE  26  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED    194  304
  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                          194                             26
  MALE                            304                             36
[1] 2 2
[1] FALSE
D50V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 25(10Q26.3) MUTATED                              12
  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
D50V5, multiclass
                                 clus
vv                                DEL PEAK 25(10Q26.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             12
  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"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED   340 158
  DEL PEAK 25(10Q26.3) WILD-TYPE  42  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED    340  158
  DEL PEAK 25(10Q26.3) WILD-TYPE   42   20
     clus
vv    DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  NO                           340                             42
  YES                          158                             20
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q26.3) MUTATED       9                        35   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                           35
  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    10 410
  DEL PEAK 25(10Q26.3) WILD-TYPE   2  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     10  410
  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                          410
                        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    21 106
  DEL PEAK 26(11P15.5) WILD-TYPE  77 356
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           127                            433 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           106                            356 
$`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        55.86        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         0.23         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        32.52 
TCGA-06-0146 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 
       20.09         9.44         5.29         2.20         2.01        40.37 
TCGA-06-0192 TCGA-06-0197 TCGA-06-0213 TCGA-06-0216 TCGA-06-0221 TCGA-06-0238 
       18.31         2.60         0.20        22.49        18.02        11.80 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-1086 
       70.52         4.70        35.01         2.04         9.40         6.35 
TCGA-06-1800 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2569 TCGA-06-2570 
       26.79        33.90        15.32         0.76         0.43        31.50 
TCGA-06-5408 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 
       11.24         3.75         7.79         7.36        34.75         3.91 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 TCGA-08-0375 TCGA-08-0380 
       10.39        53.82         6.41        22.52         9.17        10.85 
TCGA-08-0510 TCGA-08-0517 TCGA-12-0616 TCGA-12-0619 TCGA-12-0691 TCGA-12-0772 
        3.52        58.19        14.43        10.39         6.12        53.10 
TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 
       24.79        23.51        38.76         3.42         6.41        43.23 
TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
       11.74        11.97         6.21         1.35         5.39        16.50 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 
        2.04        28.93         1.15        30.18        12.43         0.99 
TCGA-14-1821 TCGA-14-1823 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 
       17.79        17.85         3.78        50.53        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 
        3.91         9.93        16.31        29.03         5.95        25.38 
TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 
        3.48         7.53         5.29         5.42         3.98        13.87 
TCGA-26-1442 TCGA-26-5133 TCGA-27-1830 TCGA-27-2521 TCGA-28-1756 TCGA-28-2502 
       31.33        14.86         4.80        10.39         2.83         0.66 
TCGA-28-2509 TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 TCGA-32-2615 TCGA-32-2632 
        4.77        13.64        21.07         0.49        15.95         8.84 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 
       21.14         3.72        10.85        11.84         7.50         2.53 
TCGA-76-6286 
       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 
        9.17         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        10.36        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 
        0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
       47.31         0.10         3.58        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       13.02         0.23         2.73        91.00        53.98        19.00 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        2.53        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        4.67         7.04         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 
        4.96        11.84        12.43         0.36        10.36        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       14.96        10.32         5.52         0.26         8.05         0.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 
       12.33         3.22         4.47         9.67        23.57        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43         3.58         8.65         7.89        13.61 
TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        6.81         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         3.95         5.39         1.48         0.49         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        3.12         2.56        22.68       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 
       13.78         7.59         3.42         1.28        15.06        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       35.64        19.53         0.95        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 
        0.30         0.56        11.77         8.52        18.44         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.01         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        43.10         5.49         9.11        14.86        14.27 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       91.76        18.48        10.62        27.78         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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61        59.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.89        26.33        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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 
        0.92        40.96         6.15         1.97         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         9.86        19.10 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07         4.31         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        14.27         3.39        10.75         9.07        12.95 
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-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         0.16         4.08        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A6J5 TCGA-26-1438 
        7.96         1.78         6.51         5.39        16.57        10.03 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 
        9.73         7.13         9.37         9.40         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 
        1.22         1.58         7.92         2.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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        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-28-1757 TCGA-28-2506 TCGA-28-2513 
        8.48         1.22         1.55         0.13         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79         4.21        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-32-1987 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-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 
       15.02         7.36        22.78        21.17        12.59        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44         0.20        11.54         7.76         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           0.2                            0.1 
  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 
                         11.24                           9.73 
[1] "0.2 - 100.0 (11.2)" "0.1 - 127.6 (9.7)" 
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    56  71
  DEL PEAK 26(11P15.5) WILD-TYPE 164 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     56   71
  DEL PEAK 26(11P15.5) WILD-TYPE  164  269
        clus
vv       DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  FEMALE                           56                            164
  MALE                             71                            269
[1] 2 2
[1] FALSE
D51V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 26(11P15.5) MUTATED                               4
  DEL PEAK 26(11P15.5) WILD-TYPE                            13
                                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
D51V5, multiclass
                                 clus
vv                                DEL PEAK 26(11P15.5) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          117
                                 clus
vv                                DEL PEAK 26(11P15.5) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               13
  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"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    88  39
  DEL PEAK 26(11P15.5) WILD-TYPE 294 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     88   39
  DEL PEAK 26(11P15.5) WILD-TYPE  294  139
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  NO                            88                            294
  YES                           39                            139
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11P15.5) MUTATED       3                         9   110
  DEL PEAK 26(11P15.5) WILD-TYPE    10                        30   375
D51V7, multiclass
                           clus
vv                          DEL PEAK 26(11P15.5) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              110
                           clus
vv                          DEL PEAK 26(11P15.5) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             30
  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     2 103
  DEL PEAK 26(11P15.5) WILD-TYPE  10 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      2  103
  DEL PEAK 26(11P15.5) WILD-TYPE   10  359
                        clus
vv                       DEL PEAK 26(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       DEL PEAK 26(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            359
[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    17  86
  DEL PEAK 27(11P11.2) WILD-TYPE  81 376
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           103                            457 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                            86                            376 
$`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         0.23 
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 
        5.29         2.20         2.01        40.37        28.47        18.31 
TCGA-06-0197 TCGA-06-0216 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
        2.60        22.49        11.80        70.52         4.70        35.01 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1805 
        2.04         9.40        46.19         6.35        26.79        33.90 
TCGA-06-1806 TCGA-06-2570 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 
       15.32        31.50         3.75         7.79         7.36        34.75 
TCGA-08-0353 TCGA-08-0510 TCGA-12-0616 TCGA-12-0619 TCGA-12-0670 TCGA-12-0772 
        6.41         3.52        14.43        10.39        25.97        53.10 
TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 
       24.79        23.51        38.76         3.42         6.41        43.23 
TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 
       11.74        11.97         6.21         5.39        16.50         2.04 
TCGA-14-0871 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 
       28.93        30.18        12.43         0.99        17.79        17.85 
TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-16-0861 
        3.78        53.19         5.52         3.91        16.31         4.31 
TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5951 
       29.03         5.95        25.38         3.48         7.53         8.02 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-5133 TCGA-27-1830 
        5.29         5.42         3.98        13.87        14.86         4.80 
TCGA-27-2521 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 TCGA-32-1986 TCGA-32-2615 
       10.39         4.77        13.64         0.49        12.69        15.95 
TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 
        8.84         3.72        10.85        11.84         7.50         2.53 
TCGA-76-6286 
       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 
        9.17         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        55.86        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        10.36        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         0.16 
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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.31         0.10         3.58        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46        11.80         2.56        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12        13.02         0.23         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       53.98        19.00         2.53        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       10.29         4.67         7.04         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        3.91         4.96        11.84         0.20        12.43         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       18.02        10.36        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.67        23.57        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        43.46         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 
        5.85         5.42        20.94         7.43         3.58         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
        7.89        13.61         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        11.24         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 
        3.95         5.39         1.48         0.49         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-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.01         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        43.10         5.49         9.11        14.86        14.27 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       91.76        18.48        10.62        27.78         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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61        59.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-0862 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-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 
        7.10         1.15         0.92        40.96         6.15         1.97 
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-16-0848 TCGA-16-0849 TCGA-16-1047 
        9.86        50.53        19.10         9.93        26.07         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 
       10.75         9.07        12.95         4.64         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
        3.25         0.13         9.67         4.87         1.08         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03         9.73        31.33         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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        2.33        16.60         9.86        18.25        33.14        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        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-28-2513 TCGA-28-2514 
        2.83         0.13         0.66         6.74         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39        21.07         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        7.36        22.78        21.17        21.14        12.59        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44         0.20        11.54         7.76         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        10.78        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         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                          0.23                           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 
                         11.80                           9.86 
[1] "0.2 - 100.0 (11.8)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.2"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    46  57
  DEL PEAK 27(11P11.2) WILD-TYPE 174 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     46   57
  DEL PEAK 27(11P11.2) WILD-TYPE  174  283
        clus
vv       DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  FEMALE                           46                            174
  MALE                             57                            283
[1] 2 2
[1] FALSE
D52V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 27(11P11.2) MUTATED                               3
  DEL PEAK 27(11P11.2) WILD-TYPE                            14
                                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
D52V5, multiclass
                                 clus
vv                                DEL PEAK 27(11P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                           94
                                 clus
vv                                DEL PEAK 27(11P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    69  34
  DEL PEAK 27(11P11.2) WILD-TYPE 313 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     69   34
  DEL PEAK 27(11P11.2) WILD-TYPE  313  144
     clus
vv    DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  NO                            69                            313
  YES                           34                            144
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(11P11.2) MUTATED       2                         9    88
  DEL PEAK 27(11P11.2) WILD-TYPE    11                        30   397
D52V7, multiclass
                           clus
vv                          DEL PEAK 27(11P11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               88
                           clus
vv                          DEL PEAK 27(11P11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             30
  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  82
  DEL PEAK 27(11P11.2) WILD-TYPE  10 380
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED      2   82
  DEL PEAK 27(11P11.2) WILD-TYPE   10  380
                        clus
vv                       DEL PEAK 27(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 27(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            380
[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    10  85
  DEL PEAK 28(11Q14.1) WILD-TYPE  88 377
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            95                            465 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            85                            377 
$`DEL PEAK 28(11Q14.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0048 
        9.17        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        10.52         9.44         5.29 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 
        2.20         2.01        40.37        28.47        10.29        18.31 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0216 TCGA-06-0238 TCGA-06-0241 TCGA-06-0409 
        7.04         2.60        22.49        11.80        14.96        70.52 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1800 
        4.70        35.01         2.04         9.40        46.19        26.79 
TCGA-06-1806 TCGA-06-5856 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 TCGA-08-0510 
       15.32         3.75         5.39         7.36        34.75         3.52 
TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 
       10.75        14.43        10.39        53.10        24.79        23.51 
TCGA-12-1091 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       30.54         3.42         9.44         6.41        43.23        11.74 
TCGA-14-0783 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1454 
        6.21         5.39        16.50         2.04        28.93        30.18 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 
       12.43         0.99        17.85         3.78         5.52         3.91 
TCGA-16-0850 TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-5959 
       16.31        29.03         5.95        25.38         3.48         5.29 
TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 
       13.87         4.80        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 TCGA-76-6661 TCGA-81-5910 
        7.50         2.53        20.98         0.23         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 
       55.86        77.65        20.12        42.74        24.59        10.36 
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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        8.65         3.19         5.46        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.04         3.12        13.02         0.23         2.73 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        53.98        19.00         2.53        73.84        26.33 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       14.93         4.67         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        4.96        11.84         0.20        12.43         0.36        18.02 
TCGA-06-0237 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       10.36        20.42        10.32         5.52         0.26         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
        0.16        12.33         3.22         4.47         9.67        23.57 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         6.35         3.58         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         1.48         0.49         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         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         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       10.59         0.30         0.56        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       58.19         1.28         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        5.52        14.01         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       18.12        28.41        12.43        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 
       14.86        14.27        91.76        18.48        10.62        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         6.25 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        3.98        25.28        13.61        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       15.12        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
       13.78         3.25         1.35         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-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        6.15         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 
       53.19         9.93        26.07         4.31         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        9.07        12.95         4.64         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-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        5.39         5.42         3.98        16.57        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-27-1831 
        8.88         1.22         1.58         7.92         2.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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        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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         7.30         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         5.42        15.39        21.07 
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-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.02         7.36        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
       21.17        21.14        12.59        19.86        10.62         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-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         4.80         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 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        8.35         4.83         5.03         9.27         7.73         7.79 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                          0.23                           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 
                         10.52                           9.86 
[1] "0.2 - 92.7 (10.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1"  
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    42  53
  DEL PEAK 28(11Q14.1) WILD-TYPE 178 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     42   53
  DEL PEAK 28(11Q14.1) WILD-TYPE  178  287
        clus
vv       DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  FEMALE                           42                            178
  MALE                             53                            287
[1] 2 2
[1] FALSE
D53V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 28(11Q14.1) MUTATED                               2
  DEL PEAK 28(11Q14.1) WILD-TYPE                            15
                                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
D53V5, multiclass
                                 clus
vv                                DEL PEAK 28(11Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        5
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 28(11Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               15
  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"
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    58  37
  DEL PEAK 28(11Q14.1) WILD-TYPE 324 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     58   37
  DEL PEAK 28(11Q14.1) WILD-TYPE  324  141
     clus
vv    DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  NO                            58                            324
  YES                           37                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11Q14.1) MUTATED       2                         6    83
  DEL PEAK 28(11Q14.1) WILD-TYPE    11                        33   402
D53V7, multiclass
                           clus
vv                          DEL PEAK 28(11Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               83
                           clus
vv                          DEL PEAK 28(11Q14.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             33
  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  77
  DEL PEAK 28(11Q14.1) WILD-TYPE  11 385
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED      1   77
  DEL PEAK 28(11Q14.1) WILD-TYPE   11  385
                        clus
vv                       DEL PEAK 28(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       DEL PEAK 28(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            385
[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    19  52
  DEL PEAK 29(12P13.1) WILD-TYPE  79 410
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            489 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            52                            410 
$`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        32.52 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0175 TCGA-06-0190 TCGA-06-0195 
       16.70         7.86         9.44         2.73        10.29         7.04 
TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0414 TCGA-06-0646 TCGA-06-1801 
        2.60        18.02        10.36        35.01         4.47         8.65 
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        34.75        10.39         7.59         0.95        15.72 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-12-0619 TCGA-12-1598 TCGA-12-1600 
        3.52         8.52         1.28        10.39         9.44        13.61 
TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 
       43.23         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        16.31         4.31         9.90 
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         1.22        30.05         5.26         3.91        15.85 
TCGA-32-2494 TCGA-32-4208 TCGA-76-4935 TCGA-76-6193 TCGA-76-6664 
       20.78        21.14        10.78         2.70         7.79 

$`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 
        9.17         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        55.86        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        10.36        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         0.23         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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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         9.80        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       11.80        12.79         8.65         3.19         5.46        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
       13.02         0.23         2.20        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       14.93        18.31         4.67         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        70.52         4.70         8.05         0.16        12.33 
TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        3.22         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 
       20.94         7.43         6.35         3.58        26.79         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37         0.43        11.24         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 
        3.95         7.79         1.48         0.49         8.32         4.77 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        1.55         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 
        3.91       108.82         1.74         4.34        13.78         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       35.64        19.53         9.17        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 
        0.30         0.56        11.77        18.44        58.19        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         6.25        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       15.85         9.11        14.53         3.98         3.42        25.28 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.41        59.41        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
        3.25         1.35         2.89        16.50        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-14-1452 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-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
        6.15        12.43         1.97        17.79        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         0.82        13.35         3.65        18.28        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         0.43        14.27         3.39 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64         3.48         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
        3.25         0.13         9.67         4.87         1.08         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        16.47         7.00         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 
        9.73        31.33         7.13         9.37        14.86         5.49 
TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        33.14        21.30        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        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-28-5207 TCGA-28-5208 
        0.66         6.74         4.77         7.30         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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-32-2495 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-32-4210 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        21.17         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        10.62         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        11.54         7.76 
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-76-6191 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-81-5910 
        4.83         5.03         0.23         9.27         7.73         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                          0.95                           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 
                          9.90                          10.19 
[1] "0.9 - 92.7 (9.9)"   "0.1 - 127.6 (10.2)"
[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 189 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED     31   40
  DEL PEAK 29(12P13.1) WILD-TYPE  189  300
        clus
vv       DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  FEMALE                           31                            189
  MALE                             40                            300
[1] 2 2
[1] FALSE
D54V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 29(12P13.1) MUTATED                               1
  DEL PEAK 29(12P13.1) WILD-TYPE                            16
                                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
D54V5, 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)                               16
  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"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED    52  19
  DEL PEAK 29(12P13.1) WILD-TYPE 330 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED     52   19
  DEL PEAK 29(12P13.1) WILD-TYPE  330  159
     clus
vv    DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  NO                            52                            330
  YES                           19                            159
[1] 2 2
[1] FALSE
                                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                        37   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                             37
  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  11 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      1   59
  DEL PEAK 29(12P13.1) WILD-TYPE   11  403
                        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                            403
[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    15  59
  DEL PEAK 30(12Q12) WILD-TYPE  83 403
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          74                          486 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          59                          403 
$`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         0.23 
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        16.70 
TCGA-06-0149 TCGA-06-0159 TCGA-06-0173 TCGA-06-0175 TCGA-06-0184 TCGA-06-0190 
        7.86         9.44         0.23         2.73        40.37        10.29 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 
        7.04         2.60        18.02        10.36         4.70        35.01 
TCGA-06-0875 TCGA-06-5856 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 
       43.46         3.75         7.79         5.39         7.36        34.75 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 
       10.39         7.59        53.82        15.72         3.52         8.52 
TCGA-12-0619 TCGA-12-0662 TCGA-12-1600 TCGA-12-3646 TCGA-14-0740 TCGA-14-0783 
       10.39        38.17        13.61        43.23        11.97         6.21 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 TCGA-14-1453 
        1.35         5.39         2.04        28.93        23.11         1.15 
TCGA-14-1458 TCGA-14-1794 TCGA-14-1821 TCGA-14-3477 TCGA-16-0849 TCGA-16-0850 
        6.15         0.99        17.79         3.78        26.07        16.31 
TCGA-16-1056 TCGA-19-0957 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-4065 
       13.35        21.90        12.95        25.38         7.53         7.04 
TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5136 TCGA-28-1746 TCGA-28-1756 
        5.42        10.03         9.40         1.22         0.20         2.83 
TCGA-32-1978 TCGA-32-2494 TCGA-32-4208 TCGA-32-4210 TCGA-41-2571 TCGA-41-5651 
       15.85        20.78        21.14         3.72         0.85        11.54 
TCGA-76-4935 TCGA-76-6193 
       10.78         2.70 

$`DEL PEAK 30(12Q12) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 
        9.21         2.20        11.74         2.33         9.80        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        3.12        13.02         2.20        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       19.00         2.53        73.84        26.33        28.47        14.93 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       18.31         4.67         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       70.52         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         1.48         0.49         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-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       13.78         3.42         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 
        3.19        10.59         0.30         0.56        11.77        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       17.33         5.52        14.01        14.43         1.64         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.17        65.92         0.10        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28         6.41        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        15.12         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       11.24        13.78         3.25         2.89        16.50        26.33 
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-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       32.05        58.78         7.10        30.18         0.92        40.96 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         1.97        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 
       53.19         5.52         3.91         9.93         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        0.82         9.90         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64         3.48         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
        3.25         0.13         9.67         4.87         1.08         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        16.47         7.00         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        5.29         3.98        16.57        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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         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-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
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-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       22.78        21.17        12.59        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        0.20         7.76         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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  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 
                       10.16                        10.06 
[1] "0.2 - 92.7 (10.2)"  "0.1 - 127.6 (10.1)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    30  44
  DEL PEAK 30(12Q12) WILD-TYPE 190 296
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     30   44
  DEL PEAK 30(12Q12) WILD-TYPE  190  296
        clus
vv       DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  FEMALE                         30                          190
  MALE                           44                          296
[1] 2 2
[1] FALSE
D55V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 30(12Q12) MUTATED                               1
  DEL PEAK 30(12Q12) WILD-TYPE                            16
                              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
D55V5, multiclass
                                 clus
vv                                DEL PEAK 30(12Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            1
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 30(12Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             16
  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"
D55V6, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    48  26
  DEL PEAK 30(12Q12) WILD-TYPE 334 152
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     48   26
  DEL PEAK 30(12Q12) WILD-TYPE  334  152
     clus
vv    DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  NO                          48                          334
  YES                         26                          152
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q12) MUTATED       0                         4    67
  DEL PEAK 30(12Q12) WILD-TYPE    13                        35   418
D55V7, multiclass
                           clus
vv                          DEL PEAK 30(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             67
                           clus
vv                          DEL PEAK 30(12Q12) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           35
  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  58
  DEL PEAK 30(12Q12) WILD-TYPE  10 404
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED      2   58
  DEL PEAK 30(12Q12) WILD-TYPE   10  404
                        clus
vv                       DEL PEAK 30(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         58
                        clus
vv                       DEL PEAK 30(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          404
[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  62
  DEL PEAK 31(12Q15) WILD-TYPE  84 400
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          76                          484 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          62                          400 
$`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         0.23 
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        16.70         7.86        11.80         9.44 
TCGA-06-0162 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0190 
        2.56         0.23         2.20         2.01        40.37        10.29 
TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
        2.60        18.02        10.36         4.70        35.01         2.04 
TCGA-06-0875 TCGA-06-0939 TCGA-06-6389 TCGA-06-6694 TCGA-06-6695 TCGA-08-0245 
       43.46        20.94         7.79         7.36         8.32        34.75 
TCGA-08-0349 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0616 TCGA-12-0619 
        7.59        15.72         3.52         8.52        14.43        10.39 
TCGA-12-1088 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-14-0740 TCGA-14-0783 
      127.59        13.61         6.41        43.23        11.97         6.21 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 TCGA-14-1453 
        1.35         5.39         2.04        28.93        23.11         1.15 
TCGA-14-1794 TCGA-14-3477 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 
        0.99         3.78        53.19        26.07        16.31        21.90 
TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-2624 TCGA-19-4065 TCGA-19-5960 
       12.95        25.38         7.53         0.16         7.04         5.42 
TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-28-5214 TCGA-32-4210 
       10.03         9.40         8.88         1.22        14.20         3.72 
TCGA-32-4211 TCGA-41-2571 TCGA-74-6584 TCGA-76-6193 
       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 
        9.17         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        55.86        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        10.36        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       23.08        22.16        10.75         9.21         2.20        11.74 
TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        2.33         9.80        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19         5.46        11.80        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       19.04         3.12        13.02         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       19.00         2.53        73.84        26.33        28.47        14.93 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       18.31         4.67         7.04         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26        70.52         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        5.39         2.70         2.17         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        22.98         5.85         5.42         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         5.39         1.48         0.49        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-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       13.78        10.39         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.77        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 
        6.54        15.98        17.33         5.52        14.01         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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-12-1089 TCGA-12-1090 TCGA-12-1091 
       38.76         8.94        20.58         5.82         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3648 
        3.98         3.42         9.44        25.28        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        15.12         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       11.24        13.78         3.25         2.89        16.50        26.33 
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-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       32.05        58.78         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
        6.15        12.43         1.97        17.79        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 
       50.53        19.10         5.52         3.91         9.93         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43        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         3.48 
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-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        1.08         4.08        16.47         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 
        5.39         5.29         3.98        16.57        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       31.33         7.13         9.37        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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 
       10.39        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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       15.58        14.53        11.77        31.27         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        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        21.17        21.14 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85        10.62        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        11.54         7.76 
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        10.78 
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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  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                       108.82 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                        9.42                        10.34 
[1] "0.2 - 127.6 (9.4)"  "0.1 - 108.8 (10.3)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    33  43
  DEL PEAK 31(12Q15) WILD-TYPE 187 297
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     33   43
  DEL PEAK 31(12Q15) WILD-TYPE  187  297
        clus
vv       DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  FEMALE                         33                          187
  MALE                           43                          297
[1] 2 2
[1] FALSE
D56V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 31(12Q15) MUTATED                               2
  DEL PEAK 31(12Q15) WILD-TYPE                            15
                              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
D56V5, multiclass
                                 clus
vv                                DEL PEAK 31(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      3
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 31(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             15
  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"
D56V6, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    48  28
  DEL PEAK 31(12Q15) WILD-TYPE 334 150
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     48   28
  DEL PEAK 31(12Q15) WILD-TYPE  334  150
     clus
vv    DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  NO                          48                          334
  YES                         28                          150
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(12Q15) MUTATED       0                         3    68
  DEL PEAK 31(12Q15) WILD-TYPE    13                        36   417
D56V7, multiclass
                           clus
vv                          DEL PEAK 31(12Q15) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             68
                           clus
vv                          DEL PEAK 31(12Q15) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           36
  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  60
  DEL PEAK 31(12Q15) WILD-TYPE   9 402
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED      3   60
  DEL PEAK 31(12Q15) WILD-TYPE    9  402
                        clus
vv                       DEL PEAK 31(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       DEL PEAK 31(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          402
[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    39 195
  DEL PEAK 32(13Q14.2) WILD-TYPE  59 267
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           234                            326 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           195                            267 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0023 
        9.17        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 
        0.26        22.72        10.52        22.16         0.20        11.74 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       16.70         7.86        11.80         5.46         9.44         2.56 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 
       56.88         5.29         2.01         2.53        40.37        28.47 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         7.04         2.60         0.39         6.48 
TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        3.91         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 
        0.26         4.70         0.16        35.01         9.67         2.04 
TCGA-06-0745 TCGA-06-0875 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        5.39        43.46         5.85        20.94         7.43         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         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 
       11.24         4.54         8.98         6.71         3.75         4.57 
TCGA-06-6389 TCGA-06-6694 TCGA-06-6701 TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 
        7.79         7.36         4.96        34.75         3.91        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0354 TCGA-08-0357 TCGA-08-0359 
       10.39         7.59         3.42        15.06        35.64         0.95 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.72         3.19         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-12-0615 TCGA-12-0620 
        8.52        18.44        58.19        10.75        14.01         5.95 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 TCGA-12-0776 
       38.17        25.97         6.12        12.43        53.10         9.11 
TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 
       30.54        21.63        11.97        11.38         9.11        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3652 
        3.42         9.44         6.41        59.41        43.23        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0787 
       11.74        13.12        15.12        11.97         6.21         2.24 
TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 TCGA-14-1034 
        3.25         5.39         2.89        16.50         2.04        15.95 
TCGA-14-1037 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 
       19.30         1.12        23.11         1.15        30.18        40.96 
TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 
        6.15        17.85         7.63         3.78         9.86        50.53 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 
       53.19         5.52         3.91        26.07        16.31        29.03 
TCGA-16-1055 TCGA-16-1060 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 
        9.90         3.65        10.75         5.95         4.64         3.48 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 
        1.08         7.53         4.08        16.47         7.04         6.64 
TCGA-19-5955 TCGA-26-1438 TCGA-26-1439 TCGA-26-5132 TCGA-26-5133 TCGA-26-5136 
        1.78        10.03        13.87         9.40        14.86         1.22 
TCGA-26-6173 TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 
        7.92         4.80         9.86        33.14        10.39        10.39 
TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 TCGA-28-2509 TCGA-28-5215 
        7.59         8.35         8.48         0.66         4.77         7.79 
TCGA-28-5216 TCGA-28-5219 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       13.64        22.68        15.39        21.07         0.49         0.10 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 
       14.86        12.23         7.36         8.84        22.78         3.72 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 
       19.86        10.85         0.85         8.94         0.99        11.84 
TCGA-41-4097 TCGA-74-6573 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 
        0.20         3.45         3.65         2.53        10.78         3.29 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-76-6662 TCGA-81-5911 
        2.70         8.35        20.98         0.23         9.27        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        55.86        77.65 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       42.74        10.36        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         0.23 
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         0.16        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 
       16.21         2.70         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 
       32.52        18.74        14.07        23.08        10.75         9.21 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
        2.20         2.33        20.09         9.80        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 
       12.79         8.65         3.19        11.80        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0194 
       53.98        19.00        73.84        26.33        14.93         4.67 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        5.49         4.96        11.84        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 
       14.96        10.32         5.52        70.52         8.05        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        3.22         4.47        23.57         9.40        22.32        19.56 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.17         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 
       22.98         5.42         6.35         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2569 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 
        5.95         6.81         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         3.95         5.39         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         8.32        12.85         4.77         1.55         4.77 
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       108.82         1.74 
TCGA-08-0346 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
        4.34        53.82         1.28         6.41        22.52        14.70 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0518 TCGA-08-0521 
       19.53         9.17        10.85        10.59         1.28         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        6.54        15.98        17.33         5.52        14.43         1.64 
TCGA-12-0619 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0692 
       10.39         7.17        65.92         0.10        24.13         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       18.12        28.41        43.10         5.49        14.86        14.27 
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         6.25 
TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
       15.85         3.98        25.28        13.61        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 
       10.95        11.77         3.22         2.04         0.95        23.05 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0866 TCGA-14-0871 TCGA-14-1043 
       11.24        13.78         1.35        26.33        28.93         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1455 
        1.38         3.75        32.05        58.78         7.10         0.92 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 TCGA-14-1829 
       12.43         0.99         1.97        17.79         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-16-0848 TCGA-16-0861 
       17.49         7.96         3.42        19.10         9.93         4.31 
TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
        0.82        13.35        18.28        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 
       21.90         8.61         0.43        14.27         3.39         9.07 
TCGA-19-1388 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       12.95        25.38         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 
        9.67         4.87         0.16         7.00        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
       18.64         4.73         7.96         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.42         3.98        16.57         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6174 TCGA-27-1831 
        9.37         5.49         8.88         1.58         2.33        16.60 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        21.30        30.05        14.04        11.51        24.76 
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-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        9.21         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         7.30         5.26         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 
       14.53        11.77        31.27        14.20         4.21        10.49 
TCGA-28-6450 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        5.42        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 
       16.93        20.78        15.02        15.95        21.17        21.14 
TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 
       12.59        10.62        13.35         9.53         4.44        11.54 
TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-6191 TCGA-76-6280 
        4.80         4.54         3.09         9.17        16.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
       17.06         4.83         5.03         7.73         7.79         1.61 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  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                         108.82 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                          9.88                          10.36 
[1] "0.1 - 127.6 (9.9)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED    90 144
  DEL PEAK 32(13Q14.2) WILD-TYPE 130 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     90  144
  DEL PEAK 32(13Q14.2) WILD-TYPE  130  196
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                           90                            130
  MALE                            144                            196
[1] 2 2
[1] FALSE
D57V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 32(13Q14.2) MUTATED                               4
  DEL PEAK 32(13Q14.2) WILD-TYPE                            13
                                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
D57V5, multiclass
                                 clus
vv                                DEL PEAK 32(13Q14.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          224
                                 clus
vv                                DEL PEAK 32(13Q14.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               13
  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"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED   157  77
  DEL PEAK 32(13Q14.2) WILD-TYPE 225 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED    157   77
  DEL PEAK 32(13Q14.2) WILD-TYPE  225  101
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  NO                           157                            225
  YES                           77                            101
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED       5                        12   211
  DEL PEAK 32(13Q14.2) WILD-TYPE     8                        27   274
D57V7, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              211
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             27
  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     5 197
  DEL PEAK 32(13Q14.2) WILD-TYPE   7 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      5  197
  DEL PEAK 32(13Q14.2) WILD-TYPE    7  265
                        clus
vv                       DEL PEAK 32(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          197
                        clus
vv                       DEL PEAK 32(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            265
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 33(14Q13.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(14Q13.1) MUTATED    35 139
  DEL PEAK 33(14Q13.1) WILD-TYPE  63 323
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                           174                            386 
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                           139                            323 
$`DEL PEAK 33(14Q13.1) MUTATED`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 
        9.17        23.18        35.41        20.71        55.86        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 
       16.21        47.31        22.72        10.52        22.16         9.21 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0162 TCGA-06-0166 TCGA-06-0188 TCGA-06-0194 
       11.74        20.09         2.56         5.29        28.47         4.67 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0397 TCGA-06-0409 
       22.49         0.36        18.02        14.96         5.52        70.52 
TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0749 
        4.70        12.33         4.47         2.04         5.39         2.17 
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         7.43         9.27 
TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 TCGA-06-6388 
       11.24         8.35         8.81         6.71         3.75         3.95 
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-08-0245 TCGA-08-0347 TCGA-08-0352 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 
       34.75        13.78         1.28        10.85        10.59         0.30 
TCGA-08-0512 TCGA-08-0520 TCGA-08-0524 TCGA-12-0616 TCGA-12-0654 TCGA-12-0662 
       11.77        10.75         6.54        14.43         7.17        38.17 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 TCGA-12-1089 
        2.63        18.12         5.49        10.62       127.59         5.82 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1096 TCGA-12-1099 TCGA-12-1598 
       30.54        21.63        11.97         9.11         3.42         9.44 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 
       25.28         6.41        11.77        11.74        13.12        15.12 
TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-1455 
        6.21         1.35         5.39         2.89        16.50         0.92 
TCGA-14-1459 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3477 
       12.43        17.85         7.63         7.17        17.49         3.78 
TCGA-15-0742 TCGA-15-1447 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-19-1389 
        9.86        53.19         9.93         4.31        29.03         4.64 
TCGA-19-1390 TCGA-19-1791 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 
       25.38         0.13         7.53         4.08        16.47         6.64 
TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        6.51         5.42         3.98        10.03        13.87         9.73 
TCGA-26-5133 TCGA-26-5134 TCGA-26-6173 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
       14.86         5.49         7.92         9.86        33.14        21.30 
TCGA-27-2519 TCGA-27-2527 TCGA-28-1750 TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 
       10.39        14.40         8.35         2.83         6.74         4.77 
TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 
        5.26         9.04        31.27         7.79        13.64        10.49 
TCGA-32-1976 TCGA-32-1980 TCGA-32-2615 TCGA-32-2634 TCGA-32-4210 TCGA-32-5222 
        0.49         1.18        15.95        22.78         3.72        10.62 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-74-6575 TCGA-74-6581 TCGA-74-6584 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 
       20.91         8.22         7.50         3.09         3.65         2.53 
TCGA-76-6191 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6664 TCGA-OX-A56R 
       16.70         2.70        17.06         8.35         7.79         5.92 

$`DEL PEAK 33(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        10.36        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         0.23 
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         0.16         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         0.26         4.04         0.10         3.58        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       18.74        14.07        23.08        10.75         0.20         2.20 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
        2.33        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       11.80        56.88        10.65        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0402 TCGA-06-0412 
       10.36        11.80        20.42        10.32         0.26         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        0.16        35.01         3.22         9.67        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 
       22.32        19.56         2.70         5.65        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        7.89        13.61        33.90        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93         2.83        30.64         5.95         6.81         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         0.49 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 
        7.36         8.32         4.77         4.77         4.96         3.12 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       22.68         3.91       108.82         1.74         4.34        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        7.59         3.42        53.82         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 
       14.70        35.64        19.53         0.95         9.17        15.72 
TCGA-08-0389 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        3.19         0.56         3.52         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        1.28         4.80        15.98        17.33         5.52        14.01 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 
        1.64        10.39         5.95        65.92         0.10        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
       24.13         6.12        28.41        12.43        53.10        43.10 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 
       23.51        27.78        38.76         8.94        20.58         6.25 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1600 TCGA-12-3644 
       11.38        15.85        14.53         3.98        13.61        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 
       43.23        25.78        11.54        10.95        34.52         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-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
       13.78         3.25        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-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 
       58.78        23.11         7.10         1.15        30.18        40.96 
TCGA-14-1458 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 TCGA-14-2555 
        6.15         0.99         1.97        17.79         5.88         7.96 
TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
        3.42        50.53        19.10         5.52         3.91        26.07 
TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       16.31         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 
        3.48         7.17        12.66         3.25         9.67         4.87 
TCGA-19-2621 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 
        1.08         0.16         7.00         7.04        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.64         4.73         7.96         1.78         5.39         5.29 
TCGA-19-A6J5 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       16.57        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 
        1.22         1.58         2.33         4.80        16.60        18.25 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        15.78         0.20         2.53         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 
        7.63         8.48         1.22         1.55         0.13         0.66 
TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 
        7.30         3.91        15.58        14.53        11.77        14.20 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
        4.21        22.68         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       15.85        19.50         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        21.17 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
       21.14        12.59        19.86        10.85         0.85        13.35 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 
       11.54         7.76         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        10.78         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         0.23         9.27         7.73         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                        127.59                         108.82 
  DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE 
                         9.485                         10.390 
[1] "0.1 - 127.6 (9.5)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(14Q13.1) MUTATED    77  97
  DEL PEAK 33(14Q13.1) WILD-TYPE 143 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(14Q13.1) MUTATED     77   97
  DEL PEAK 33(14Q13.1) WILD-TYPE  143  243
        clus
vv       DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE
  FEMALE                           77                            143
  MALE                             97                            243
[1] 2 2
[1] FALSE
D58V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 33(14Q13.1) MUTATED                               4
  DEL PEAK 33(14Q13.1) WILD-TYPE                            13
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 33(14Q13.1) MUTATED                     6
  DEL PEAK 33(14Q13.1) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 33(14Q13.1) MUTATED                               164
  DEL PEAK 33(14Q13.1) WILD-TYPE                             361
D58V5, multiclass
                                 clus
vv                                DEL PEAK 33(14Q13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          164
                                 clus
vv                                DEL PEAK 33(14Q13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               13
  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"
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(14Q13.1) MUTATED   121  53
  DEL PEAK 33(14Q13.1) WILD-TYPE 261 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(14Q13.1) MUTATED    121   53
  DEL PEAK 33(14Q13.1) WILD-TYPE  261  125
     clus
vv    DEL PEAK 33(14Q13.1) MUTATED DEL PEAK 33(14Q13.1) WILD-TYPE
  NO                           121                            261
  YES                           53                            125
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(14Q13.1) MUTATED       2                        17   147
  DEL PEAK 33(14Q13.1) WILD-TYPE    11                        22   338
D58V7, multiclass
                           clus
vv                          DEL PEAK 33(14Q13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              147
                           clus
vv                          DEL PEAK 33(14Q13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             22
  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"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(14Q13.1) MUTATED     1 143
  DEL PEAK 33(14Q13.1) WILD-TYPE  11 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(14Q13.1) MUTATED      1  143
  DEL PEAK 33(14Q13.1) WILD-TYPE   11  319
                        clus
vv                       DEL PEAK 33(14Q13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       DEL PEAK 33(14Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            319
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 34(14Q24.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q24.2) MUTATED    32 138
  DEL PEAK 34(14Q24.2) WILD-TYPE  66 324
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                           170                            390 
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                           138                            324 
$`DEL PEAK 34(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        55.86        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        32.52 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 TCGA-06-0146 TCGA-06-0155 
       10.52        22.16         9.21        11.74        20.09         8.65 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0171 TCGA-06-0188 TCGA-06-0194 TCGA-06-0214 
        2.56         5.29        13.02        28.47         4.67        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 
       22.49         0.36        18.02        14.96        70.52         4.70 
TCGA-06-0412 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0750 
        8.05        12.33         4.47         2.04         5.39         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         9.27        11.24         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-08-0245 TCGA-08-0380 TCGA-08-0390 
        1.55         1.87         2.56        34.75        10.85        10.59 
TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 TCGA-12-0615 TCGA-12-0616 
        0.30        11.77        58.19        10.75        14.01        14.43 
TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0776 TCGA-12-0821 
        7.17        38.17         6.12         2.63         9.11        10.62 
TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1096 
       38.76       127.59         5.82        30.54        21.63         9.11 
TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
        9.44        13.61         6.41        11.77        11.74        13.12 
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-14-1396 TCGA-14-1401 TCGA-14-1453 TCGA-14-1455 TCGA-14-1821 TCGA-14-1823 
        1.12         3.75         1.15         0.92        17.79        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-3477 TCGA-14-4157 TCGA-15-1447 TCGA-16-0848 
        7.63         7.17         3.78         3.42        53.19         9.93 
TCGA-16-0861 TCGA-16-1045 TCGA-19-0962 TCGA-19-1389 TCGA-19-1390 TCGA-19-1791 
        4.31        29.03         0.43         4.64        25.38         0.13 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 
        7.53         4.08        16.47         6.64         6.51         5.42 
TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1440 TCGA-26-5133 TCGA-26-5134 TCGA-27-1832 
        3.98        13.87         9.73        14.86         5.49         9.86 
TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2527 TCGA-28-1750 TCGA-28-1756 
       33.14        21.30        10.39        14.40         8.35         2.83 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 
        6.74         4.77         5.26         9.04        31.27         7.79 
TCGA-28-5216 TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 TCGA-32-2494 TCGA-32-2615 
       13.64        10.49         0.49         1.18        20.78        15.95 
TCGA-32-2616 TCGA-32-2634 TCGA-32-4208 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
        7.36        22.78        21.14         8.94         9.53         0.99 
TCGA-41-4097 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-6193 TCGA-76-6282 
        0.20         3.09         3.65         2.53         2.70        17.06 
TCGA-76-6285 TCGA-OX-A56R 
        8.35         5.92 

$`DEL PEAK 34(14Q24.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
        9.17         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        10.36        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         0.23        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         0.16         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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       47.31         0.10         3.58        18.74        14.07        23.08 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
       10.75         0.20         2.20         2.33        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 
        7.86        19.46        46.59        11.80        12.79         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        5.46         9.44        11.80        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.12         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29        18.31         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       10.36        11.80        20.42        10.32         5.52         0.26 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        0.16        35.01         3.22         9.67        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0877 TCGA-06-0879 
       22.32        19.56         2.70         2.17         5.65        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 
        6.81         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 
        3.95         1.48         0.49         7.36         8.32         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        4.77         4.96         3.12        22.68         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 
       35.64        19.53         0.95         9.17        15.72         3.19 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 
        0.56         3.52         8.52        18.44         1.28         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 
        6.54        15.98        17.33         5.52         1.64        10.39 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 
        5.95        65.92         0.10        25.97        24.13        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        12.43        53.10        43.10         5.49        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 
       14.27        91.76        24.79        18.48        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        8.94        20.58         6.25        11.97        11.38        15.85 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 
       14.53         3.98         3.42        25.28        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 
       25.78        11.54        10.95        34.52         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-14-0812 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        3.25        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        0.79         1.38        32.05        58.78        23.11         7.10 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18        40.96         6.15        12.43         0.99         1.97 
TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        5.88        17.49         7.96         9.86        50.53        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 
        5.52         3.91        26.07        16.31         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95        12.95         3.48         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 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 
        5.39         5.29        16.57        10.03        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.37         9.40         8.88         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 
        2.33         4.80        16.60        18.25        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         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       15.58        14.53        11.77        14.20         4.21        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-32-2495 
        4.67        12.69        14.86        16.93        12.23        15.02 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        21.17         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 
       10.62         0.85        13.35         4.44        11.84        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        7.50         4.80         4.54         9.17        10.78        16.70 
TCGA-76-6192 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        3.29        11.38        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 

  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                        127.59                         108.82 
  DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE 
                          9.63                          10.36 
[1] "0.1 - 127.6 (9.6)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1"  
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q24.2) MUTATED    73  97
  DEL PEAK 34(14Q24.2) WILD-TYPE 147 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q24.2) MUTATED     73   97
  DEL PEAK 34(14Q24.2) WILD-TYPE  147  243
        clus
vv       DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE
  FEMALE                           73                            147
  MALE                             97                            243
[1] 2 2
[1] FALSE
D59V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 34(14Q24.2) MUTATED                               4
  DEL PEAK 34(14Q24.2) WILD-TYPE                            13
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 34(14Q24.2) MUTATED                     7
  DEL PEAK 34(14Q24.2) WILD-TYPE                  11
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 34(14Q24.2) MUTATED                               159
  DEL PEAK 34(14Q24.2) WILD-TYPE                             366
D59V5, multiclass
                                 clus
vv                                DEL PEAK 34(14Q24.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                          159
                                 clus
vv                                DEL PEAK 34(14Q24.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               13
  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"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q24.2) MUTATED   119  51
  DEL PEAK 34(14Q24.2) WILD-TYPE 263 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q24.2) MUTATED    119   51
  DEL PEAK 34(14Q24.2) WILD-TYPE  263  127
     clus
vv    DEL PEAK 34(14Q24.2) MUTATED DEL PEAK 34(14Q24.2) WILD-TYPE
  NO                           119                            263
  YES                           51                            127
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q24.2) MUTATED       5                        15   145
  DEL PEAK 34(14Q24.2) WILD-TYPE     8                        24   340
D59V7, multiclass
                           clus
vv                          DEL PEAK 34(14Q24.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              145
                           clus
vv                          DEL PEAK 34(14Q24.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             24
  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"
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q24.2) MUTATED     3 140
  DEL PEAK 34(14Q24.2) WILD-TYPE   9 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q24.2) MUTATED      3  140
  DEL PEAK 34(14Q24.2) WILD-TYPE    9  322
                        clus
vv                       DEL PEAK 34(14Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          140
                        clus
vv                       DEL PEAK 34(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            322
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 35(15Q14) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 35(15Q14) MUTATED    23 124
  DEL PEAK 35(15Q14) WILD-TYPE  75 338
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                         147                          413 
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                         124                          338 
$`DEL PEAK 35(15Q14) MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0026 
        9.17         4.73        20.71        55.86        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         0.23        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         4.04        22.72        32.52         9.21 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 
        5.29         2.20         2.01        28.47        10.29        18.31 
TCGA-06-0201 TCGA-06-0209 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 
        0.39         3.91         0.20        22.49        10.36        11.80 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.26         4.70         3.22         4.47         9.67         2.04 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0875 TCGA-06-1801 TCGA-06-2558 TCGA-06-2562 
        9.40         5.39        43.46         8.65         0.76         2.83 
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-08-0246 TCGA-08-0344 TCGA-08-0348 TCGA-08-0349 TCGA-08-0355 TCGA-08-0359 
        3.91       108.82        10.39         7.59        22.52         0.95 
TCGA-08-0386 TCGA-08-0510 TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 TCGA-12-0707 
       15.72         3.52        15.98         1.64        10.39        28.41 
TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
        5.49        10.62       127.59         9.11        14.53         3.42 
TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 TCGA-12-3651 
        9.44        13.61         6.41        43.23        25.78        11.77 
TCGA-14-0736 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-1459 TCGA-14-1794 
       15.12         6.21         5.39         2.04        12.43         0.99 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-1045 TCGA-16-1063 TCGA-19-0963 TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 
       29.03        13.97        14.27        10.75         5.95        12.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 TCGA-19-5955 TCGA-19-5956 
       25.38         3.48        16.47         7.04         1.78         6.51 
TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-6174 TCGA-27-1830 TCGA-27-1834 
        5.42        10.03        13.87         2.33         4.80        33.14 
TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 TCGA-28-1750 TCGA-28-1756 
       10.39         7.59         2.86         0.20         8.35         2.83 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5215 TCGA-28-5219 TCGA-32-1970 TCGA-32-1973 
        7.30         5.26         7.79        22.68        15.39        21.07 
TCGA-32-1976 TCGA-32-2494 TCGA-32-2616 TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 
        0.49        20.78         7.36        22.78         3.72        12.59 
TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3915 
       10.85         0.85         8.94         9.53         0.99        11.84 
TCGA-41-5651 TCGA-74-6578 TCGA-76-4925 TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 
       11.54        14.33         4.80         3.65        10.78        16.70 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 
        2.70         8.35        20.98 

$`DEL PEAK 35(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        10.36        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         0.16        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        16.21 
TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 
        0.26        47.31         0.10         3.58        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       14.07        23.08        22.16        10.75         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12        13.02         0.23         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 TCGA-06-0208 
       14.93         4.67         7.04         2.60         6.48         5.49 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 
        4.96        11.84        12.43         0.36        18.02        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       14.96        10.32         5.52        70.52         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.01        12.33        23.57        22.32        19.56         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        46.19         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79         7.89        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         9.27        30.64         5.95         6.81         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        11.24         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 
        3.95         7.79         5.39         1.48         0.49         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S1 
       12.85         4.77         1.55         4.77         4.96         2.56 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 
       22.68        34.75         1.74         4.34        13.78         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28         6.41        15.06        14.70        35.64 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       19.53         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         6.54        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       14.43         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 
       25.97        24.13         6.12         2.63        18.12        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.10        43.10         9.11        14.86        14.27        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-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58         5.82         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-3644 TCGA-12-3649 
       11.38        15.85         3.98        25.28        59.41        11.54 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.52        11.74        13.12         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-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        3.25         1.35         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-14-1795 TCGA-14-1821 TCGA-14-1823 
        0.92        40.96         6.15         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-16-0861 TCGA-16-1047 
        3.42         9.86        50.53        19.10         4.31         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 
        9.90        13.35         3.65        18.28         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0964 TCGA-19-1386 TCGA-19-1389 
       21.90         8.61         0.43         3.39         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-19-2631 TCGA-19-5947 
        1.08         7.53         0.16         4.08         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5958 
       11.28         8.02        18.64         4.73         7.96         5.39 
TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.29         3.98        16.57         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        1.58         7.92        16.60         9.86        18.25        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       14.40        15.78         2.53         9.21         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-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 
       14.20        13.64         4.21        10.49         5.42         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-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 
       16.93        12.23        15.02        15.95         8.84        21.17 
TCGA-32-4208 TCGA-32-4213 TCGA-32-5222 TCGA-41-2572 TCGA-41-3393 TCGA-41-4097 
       21.14        19.86        10.62        13.35         4.44         0.20 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 
        7.76         3.45        20.91         4.34         8.22         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-6192 TCGA-76-6280 
        4.54         3.09         9.17         2.53         3.29        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       17.06         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                      127.59                        99.98 
  DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE 
                        9.44                        10.52 
[1] "0.2 - 127.6 (9.4)"  "0.1 - 100.0 (10.5)"
[1] "hr=" "1.1"
D60V2, continuous
D60V3, binary
                              cls
clus                             0   1
  DEL PEAK 35(15Q14) MUTATED    56  91
  DEL PEAK 35(15Q14) WILD-TYPE 164 249
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(15Q14) MUTATED     56   91
  DEL PEAK 35(15Q14) WILD-TYPE  164  249
        clus
vv       DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE
  FEMALE                         56                          164
  MALE                           91                          249
[1] 2 2
[1] FALSE
D60V4, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 35(15Q14) MUTATED                               3
  DEL PEAK 35(15Q14) WILD-TYPE                            14
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 35(15Q14) MUTATED                     4
  DEL PEAK 35(15Q14) WILD-TYPE                  14
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 35(15Q14) MUTATED                               140
  DEL PEAK 35(15Q14) WILD-TYPE                             385
D60V5, multiclass
                                 clus
vv                                DEL PEAK 35(15Q14) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            3
  TREATED PRIMARY GBM                                      4
  UNTREATED PRIMARY (DE NOVO) GBM                        140
                                 clus
vv                                DEL PEAK 35(15Q14) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             14
  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"
D60V6, binary
                              cls
clus                             0   1
  DEL PEAK 35(15Q14) MUTATED    96  51
  DEL PEAK 35(15Q14) WILD-TYPE 286 127
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(15Q14) MUTATED     96   51
  DEL PEAK 35(15Q14) WILD-TYPE  286  127
     clus
vv    DEL PEAK 35(15Q14) MUTATED DEL PEAK 35(15Q14) WILD-TYPE
  NO                          96                          286
  YES                         51                          127
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(15Q14) MUTATED       5                         6   129
  DEL PEAK 35(15Q14) WILD-TYPE     8                        33   356
D60V7, multiclass
                           clus
vv                          DEL PEAK 35(15Q14) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                            129
                           clus
vv                          DEL PEAK 35(15Q14) WILD-TYPE
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           33
  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"
D60V8, binary
                              cls
clus                             0   1
  DEL PEAK 35(15Q14) MUTATED     5 125
  DEL PEAK 35(15Q14) WILD-TYPE   7 337
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(15Q14) MUTATED      5  125
  DEL PEAK 35(15Q14) WILD-TYPE    7  337
                        clus
vv                       DEL PEAK 35(15Q14) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        125
                        clus
vv                       DEL PEAK 35(15Q14) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          337
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 36(16P12.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16P12.2) MUTATED    11  81
  DEL PEAK 36(16P12.2) WILD-TYPE  87 381
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                            92                            468 
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                            81                            381 
$`DEL PEAK 36(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        16.21        18.74 
TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 TCGA-06-0216 
       56.88        19.04        13.02         2.01        12.43        22.49 
TCGA-06-0221 TCGA-06-0394 TCGA-06-0414 TCGA-06-0645 TCGA-06-0649 TCGA-06-0686 
       18.02        10.32        35.01         3.22         2.04         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 TCGA-06-2557 
       22.32        19.56        22.98         5.42         3.58         1.08 
TCGA-06-2569 TCGA-06-5418 TCGA-06-6389 TCGA-06-6698 TCGA-06-6700 TCGA-06-A5U1 
        0.43         2.73         7.79         4.77         4.77         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0347 TCGA-08-0353 TCGA-08-0386 TCGA-08-0392 
        3.12         2.56        13.78         6.41        15.72         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 
        0.56         3.52         8.52        15.98        10.39         5.95 
TCGA-12-0776 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-1099 TCGA-12-1600 
        9.11        23.51        27.78        38.76         3.42        13.61 
TCGA-12-3649 TCGA-12-3651 TCGA-12-3653 TCGA-12-5301 TCGA-14-0736 TCGA-14-0812 
       11.54        11.77        11.74         2.04        15.12         3.25 
TCGA-14-0813 TCGA-14-0871 TCGA-14-1823 TCGA-16-0861 TCGA-19-0962 TCGA-19-1389 
        1.35        28.93        17.85         4.31         0.43         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-2620 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 
        3.48         7.17         4.87         4.73         1.78         6.51 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 
       33.14        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         3.91        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 36(16P12.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 
        0.10         3.58        22.72        32.52        10.52        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 
        5.46         9.44        11.80         2.56        10.65         5.29 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.12         0.23         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.20         0.36        10.36        11.80        20.42        14.96 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 
       12.33         4.47         9.67        23.57         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
        5.85        20.94         7.43         6.35        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90        15.32         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.24         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         6.71         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        4.57         3.95         5.39         1.48         0.49         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6701 TCGA-08-0244 TCGA-08-0245 
        8.32        12.85         1.55         4.96        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 
        3.91       108.82         1.74         4.34        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        3.42        53.82         1.28        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       10.59        11.77        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        4.80         6.54        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        1.64         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.10        43.10         5.49        14.86        14.27        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        18.48        10.62         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         6.25        30.54        21.63        11.97        11.38 
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         9.44        25.28 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3652 
        6.41        59.41        43.23        25.78        10.95        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
       13.12         3.22        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
        2.24        11.24        13.78         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-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.15        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       16.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1390 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 
       25.38        12.66         3.25         0.13         9.67         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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        6.64        11.28         8.02        18.64         7.96         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1837 TCGA-27-1838 
        4.80        16.60         9.86        18.25        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        10.39        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1755 
        0.20         2.53         9.21         7.63         8.48         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-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 
       15.39        21.07         0.49         0.10        19.50         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        16.93        12.23        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        9.53         4.44         0.20        11.54         7.76         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 
        4.34        14.33         8.22         7.50         4.54         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17         2.53        10.78         3.29         2.70        11.38 
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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                           0.3                            0.1 
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                         56.88                         127.59 
  DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE 
                         9.255                         10.325 
[1] "0.3 - 56.9 (9.3)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.3"
D61V2, continuous
D61V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P12.2) MUTATED    32  60
  DEL PEAK 36(16P12.2) WILD-TYPE 188 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P12.2) MUTATED     32   60
  DEL PEAK 36(16P12.2) WILD-TYPE  188  280
        clus
vv       DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE
  FEMALE                           32                            188
  MALE                             60                            280
[1] 2 2
[1] FALSE
D61V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 36(16P12.2) MUTATED                               3
  DEL PEAK 36(16P12.2) WILD-TYPE                            14
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 36(16P12.2) MUTATED                     1
  DEL PEAK 36(16P12.2) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 36(16P12.2) MUTATED                                88
  DEL PEAK 36(16P12.2) WILD-TYPE                             437
D61V5, multiclass
                                 clus
vv                                DEL PEAK 36(16P12.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 36(16P12.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P12.2) MUTATED    59  33
  DEL PEAK 36(16P12.2) WILD-TYPE 323 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P12.2) MUTATED     59   33
  DEL PEAK 36(16P12.2) WILD-TYPE  323  145
     clus
vv    DEL PEAK 36(16P12.2) MUTATED DEL PEAK 36(16P12.2) WILD-TYPE
  NO                            59                            323
  YES                           33                            145
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16P12.2) MUTATED       2                         9    77
  DEL PEAK 36(16P12.2) WILD-TYPE    11                        30   408
D61V7, multiclass
                           clus
vv                          DEL PEAK 36(16P12.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               77
                           clus
vv                          DEL PEAK 36(16P12.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             30
  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"
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P12.2) MUTATED     2  78
  DEL PEAK 36(16P12.2) WILD-TYPE  10 384
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P12.2) MUTATED      2   78
  DEL PEAK 36(16P12.2) WILD-TYPE   10  384
                        clus
vv                       DEL PEAK 36(16P12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 36(16P12.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            384
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 37(16Q23.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q23.3) MUTATED     9  86
  DEL PEAK 37(16Q23.3) WILD-TYPE  89 376
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                            95                            465 
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                            86                            376 
$`DEL PEAK 37(16Q23.3) MUTATED`
TCGA-02-0009 TCGA-02-0026 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 TCGA-02-0114 
       10.59        24.59        12.59         2.50        10.19        99.98 
TCGA-02-0258 TCGA-02-0281 TCGA-02-0321 TCGA-02-0337 TCGA-02-0456 TCGA-02-2470 
       16.54         3.98         9.90        25.12         3.35        12.92 
TCGA-02-2486 TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 
       16.21        18.74        56.88        19.04        13.02         2.01 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 
       12.43        22.49        18.02        35.01         3.22         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0749 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 
       22.32        19.56         2.17        22.98         5.42         3.58 
TCGA-06-2557 TCGA-06-2567 TCGA-06-2569 TCGA-06-5410 TCGA-06-5418 TCGA-06-5859 
        1.08         4.37         0.43         3.55         2.73         4.57 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6698 TCGA-06-6700 TCGA-06-A6S0 TCGA-06-A6S1 
        7.79         0.49         4.77         4.77         3.12         2.56 
TCGA-08-0353 TCGA-08-0380 TCGA-08-0392 TCGA-08-0509 TCGA-08-0520 TCGA-08-0525 
        6.41        10.85         0.30         0.56        10.75        15.98 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 TCGA-12-0692 TCGA-12-0826 TCGA-12-1088 
        1.64        10.39         7.17         2.63        27.78       127.59 
TCGA-12-1091 TCGA-12-1099 TCGA-12-1600 TCGA-12-3649 TCGA-12-3653 TCGA-12-5295 
       30.54         3.42        13.61        11.54        11.74        13.12 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        2.04        15.12         2.24         3.25         1.35         2.89 
TCGA-14-0871 TCGA-14-1453 TCGA-14-1823 TCGA-14-2554 TCGA-16-1045 TCGA-19-1389 
       28.93         1.15        17.85        17.49        29.03         4.64 
TCGA-19-1392 TCGA-19-5947 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-27-1832 
        3.48         6.64         4.73         1.78         6.51         9.86 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1755 TCGA-28-5204 TCGA-28-5216 
       10.39         7.59         8.35         1.55         3.91        13.64 
TCGA-32-1973 TCGA-32-1978 TCGA-32-1980 TCGA-32-1987 TCGA-32-2494 TCGA-32-4210 
       21.07        15.85         1.18        14.86        20.78         3.72 
TCGA-41-3915 TCGA-41-5651 TCGA-74-6578 TCGA-76-4928 TCGA-OX-A56R 
       11.84        11.54        14.33         3.09         5.92 

$`DEL PEAK 37(16Q23.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
        9.17         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        55.86        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        10.36        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-02-0075 
       19.73        26.43        28.70        25.05         5.49        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         0.23        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-02-0115 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-02-0285 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-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       12.23         7.73        10.62         0.16        15.91        25.71 
TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
        4.37        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 
       11.34         9.27        16.21        16.80        15.32        15.45 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        10.52        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 
       11.80         2.56        10.65         5.29         3.12         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 
        5.49         3.91         4.96        11.84         0.20         0.36 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        70.52         4.70         8.05         0.16        12.33 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 
        4.47         9.67         2.04        23.57         5.39         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         5.85 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         6.35        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2570 
        2.83        30.64         5.95         6.81         5.98        31.50 
TCGA-06-5408 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.24         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        6.71         3.75         6.15         3.95         5.39         1.48 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U1 
        7.36         8.32        12.85         1.55         4.96         1.87 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 TCGA-08-0512 
        9.17        15.72         3.19        10.59         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
        8.52        18.44        58.19         1.28         4.80         6.54 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0620 TCGA-12-0656 
       17.33         5.52        14.01        14.43         5.95        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 
        0.10        38.17        25.97        24.13         6.12        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 
       23.51        38.76         8.94        20.58         5.82         6.25 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.98         9.44        25.28         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-14-0740 
       25.78        10.95        11.77        34.52         3.22        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 
        0.95         6.21        23.05        11.24        13.78         5.39 
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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.15        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
       25.38         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        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 
        7.00         7.04        11.28         8.02        18.64         7.96 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        5.39         5.29         5.42         3.98        16.57        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        2.33         4.80        16.60        18.25        33.14        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        10.39        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-28-1756 TCGA-28-1757 TCGA-28-2502 
        7.63         8.48         1.22         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 
        6.74         4.77         7.30         5.26         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       14.53        11.77        31.27        14.20         7.79         4.21 
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-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 
       19.50         4.67        12.69        16.93        12.23        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        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 
        8.94         9.53         0.99         4.44         0.20         7.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34         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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                           0.3                            0.1 
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                        127.59                         108.82 
  DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE 
                          9.40                          10.36 
[1] "0.3 - 127.6 (9.4)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1.3"
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.3) MUTATED    40  55
  DEL PEAK 37(16Q23.3) WILD-TYPE 180 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.3) MUTATED     40   55
  DEL PEAK 37(16Q23.3) WILD-TYPE  180  285
        clus
vv       DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE
  FEMALE                           40                            180
  MALE                             55                            285
[1] 2 2
[1] FALSE
D62V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 37(16Q23.3) MUTATED                               3
  DEL PEAK 37(16Q23.3) WILD-TYPE                            14
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 37(16Q23.3) MUTATED                     2
  DEL PEAK 37(16Q23.3) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 37(16Q23.3) MUTATED                                90
  DEL PEAK 37(16Q23.3) WILD-TYPE                             435
D62V5, multiclass
                                 clus
vv                                DEL PEAK 37(16Q23.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           90
                                 clus
vv                                DEL PEAK 37(16Q23.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  TREATED PRIMARY GBM                                         16
  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"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.3) MUTATED    54  41
  DEL PEAK 37(16Q23.3) WILD-TYPE 328 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.3) MUTATED     54   41
  DEL PEAK 37(16Q23.3) WILD-TYPE  328  137
     clus
vv    DEL PEAK 37(16Q23.3) MUTATED DEL PEAK 37(16Q23.3) WILD-TYPE
  NO                            54                            328
  YES                           41                            137
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.3) MUTATED       2                        11    79
  DEL PEAK 37(16Q23.3) WILD-TYPE    11                        28   406
D62V7, multiclass
                           clus
vv                          DEL PEAK 37(16Q23.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               79
                           clus
vv                          DEL PEAK 37(16Q23.3) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             28
  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"
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.3) MUTATED     1  81
  DEL PEAK 37(16Q23.3) WILD-TYPE  11 381
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.3) MUTATED      1   81
  DEL PEAK 37(16Q23.3) WILD-TYPE   11  381
                        clus
vv                       DEL PEAK 37(16Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 37(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            381
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 38(17P13.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(17P13.2) MUTATED    15  67
  DEL PEAK 38(17P13.2) WILD-TYPE  83 395
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                            82                            478 
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                            67                            395 
$`DEL PEAK 38(17P13.2) MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0079 
        9.17         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        10.52 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 TCGA-06-0177 TCGA-06-0184 
       16.70         7.86        11.80         9.44         2.01        40.37 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 
       26.33        28.47        14.93        10.29        18.31         2.60 
TCGA-06-0206 TCGA-06-0241 TCGA-06-0410 TCGA-06-0644 TCGA-06-0744 TCGA-06-1086 
        6.48        14.96         4.70        12.33        19.56         6.35 
TCGA-06-2561 TCGA-06-2569 TCGA-06-5408 TCGA-06-6700 TCGA-08-0245 TCGA-08-0353 
        9.27         0.43        11.24         4.77        34.75         6.41 
TCGA-08-0386 TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 TCGA-12-0780 TCGA-12-0826 
       15.72        10.59        10.39        53.10        14.27        27.78 
TCGA-12-1098 TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-14-0783 TCGA-14-0871 
        3.98         9.44        43.23        11.74         6.21        28.93 
TCGA-14-1453 TCGA-14-1794 TCGA-14-2555 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 
        1.15         0.99         7.96         3.78         5.52         3.91 
TCGA-16-1060 TCGA-19-0960 TCGA-19-2623 TCGA-19-2629 TCGA-19-4065 TCGA-26-1442 
        3.65         8.61         7.53        16.47         7.04        31.33 
TCGA-26-5133 TCGA-27-1835 TCGA-28-1756 TCGA-28-2509 TCGA-28-5215 TCGA-32-1976 
       14.86        21.30         2.83         4.77         7.79         0.49 
TCGA-32-2491 TCGA-32-2616 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 
       12.23         7.36         8.94         0.99        11.84        11.54 
TCGA-76-4925 TCGA-76-4934 TCGA-76-6285 TCGA-76-6662 
        4.80         2.53         8.35         9.27 

$`DEL PEAK 38(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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        32.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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         9.80        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 
       12.79         8.65         3.19         5.46        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 
        2.53        73.84         4.67         7.04         0.39         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 
        0.36        18.02        10.36        11.80        20.42        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        5.52         0.26        70.52         8.05         0.16        35.01 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       22.32         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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 
        3.95         7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
        0.95         9.17        10.85         3.19         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       18.12        28.41        12.43        43.10         5.49         9.11 
TCGA-12-0778 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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       14.53         3.42        25.28        13.61         6.41        59.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-1034 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.17        17.49         3.42         9.86        50.53        19.10 
TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       53.19         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        0.82         9.90        13.35        18.28        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         0.43        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         3.48 
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-19-2631 TCGA-19-5947 TCGA-19-5950 
        1.08         0.16         4.08         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        5.39         5.29         5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        33.14        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        10.39        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-28-1752 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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         7.30         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       15.58        14.53        11.77        31.27        14.20        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         5.42        15.39        21.07 
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-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       14.86        16.93        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        21.17        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 
       10.85        10.62         0.85        13.35         9.53         4.44 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        0.20         7.76         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 
       10.78        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         0.23         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE 
                         9.735                         10.255 
[1] "0.4 - 92.7 (9.7)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.2) MUTATED    37  45
  DEL PEAK 38(17P13.2) WILD-TYPE 183 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.2) MUTATED     37   45
  DEL PEAK 38(17P13.2) WILD-TYPE  183  295
        clus
vv       DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE
  FEMALE                           37                            183
  MALE                             45                            295
[1] 2 2
[1] FALSE
D63V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 38(17P13.2) MUTATED                               1
  DEL PEAK 38(17P13.2) WILD-TYPE                            16
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 38(17P13.2) MUTATED                     2
  DEL PEAK 38(17P13.2) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 38(17P13.2) MUTATED                                79
  DEL PEAK 38(17P13.2) WILD-TYPE                             446
D63V5, multiclass
                                 clus
vv                                DEL PEAK 38(17P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           79
                                 clus
vv                                DEL PEAK 38(17P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               16
  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"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.2) MUTATED    55  27
  DEL PEAK 38(17P13.2) WILD-TYPE 327 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.2) MUTATED     55   27
  DEL PEAK 38(17P13.2) WILD-TYPE  327  151
     clus
vv    DEL PEAK 38(17P13.2) MUTATED DEL PEAK 38(17P13.2) WILD-TYPE
  NO                            55                            327
  YES                           27                            151
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17P13.2) MUTATED       2                         6    73
  DEL PEAK 38(17P13.2) WILD-TYPE    11                        33   412
D63V7, multiclass
                           clus
vv                          DEL PEAK 38(17P13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               73
                           clus
vv                          DEL PEAK 38(17P13.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             33
  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"
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.2) MUTATED     2  70
  DEL PEAK 38(17P13.2) WILD-TYPE  10 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.2) MUTATED      2   70
  DEL PEAK 38(17P13.2) WILD-TYPE   10  392
                        clus
vv                       DEL PEAK 38(17P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       DEL PEAK 38(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            392
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 39(17P13.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P13.1) MUTATED    15  77
  DEL PEAK 39(17P13.1) WILD-TYPE  83 385
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            92                            468 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            77                            385 
$`DEL PEAK 39(17P13.1) MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0033 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
        9.17        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        10.52        16.70         7.86        11.80         9.44 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        2.01        40.37        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 TCGA-06-0213 TCGA-06-0241 TCGA-06-0397 
       18.31         2.60         6.48         0.20        14.96         5.52 
TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0744 TCGA-06-0875 TCGA-06-1086 
        4.70        12.33         4.47        19.56        43.46         6.35 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2569 TCGA-06-5408 TCGA-06-6694 
        1.08         0.76         9.27         0.43        11.24         7.36 
TCGA-08-0245 TCGA-08-0353 TCGA-08-0386 TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 
       34.75         6.41        15.72        10.59        10.39        53.10 
TCGA-12-0826 TCGA-12-1098 TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-14-0783 
       27.78         3.98         9.44        43.23        11.74         6.21 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1396 TCGA-14-1453 TCGA-14-1794 TCGA-14-3477 
       28.93        15.95         1.12         1.15         0.99         3.78 
TCGA-15-1449 TCGA-16-0846 TCGA-19-0960 TCGA-19-1791 TCGA-19-2623 TCGA-19-2629 
        5.52         3.91         8.61         0.13         7.53        16.47 
TCGA-19-4065 TCGA-26-1442 TCGA-26-5133 TCGA-27-1835 TCGA-28-1756 TCGA-28-2509 
        7.04        31.33        14.86        21.30         2.83         4.77 
TCGA-28-5215 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2616 TCGA-32-4210 
        7.79         0.49        14.86        12.23         7.36         3.72 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-76-4925 TCGA-76-4934 
        8.94         0.99        11.84        11.54         4.80         2.53 
TCGA-76-6285 TCGA-76-6662 
        8.35         9.27 

$`DEL PEAK 39(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        55.86        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        10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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         9.80        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        2.73        91.00        53.98        19.00         2.53        73.84 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        4.67         7.04         0.39         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84        12.43        22.49         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       11.80        20.42        10.32         0.26        70.52         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        0.16        35.01         3.22         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        22.32         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         3.58        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       13.61        33.90        15.32         4.93         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5410 
        5.95         6.81         5.98         4.37        31.50         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       10.39         7.59         3.42        53.82         1.28        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       10.85         3.19         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
        3.42        25.28        13.61         6.41        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0813 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-14-1037 TCGA-14-1043 TCGA-14-1395 
       16.50        26.33         2.04        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-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96         6.15        12.43         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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 
        3.42         9.86        50.53        19.10        53.19         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        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         3.48         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-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        10.03        13.87         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        33.14        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 
       10.39        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-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         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         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        14.20        13.64         4.21        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-32-1986 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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        9.53         4.44         0.20         7.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         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        10.78        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         0.23 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                          9.44                          10.36 
[1] "0.1 - 92.7 (9.4)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.1) MUTATED    44  48
  DEL PEAK 39(17P13.1) WILD-TYPE 176 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED     44   48
  DEL PEAK 39(17P13.1) WILD-TYPE  176  292
        clus
vv       DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE
  FEMALE                           44                            176
  MALE                             48                            292
[1] 2 2
[1] FALSE
D64V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 39(17P13.1) MUTATED                               1
  DEL PEAK 39(17P13.1) WILD-TYPE                            16
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 39(17P13.1) MUTATED                     3
  DEL PEAK 39(17P13.1) WILD-TYPE                  15
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 39(17P13.1) MUTATED                                88
  DEL PEAK 39(17P13.1) WILD-TYPE                             437
D64V5, multiclass
                                 clus
vv                                DEL PEAK 39(17P13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 39(17P13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               16
  TREATED PRIMARY GBM                                         15
  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"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.1) MUTATED    57  35
  DEL PEAK 39(17P13.1) WILD-TYPE 325 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED     57   35
  DEL PEAK 39(17P13.1) WILD-TYPE  325  143
     clus
vv    DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE
  NO                            57                            325
  YES                           35                            143
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17P13.1) MUTATED       2                         7    81
  DEL PEAK 39(17P13.1) WILD-TYPE    11                        32   404
D64V7, multiclass
                           clus
vv                          DEL PEAK 39(17P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               81
                           clus
vv                          DEL PEAK 39(17P13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             32
  WHITE                                                404
[1] 3 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(17P13.1) MUTATED     2  79
  DEL PEAK 39(17P13.1) WILD-TYPE  10 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED      2   79
  DEL PEAK 39(17P13.1) WILD-TYPE   10  383
                        clus
vv                       DEL PEAK 39(17P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 39(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            383
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 40(17Q11.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17Q11.2) MUTATED     9  59
  DEL PEAK 40(17Q11.2) WILD-TYPE  89 403
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            68                            492 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            59                            403 
$`DEL PEAK 40(17Q11.2) MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0039 TCGA-02-0055 TCGA-02-0059 TCGA-02-0079 
        9.17         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        10.52        16.70         7.86        11.80         9.44 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0175 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
       56.88         5.29         2.73         2.01        40.37        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 TCGA-06-0644 
       14.93        10.29        18.31         2.60         6.48        12.33 
TCGA-06-0744 TCGA-06-0882 TCGA-06-2569 TCGA-06-5408 TCGA-06-6697 TCGA-08-0353 
       19.56         5.42         0.43        11.24        12.85         6.41 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0512 TCGA-12-0619 TCGA-12-0703 TCGA-12-0772 
       15.72        10.59        11.77        10.39        18.12        53.10 
TCGA-12-0775 TCGA-12-0826 TCGA-12-1098 TCGA-12-3653 TCGA-14-0862 TCGA-14-0871 
        5.49        27.78         3.98        11.74         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-26-5133 TCGA-27-2527 TCGA-28-2502 TCGA-28-2509 
        6.64         4.73        14.86        14.40         0.66         4.77 
TCGA-32-1986 TCGA-32-2491 TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 TCGA-74-6573 
       12.69        12.23         0.99         0.20        11.54         3.45 
TCGA-76-4934 TCGA-76-6285 
        2.53         8.35 

$`DEL PEAK 40(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        55.86        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        10.36        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         0.23        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 
        0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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         9.80        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0168 
        3.19         5.46        11.80         2.56        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 
        3.12        13.02         0.23         2.20        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0194 TCGA-06-0195 
       19.00         2.53        73.84        28.47         4.67         7.04 
TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        35.01         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 
        9.67         2.04        23.57         9.40        22.32         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95         6.81         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         8.32 
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-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
        0.95         9.17        10.85         3.19         0.30         0.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        3.52         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 
       38.17        25.97        24.13         6.12         2.63        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       12.43        43.10         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       11.97        11.38        15.85         9.11        14.53         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 
        5.39        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-14-1794 
       30.18         0.92        40.96         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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-19-1787 
       12.95         4.64        25.38         3.48         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
        3.25         0.13         9.67         4.87         1.08         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08        16.47         7.00        11.28         8.02        18.64 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        10.03        13.87         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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        10.39        10.39        16.08         7.59         2.86 
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-28-2506 
        8.48         1.22         1.55         2.83         0.13         6.74 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
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-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       16.93        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        21.17        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        10.62         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.44        11.84         7.76        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        10.78        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         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 

  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                           0.2                            0.1 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                        10.455                          9.915 
[1] "0.2 - 92.7 (10.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    26  42
  DEL PEAK 40(17Q11.2) WILD-TYPE 194 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     26   42
  DEL PEAK 40(17Q11.2) WILD-TYPE  194  298
        clus
vv       DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  FEMALE                           26                            194
  MALE                             42                            298
[1] 2 2
[1] FALSE
D65V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 40(17Q11.2) MUTATED                               1
  DEL PEAK 40(17Q11.2) WILD-TYPE                            16
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 40(17Q11.2) MUTATED                     2
  DEL PEAK 40(17Q11.2) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 40(17Q11.2) MUTATED                                65
  DEL PEAK 40(17Q11.2) WILD-TYPE                             460
D65V5, multiclass
                                 clus
vv                                DEL PEAK 40(17Q11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           65
                                 clus
vv                                DEL PEAK 40(17Q11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               16
  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"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    40  28
  DEL PEAK 40(17Q11.2) WILD-TYPE 342 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     40   28
  DEL PEAK 40(17Q11.2) WILD-TYPE  342  150
     clus
vv    DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  NO                            40                            342
  YES                           28                            150
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17Q11.2) MUTATED       2                         5    59
  DEL PEAK 40(17Q11.2) WILD-TYPE    11                        34   426
D65V7, multiclass
                           clus
vv                          DEL PEAK 40(17Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               59
                           clus
vv                          DEL PEAK 40(17Q11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             34
  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"
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED     1  57
  DEL PEAK 40(17Q11.2) WILD-TYPE  11 405
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED      1   57
  DEL PEAK 40(17Q11.2) WILD-TYPE   11  405
                        clus
vv                       DEL PEAK 40(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 40(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            405
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 41(18Q22.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q22.3) MUTATED    18  62
  DEL PEAK 41(18Q22.3) WILD-TYPE  80 400
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            80                            480 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            62                            400 
$`DEL PEAK 41(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 
       32.52        46.59         0.23         6.48        10.36         9.67 
TCGA-06-0649 TCGA-06-0749 TCGA-06-1086 TCGA-06-1800 TCGA-06-1806 TCGA-06-2559 
        2.04         2.17         6.35        26.79        15.32         4.93 
TCGA-06-5413 TCGA-06-5859 TCGA-06-6388 TCGA-06-6694 TCGA-06-A5U1 TCGA-08-0245 
        8.81         4.57         3.95         7.36         1.87        34.75 
TCGA-08-0357 TCGA-08-0359 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0525 
       35.64         0.95         3.52         8.52         1.28        15.98 
TCGA-12-0691 TCGA-12-0775 TCGA-12-0776 TCGA-12-0826 TCGA-12-1096 TCGA-12-1098 
        6.12         5.49         9.11        27.78         9.11         3.98 
TCGA-12-5301 TCGA-14-0812 TCGA-14-0817 TCGA-14-0865 TCGA-16-0846 TCGA-16-0849 
        2.04         3.25         5.39        16.50         3.91        26.07 
TCGA-19-0962 TCGA-19-1388 TCGA-19-1390 TCGA-19-2619 TCGA-19-4065 TCGA-19-5960 
        0.43        12.95        25.38         9.67         7.04         5.42 
TCGA-26-1438 TCGA-26-1439 TCGA-26-5133 TCGA-26-5136 TCGA-26-6173 TCGA-27-1834 
       10.03        13.87        14.86         1.22         7.92        33.14 
TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5216 
       11.51         8.35         5.26         9.04        31.27        13.64 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2634 TCGA-32-4210 
       21.07         0.49        14.86        12.23        22.78         3.72 
TCGA-41-3392 TCGA-74-6575 TCGA-76-4929 TCGA-76-4934 TCGA-76-6285 TCGA-76-6286 
        0.99        20.91         3.65         2.53         8.35        20.98 
TCGA-76-6662 TCGA-81-5911 
        9.27        17.72 

$`DEL PEAK 41(18Q22.3) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
        9.17         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        55.86        77.65        20.12        24.59        10.36 
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 
        0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.12        13.02         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        2.60         0.39         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.20        12.43        22.49         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        4.47        23.57         9.40        22.32        19.56         5.39 
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 
       22.98         5.85         5.42        20.94         7.43         3.58 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        33.90         1.08         0.76 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0375 
        6.41        15.06        22.52        14.70        19.53         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.77        18.44        58.19        10.75         4.80         6.54 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
       43.10        14.86        14.27        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         6.25        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       15.85        14.53         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 
       11.77        34.52        11.74        13.12         3.22        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-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
       13.78         1.35         2.89        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-14-1795 
        0.92        40.96         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       53.19         5.52         9.93        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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-19-1389 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07         5.95         4.64         3.48         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-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        16.47         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 
        5.39         5.29         3.98        16.57         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
        7.13         9.37         9.40         5.49         8.88         1.58 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        2.33         4.80        16.60         9.86        18.25        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        10.39        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-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         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         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       15.58        14.53        11.77        14.20         7.79         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 
       22.68        10.49         5.42        15.39         0.10        15.85 
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-32-2638 TCGA-32-4208 
       15.02        15.95         7.36         8.84        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76         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        10.78        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 
        0.23         7.73         7.79         1.61        26.30         5.92 

  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                          0.23                           0.10 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                          9.47                          10.34 
[1] "0.2 - 92.7 (9.5)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.3) MUTATED    30  50
  DEL PEAK 41(18Q22.3) WILD-TYPE 190 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED     30   50
  DEL PEAK 41(18Q22.3) WILD-TYPE  190  290
        clus
vv       DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE
  FEMALE                           30                            190
  MALE                             50                            290
[1] 2 2
[1] FALSE
D66V4, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 41(18Q22.3) MUTATED                               3
  DEL PEAK 41(18Q22.3) WILD-TYPE                            14
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 41(18Q22.3) MUTATED                     2
  DEL PEAK 41(18Q22.3) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 41(18Q22.3) MUTATED                                75
  DEL PEAK 41(18Q22.3) WILD-TYPE                             450
D66V5, multiclass
                                 clus
vv                                DEL PEAK 41(18Q22.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           75
                                 clus
vv                                DEL PEAK 41(18Q22.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               14
  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"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.3) MUTATED    53  27
  DEL PEAK 41(18Q22.3) WILD-TYPE 329 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED     53   27
  DEL PEAK 41(18Q22.3) WILD-TYPE  329  151
     clus
vv    DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE
  NO                            53                            329
  YES                           27                            151
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q22.3) MUTATED       3                         7    67
  DEL PEAK 41(18Q22.3) WILD-TYPE    10                        32   418
D66V7, multiclass
                           clus
vv                          DEL PEAK 41(18Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               67
                           clus
vv                          DEL PEAK 41(18Q22.3) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             32
  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"
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.3) MUTATED     3  67
  DEL PEAK 41(18Q22.3) WILD-TYPE   9 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED      3   67
  DEL PEAK 41(18Q22.3) WILD-TYPE    9  395
                        clus
vv                       DEL PEAK 41(18Q22.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 41(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            395
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 42(19Q13.41) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 42(19Q13.41) MUTATED    19  79
  DEL PEAK 42(19Q13.41) WILD-TYPE  79 383
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             98                             462 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             79                             383 
$`DEL PEAK 42(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        18.74         7.86        11.80        10.36        10.32 
TCGA-06-0745 TCGA-06-0875 TCGA-06-0878 TCGA-06-1084 TCGA-06-2561 TCGA-06-2562 
        5.39        43.46         7.17         7.43         9.27         2.83 
TCGA-06-2563 TCGA-06-2569 TCGA-06-5411 TCGA-06-5415 TCGA-06-6693 TCGA-06-A6S1 
       30.64         0.43         8.35         8.55         0.49         2.56 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 
       22.68        34.75       108.82         4.34        10.39         7.59 
TCGA-08-0351 TCGA-08-0358 TCGA-08-0386 TCGA-08-0392 TCGA-08-0517 TCGA-12-0619 
       53.82        19.53        15.72         0.30        58.19        10.39 
TCGA-12-0656 TCGA-12-0772 TCGA-12-0827 TCGA-12-1088 TCGA-12-1094 TCGA-12-1095 
       65.92        53.10        38.76       127.59        11.38        15.85 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-3651 TCGA-14-0740 TCGA-14-0783 
       14.53         3.42         9.44        11.77        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         6.15         3.42        50.53 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-0960 TCGA-19-1388 TCGA-19-1390 
       16.31         4.31         6.41         8.61        12.95        25.38 
TCGA-19-2629 TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 TCGA-28-1746 
       16.47         1.22        33.14        10.39        10.39         0.20 
TCGA-28-2514 TCGA-28-5211 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 
        5.26        11.77        15.39        21.07         0.49        15.85 
TCGA-32-1987 TCGA-32-2491 TCGA-32-4208 TCGA-32-4210 TCGA-41-2575 TCGA-41-5651 
       14.86        12.23        21.14         3.72         9.53        11.54 
TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 TCGA-76-6193 TCGA-76-6285 TCGA-76-6662 
        4.80         3.65         9.17         2.70         8.35         9.27 
TCGA-76-6664 TCGA-87-5896 
        7.79        26.30 

$`DEL PEAK 42(19Q13.41) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36         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 
        0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        10.52        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80        19.46        46.59        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.20        12.43        22.49         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       20.42        14.96         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.70         2.17         0.92        46.19         5.65        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.85         5.42        20.94         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.24         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         3.95 
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-08-0246 TCGA-08-0345 TCGA-08-0347 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 
        3.91         1.74        13.78         3.42         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 
       15.06        22.52        14.70        35.64         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       10.85         3.19        10.59         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
        8.52        18.44         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        5.95         7.17         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
        6.12         2.63        18.12        28.41        12.43        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
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-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1096 
        5.82         6.25        30.54        21.63        11.97         9.11 
TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.98        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       25.78        11.54        10.95        34.52        11.74        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        15.12         0.95        23.05         2.24 
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-14-1396 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-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92        40.96        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-15-1446 TCGA-15-1447 TCGA-15-1449 
        7.96         3.78         9.86        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91         9.93        26.07        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       13.35         3.65        18.28        13.97        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.43        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         3.48         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-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        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-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 
        7.30         3.91         9.04        15.58        14.53        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
TCGA-28-6450 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        5.42         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       16.93        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       22.78        21.17        12.59        19.86        10.85        10.62 
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-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        0.20         7.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 
        8.22         7.50         4.54         3.09         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29        11.38        17.06        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-OX-A56R 
        5.03         0.23         7.73         1.61        17.72         5.92 

  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                            0.2                             0.1 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                         127.59                           92.65 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                         10.505                           9.765 
[1] "0.2 - 127.6 (10.5)" "0.1 - 92.7 (9.8)"  
[1] "hr=" "1.3"
D67V2, continuous
D67V3, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED    39  59
  DEL PEAK 42(19Q13.41) WILD-TYPE 181 281
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED     39   59
  DEL PEAK 42(19Q13.41) WILD-TYPE  181  281
        clus
vv       DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE
  FEMALE                            39                             181
  MALE                              59                             281
[1] 2 2
[1] FALSE
D67V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 42(19Q13.41) MUTATED                               2
  DEL PEAK 42(19Q13.41) WILD-TYPE                            15
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 42(19Q13.41) MUTATED                     4
  DEL PEAK 42(19Q13.41) WILD-TYPE                  14
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 42(19Q13.41) MUTATED                                92
  DEL PEAK 42(19Q13.41) WILD-TYPE                             433
D67V5, multiclass
                                 clus
vv                                DEL PEAK 42(19Q13.41) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               2
  TREATED PRIMARY GBM                                         4
  UNTREATED PRIMARY (DE NOVO) GBM                            92
                                 clus
vv                                DEL PEAK 42(19Q13.41) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                15
  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"
D67V6, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED    67  31
  DEL PEAK 42(19Q13.41) WILD-TYPE 315 147
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED     67   31
  DEL PEAK 42(19Q13.41) WILD-TYPE  315  147
     clus
vv    DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE
  NO                             67                             315
  YES                            31                             147
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(19Q13.41) MUTATED       2                        10    83
  DEL PEAK 42(19Q13.41) WILD-TYPE    11                        29   402
D67V7, multiclass
                           clus
vv                          DEL PEAK 42(19Q13.41) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                                83
                           clus
vv                          DEL PEAK 42(19Q13.41) WILD-TYPE
  ASIAN                                                  11
  BLACK OR AFRICAN AMERICAN                              29
  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"
D67V8, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED     2  81
  DEL PEAK 42(19Q13.41) WILD-TYPE  10 381
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED      2   81
  DEL PEAK 42(19Q13.41) WILD-TYPE   10  381
                        clus
vv                       DEL PEAK 42(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            81
                        clus
vv                       DEL PEAK 42(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             381
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 43(21Q22.11) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 43(21Q22.11) MUTATED     7  39
  DEL PEAK 43(21Q22.11) WILD-TYPE  91 423
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                             46                             514 
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                             39                             423 
$`DEL PEAK 43(21Q22.11) MUTATED`
TCGA-02-0011 TCGA-02-0015 TCGA-02-0051 TCGA-02-0069 TCGA-02-0106 TCGA-02-0114 
       20.71        20.61        15.09        28.70        11.67        99.98 
TCGA-02-0258 TCGA-02-0266 TCGA-02-0281 TCGA-02-0339 TCGA-06-0209 TCGA-06-0221 
       16.54        17.72         3.98        12.39         3.91        18.02 
TCGA-06-0402 TCGA-06-0414 TCGA-06-0648 TCGA-06-0875 TCGA-06-5856 TCGA-06-6389 
        0.26        35.01         9.67        43.46         3.75         7.79 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0353 TCGA-08-0516 TCGA-12-0820 TCGA-12-0826 
        0.49         7.36         6.41        18.44        18.48        27.78 
TCGA-12-0827 TCGA-12-1099 TCGA-12-1600 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 
       38.76         3.42        13.61        11.74        11.97         5.39 
TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-16-0848 TCGA-16-0850 TCGA-19-0960 
       17.85         3.78         9.86         9.93        16.31         8.61 
TCGA-19-2629 TCGA-19-5958 TCGA-27-2521 TCGA-28-2514 TCGA-32-1973 TCGA-32-1978 
       16.47         5.39        10.39         5.26        21.07        15.85 
TCGA-32-4210 TCGA-41-3392 TCGA-76-4925 TCGA-76-4934 
        3.72         0.99         4.80         2.53 

$`DEL PEAK 43(21Q22.11) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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-02-0070 TCGA-02-0071 TCGA-02-0074 
        6.02        19.73        26.43        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         0.23        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-02-0260 
       17.65        23.18        92.65        15.65        48.95        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         0.16        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-02-0456 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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         5.49         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       12.43        22.49         0.36        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         5.52        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 
        0.16        12.33         3.22         4.47         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        46.19         5.65         7.17        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        6.71         2.73         6.15         4.57         3.95         5.39 
TCGA-06-6391 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        1.48         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        7.59         3.42        53.82         1.28        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.77         8.52        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
       14.86        14.27        91.76        24.79        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.98         9.44        25.28         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         0.95         6.21        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-14-0867 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-14-1452 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 
        6.15        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 
        5.88         7.17        17.49         7.96         3.42        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0861 
       19.10        53.19         5.52         3.91        26.07         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43        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         3.48         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-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
        4.73         7.96         1.78         6.51         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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        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-28-5204 TCGA-28-5207 
        0.66         6.74         4.77         7.30         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        10.49         5.42        15.39 
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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        11.54         7.76 
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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                           0.26                            0.10 
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                          99.98                          127.59 
  DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE 
                         11.705                           9.900 
[1] "0.3 - 100.0 (11.7)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1"  
D68V2, continuous
D68V3, binary
                                 cls
clus                                0   1
  DEL PEAK 43(21Q22.11) MUTATED    19  27
  DEL PEAK 43(21Q22.11) WILD-TYPE 201 313
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(21Q22.11) MUTATED     19   27
  DEL PEAK 43(21Q22.11) WILD-TYPE  201  313
        clus
vv       DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE
  FEMALE                            19                             201
  MALE                              27                             313
[1] 2 2
[1] FALSE
D68V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 43(21Q22.11) MUTATED                               0
  DEL PEAK 43(21Q22.11) WILD-TYPE                            17
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 43(21Q22.11) MUTATED                     1
  DEL PEAK 43(21Q22.11) WILD-TYPE                  17
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 43(21Q22.11) MUTATED                                45
  DEL PEAK 43(21Q22.11) WILD-TYPE                             480
D68V5, multiclass
                                 clus
vv                                DEL PEAK 43(21Q22.11) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               0
  TREATED PRIMARY GBM                                         1
  UNTREATED PRIMARY (DE NOVO) GBM                            45
                                 clus
vv                                DEL PEAK 43(21Q22.11) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                17
  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"
D68V6, binary
                                 cls
clus                                0   1
  DEL PEAK 43(21Q22.11) MUTATED    28  18
  DEL PEAK 43(21Q22.11) WILD-TYPE 354 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(21Q22.11) MUTATED     28   18
  DEL PEAK 43(21Q22.11) WILD-TYPE  354  160
     clus
vv    DEL PEAK 43(21Q22.11) MUTATED DEL PEAK 43(21Q22.11) WILD-TYPE
  NO                             28                             354
  YES                            18                             160
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(21Q22.11) MUTATED       2                         2    41
  DEL PEAK 43(21Q22.11) WILD-TYPE    11                        37   444
D68V7, multiclass
                           clus
vv                          DEL PEAK 43(21Q22.11) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                41
                           clus
vv                          DEL PEAK 43(21Q22.11) WILD-TYPE
  ASIAN                                                  11
  BLACK OR AFRICAN AMERICAN                              37
  WHITE                                                 444
[1] 3 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(21Q22.11) MUTATED     3  39
  DEL PEAK 43(21Q22.11) WILD-TYPE   9 423
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(21Q22.11) MUTATED      3   39
  DEL PEAK 43(21Q22.11) WILD-TYPE    9  423
                        clus
vv                       DEL PEAK 43(21Q22.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            39
                        clus
vv                       DEL PEAK 43(21Q22.11) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             423
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 44(22Q13.32) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(22Q13.32) MUTATED    33 177
  DEL PEAK 44(22Q13.32) WILD-TYPE  65 285
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            210                             350 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            177                             285 
$`DEL PEAK 44(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        55.86        24.59        10.36 
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         0.16 
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        16.21        32.52 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 TCGA-06-0147 TCGA-06-0152 TCGA-06-0158 
        0.20         9.21         2.33        16.70        11.80         5.46 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0175 
        9.44         2.56        56.88         5.29        19.04         2.73 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 
        2.53        73.84        26.33        28.47        14.93         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0211 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        7.04         2.60        11.84        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0744 
       10.36        14.96         5.52         0.26         4.70        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0875 TCGA-06-0878 TCGA-06-0882 TCGA-06-0939 
        5.39         2.70        43.46         7.17         5.42        20.94 
TCGA-06-1084 TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2562 TCGA-06-2565 
        7.43        13.61        15.32         0.76         2.83         6.81 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5418 TCGA-06-5856 
        4.37        11.24         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         0.49        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        34.75         3.91         7.59         3.42 
TCGA-08-0354 TCGA-08-0357 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       15.06        35.64        15.72         3.19         0.30        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0520 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 
        8.52        18.44        10.75        15.98        10.39         5.95 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0707 TCGA-12-0820 TCGA-12-0821 
       65.92        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        30.54         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 
        3.98         9.44        13.61        43.23        11.77        11.74 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0862 
       13.12        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 
        9.86        50.53        53.19        13.35        18.28         0.43 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1389 TCGA-19-1392 TCGA-19-1791 TCGA-19-2620 
        3.39        10.75         4.64         3.48         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        16.47         7.00         6.64         6.51 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1442 TCGA-26-5132 TCGA-26-5136 
        5.39         5.42         3.98        31.33         9.40         1.22 
TCGA-26-6173 TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 
        7.92         4.80         9.86        33.14        21.30        11.51 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-28-1746 TCGA-28-1752 
       10.39        10.39        16.08        14.40         0.20         8.48 
TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5208 TCGA-28-5213 
        2.83         6.74         4.77         9.04        15.58        31.27 
TCGA-28-5214 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 TCGA-32-1980 
       14.20        15.39        21.07         0.49        15.85         1.18 
TCGA-32-1986 TCGA-32-2491 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-4208 
       12.69        12.23        15.95         8.84        22.78        21.14 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
       13.35         8.94         9.53        11.84         0.20         7.76 
TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 
       20.91         8.22         4.80         4.54         3.65         9.17 
TCGA-76-4934 TCGA-76-6280 TCGA-76-6285 TCGA-76-6657 TCGA-87-5896 TCGA-OX-A56R 
        2.53        11.38         8.35         5.03        26.30         5.92 

$`DEL PEAK 44(22Q13.32) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
        9.17         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 
        0.23        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         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 
       23.08        22.16        10.75         2.20        11.74        20.09 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0160 TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
        3.19        11.80        10.65         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 
        2.20        91.00         2.01        53.98        19.00        40.37 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       10.29        18.31         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 
        4.96         0.20        12.43        11.80        20.42        10.32 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       70.52         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 
        2.17         0.92        46.19         5.65        22.98         5.85 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1805 
        6.35         3.58        26.79         8.65         7.89        33.90 
TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 
        1.08         4.93         9.27        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         3.95         1.48         7.36 
TCGA-06-6695 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0344 
        8.32         1.55         4.77         4.96         3.12       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 
        1.74         4.34        13.78        10.39        53.82         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
        6.41        22.52        14.70        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0517 TCGA-08-0518 
       10.85        10.59         0.56         3.52        58.19         1.28 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        4.80         6.54        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0654 TCGA-12-0657 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        1.64         7.17         0.10        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       18.12        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0822 TCGA-12-0828 
       14.86        14.27        91.76        24.79        23.51         8.94 
TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
       20.58         5.82         6.25        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1099 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
       15.85         3.42        25.28         6.41        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       11.54        10.95        34.52         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        0.95        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0866 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 
       26.33         0.79         1.38         1.12         3.75        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         6.15        12.43 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 
        1.97        17.85         7.63         5.88         7.17         7.96 
TCGA-14-4157 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
        3.42        19.10         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 
       16.31         4.31        29.03         0.82         9.90         3.65 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 
       13.97         6.41        11.77        21.90         8.61        14.27 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95        12.95        25.38         7.17        12.66 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 TCGA-19-2624 TCGA-19-4065 TCGA-19-5950 
        3.25         9.67         1.08         0.16         7.04        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 
        8.02        18.64         4.73         7.96         1.78         5.29 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6174 TCGA-27-1831 
       14.86         5.49         8.88         1.58         2.33        16.60 
TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2524 TCGA-27-2526 
       18.25        30.05        14.04        24.76         7.59         2.86 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 
       15.78         2.53         9.21         8.35         7.63         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.55         0.13         0.66         7.30         5.26         3.91 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
       10.49         5.42         0.10        19.50         4.67        14.86 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2638 TCGA-32-4210 
       16.93        20.78        15.02         7.36        21.17         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-3392 
       12.59        19.86        10.85        10.62         0.85         0.99 
TCGA-41-3393 TCGA-41-5651 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 
        4.44        11.54         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        10.78        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         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 
        1.61        17.72 

  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                           0.13                            0.10 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                         127.59                          108.82 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                          10.39                            9.85 
[1] "0.1 - 127.6 (10.4)" "0.1 - 108.8 (9.9)" 
[1] "hr=" "1"  
D69V2, continuous
D69V3, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED    84 126
  DEL PEAK 44(22Q13.32) WILD-TYPE 136 214
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED     84  126
  DEL PEAK 44(22Q13.32) WILD-TYPE  136  214
        clus
vv       DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  FEMALE                            84                             136
  MALE                             126                             214
[1] 2 2
[1] FALSE
D69V4, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 44(22Q13.32) MUTATED                               8
  DEL PEAK 44(22Q13.32) WILD-TYPE                             9
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 44(22Q13.32) MUTATED                     6
  DEL PEAK 44(22Q13.32) WILD-TYPE                  12
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 44(22Q13.32) MUTATED                               196
  DEL PEAK 44(22Q13.32) WILD-TYPE                             329
D69V5, multiclass
                                 clus
vv                                DEL PEAK 44(22Q13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               8
  TREATED PRIMARY GBM                                         6
  UNTREATED PRIMARY (DE NOVO) GBM                           196
                                 clus
vv                                DEL PEAK 44(22Q13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 9
  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"
D69V6, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   140  70
  DEL PEAK 44(22Q13.32) WILD-TYPE 242 108
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    140   70
  DEL PEAK 44(22Q13.32) WILD-TYPE  242  108
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  NO                            140                             242
  YES                            70                             108
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(22Q13.32) MUTATED       6                        11   184
  DEL PEAK 44(22Q13.32) WILD-TYPE     7                        28   301
D69V7, multiclass
                           clus
vv                          DEL PEAK 44(22Q13.32) MUTATED
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               184
                           clus
vv                          DEL PEAK 44(22Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              28
  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"
D69V8, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED     4 178
  DEL PEAK 44(22Q13.32) WILD-TYPE   8 284
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      4  178
  DEL PEAK 44(22Q13.32) WILD-TYPE    8  284
                        clus
vv                       DEL PEAK 44(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           178
                        clus
vv                       DEL PEAK 44(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             284
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 45(XP22.2) MUTATION ANALYSIS
D70V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 45(XP22.2) MUTATED    19  96
  DEL PEAK 45(XP22.2) WILD-TYPE  79 366
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          115                           445 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                           96                           366 
$`DEL PEAK 45(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 
       22.16        11.80         5.46        13.02         2.73        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0743 
       73.84        26.33        12.43         0.36        18.02        22.32 
TCGA-06-1800 TCGA-06-2558 TCGA-06-2561 TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 
       26.79         0.76         9.27        31.50        11.24         6.71 
TCGA-06-5418 TCGA-06-5859 TCGA-06-6693 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0348 
        2.73         4.57         0.49         2.56        34.75        10.39 
TCGA-08-0354 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 
       15.06         3.19         0.30        11.77        58.19        10.75 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0818 TCGA-12-0821 TCGA-12-0827 TCGA-12-1091 
       15.98        14.01        91.76        10.62        38.76        30.54 
TCGA-12-1093 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       11.97        59.41        43.23        11.77        34.52        13.12 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 
       15.12        11.97         6.21         2.24         2.89        16.50 
TCGA-14-0871 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 
       28.93         1.15        17.79         3.78         9.86        50.53 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-19-0964 TCGA-19-1388 TCGA-19-1390 
       16.31         4.31        29.03         3.39        12.95        25.38 
TCGA-19-1392 TCGA-19-1787 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 
        3.48        12.66         9.67         1.08         7.53         4.08 
TCGA-19-2629 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-5133 TCGA-27-1830 
       16.47         6.51         5.42        13.87        14.86         4.80 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-2514 TCGA-28-5204 TCGA-28-5220 
       10.39         7.59         8.35         5.26         3.91        10.49 
TCGA-32-1978 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 
       15.85        12.23        20.78        15.95        22.78        21.14 
TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
        3.72        19.86        10.85        13.35         9.53         0.99 
TCGA-74-6575 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6285 
       20.91         3.65         9.17         2.53        10.78         8.35 
TCGA-OX-A56R 
        5.92 

$`DEL PEAK 45(XP22.2) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
        9.17         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 
       55.86        77.65        20.12        53.10        42.74        10.36 
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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       23.08        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 
       46.59        12.79         8.65         3.19         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
        2.53        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 
        4.96        11.84         0.20        22.49        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35         3.58         8.65         7.89        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         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-5410 
        5.95         6.81         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         3.95         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        1.87         3.12        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
        6.41        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
        9.17        10.85        15.72        10.59         0.56         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
        8.52        18.44         1.28         4.80         6.54        17.33 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        5.52        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        5.49         9.11        14.86        14.27        24.79        18.48 
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-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
        6.25        21.63        11.38        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         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 
       25.78        11.54        10.95        11.74         3.22         2.04 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
        0.95        23.05        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        5.39        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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.15        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-15-1446 TCGA-15-1447 TCGA-15-1449 
       17.49         7.96         3.42        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.91         9.93        26.07         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        8.61         0.43        14.27        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 
        4.64         7.17         3.25         0.13         4.87         0.16 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 
        4.73         7.96         1.78         5.39         5.29         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        10.03         9.73        31.33         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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        2.33        16.60         9.86        18.25        33.14        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        10.39        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-28-1757 
        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-28-5207 TCGA-28-5208 
        0.66         6.74         4.77         7.30         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        4.21        22.68         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-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4211 
       16.93        15.02         7.36         8.84        21.17        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
       10.62         0.85         8.94         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       11.54         7.76         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-6191 TCGA-76-6192 
        7.50         4.80         4.54         3.09        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38        17.06        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                          0.3                           0.1 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                        91.76                        127.59 
  DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE 
                        11.97                          9.37 
[1] "0.3 - 91.8 (12.0)" "0.1 - 127.6 (9.4)"
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED    44  71
  DEL PEAK 45(XP22.2) WILD-TYPE 176 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED     44   71
  DEL PEAK 45(XP22.2) WILD-TYPE  176  269
        clus
vv       DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  FEMALE                          44                           176
  MALE                            71                           269
[1] 2 2
[1] FALSE
D70V4, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 45(XP22.2) MUTATED                               3
  DEL PEAK 45(XP22.2) WILD-TYPE                            14
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 45(XP22.2) MUTATED                     4
  DEL PEAK 45(XP22.2) WILD-TYPE                  14
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 45(XP22.2) MUTATED                               108
  DEL PEAK 45(XP22.2) WILD-TYPE                             417
D70V5, multiclass
                                 clus
vv                                DEL PEAK 45(XP22.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       4
  UNTREATED PRIMARY (DE NOVO) GBM                         108
                                 clus
vv                                DEL PEAK 45(XP22.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              14
  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"
D70V6, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED    79  36
  DEL PEAK 45(XP22.2) WILD-TYPE 303 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED     79   36
  DEL PEAK 45(XP22.2) WILD-TYPE  303  142
     clus
vv    DEL PEAK 45(XP22.2) MUTATED DEL PEAK 45(XP22.2) WILD-TYPE
  NO                           79                           303
  YES                          36                           142
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(XP22.2) MUTATED       4                         7   100
  DEL PEAK 45(XP22.2) WILD-TYPE     9                        32   385
D70V7, multiclass
                           clus
vv                          DEL PEAK 45(XP22.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             100
                           clus
vv                          DEL PEAK 45(XP22.2) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            32
  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"
D70V8, binary
                               cls
clus                              0   1
  DEL PEAK 45(XP22.2) MUTATED     1  97
  DEL PEAK 45(XP22.2) WILD-TYPE  11 365
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 45(XP22.2) MUTATED      1   97
  DEL PEAK 45(XP22.2) WILD-TYPE   11  365
                        clus
vv                       DEL PEAK 45(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK 45(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           365
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 46(XQ23) MUTATION ANALYSIS
D71V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 46(XQ23) MUTATED    23  83
  DEL PEAK 46(XQ23) WILD-TYPE  75 379
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                        106                         454 
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                         83                         379 
$`DEL PEAK 46(XQ23) MUTATED`
TCGA-02-0007 TCGA-02-0011 TCGA-02-0016 TCGA-02-0026 TCGA-02-0034 TCGA-02-0039 
       23.18        20.71        55.86        24.59        14.14        10.52 
TCGA-02-0048 TCGA-02-0068 TCGA-02-0070 TCGA-02-0099 TCGA-02-0330 TCGA-02-0339 
        3.22        26.43        25.05         3.48        15.91        12.39 
TCGA-02-2466 TCGA-06-0129 TCGA-06-0138 TCGA-06-0152 TCGA-06-0162 TCGA-06-0171 
       16.80        32.52        22.16        11.80         2.56        13.02 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0214 TCGA-06-0219 TCGA-06-0875 TCGA-06-1800 
       40.37        73.84        12.43         0.36        43.46        26.79 
TCGA-06-2558 TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        0.76        31.50        11.24         6.71         2.73         3.75 
TCGA-06-5859 TCGA-06-6693 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0348 
        4.57         0.49         1.87         2.56        34.75        10.39 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 
       15.06        22.52         3.19         0.30        11.77        58.19 
TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0821 TCGA-12-1091 TCGA-12-1097 
       10.75        15.98        14.01        10.62        30.54        14.53 
TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
        9.44        59.41        43.23        11.77        34.52        13.12 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-1453 
       15.12        11.97         2.24         2.89        16.50         1.15 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1447 TCGA-16-0861 TCGA-16-1045 TCGA-19-1390 
        3.78         9.86        53.19         4.31        29.03        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 
        3.48         7.17         9.67         1.08         7.53         4.08 
TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-5133 
       16.47         6.64         6.51         5.42        13.87        14.86 
TCGA-26-5134 TCGA-27-2524 TCGA-28-1750 TCGA-28-2514 TCGA-28-5204 TCGA-28-5209 
        5.49         7.59         8.35         5.26         3.91        14.53 
TCGA-28-5220 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-2494 TCGA-32-2615 
       10.49        21.07         0.10        15.85        20.78        15.95 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2575 TCGA-41-3392 
       22.78        21.14        19.86        10.85         9.53         0.99 
TCGA-74-6573 TCGA-74-6575 TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        3.45        20.91         4.80         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6285 TCGA-76-6286 TCGA-OX-A56R 
       10.78         8.35        20.98         5.92 

$`DEL PEAK 46(XQ23) WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
        9.17         4.73        18.35        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 
       20.61        77.65        20.12        53.10        42.74        10.36 
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-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0069 TCGA-02-0071 
        8.35         9.57         6.02        19.73        28.70         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         0.23 
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-02-0106 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-02-0289 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         0.16        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-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
       22.72        10.52        18.74        14.07        23.08        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       16.70         9.80         7.86        19.46        46.59        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
        8.65         3.19         5.46         9.44        11.80        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
       10.65         5.29        19.04         3.12         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.73        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 
        4.96        11.84         0.20        22.49        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       70.52         4.70         8.05         0.16        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         6.35         3.58         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32         1.08         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2569 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        0.43         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        8.55         6.15         3.95         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-A6S0 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        4.96         3.12        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
        6.41        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       10.85        15.72        10.59         0.56         3.52         8.52 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 
       18.44         1.28         4.80         6.54        17.33         5.52 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
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-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         6.25        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        9.11         3.98         3.42        25.28        13.61         6.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 
       25.78        11.54        10.95        11.74         3.22         2.04 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        0.95         6.21        23.05        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-14-1451 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 
        6.15        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-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       16.31         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 
        4.64        12.66         3.25         0.13         4.87         0.16 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         7.04        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 
        7.96         1.78         5.39         5.29         3.98        16.57 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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        10.39        10.39        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-28-1757 
        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-28-5207 TCGA-28-5208 
        0.66         6.74         4.77         7.30         9.04        15.58 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1979 TCGA-32-1980 
       22.68         5.42        15.39         0.49        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-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 
        7.36         8.84        21.17         3.72        12.59        10.62 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        0.85        13.35         8.94         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       11.54         7.76         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        4.54         3.09        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       17.06         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.79         1.61        17.72        26.30 

  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                        0.1                         0.1 
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                      73.84                      127.59 
  DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE 
                     11.505                       9.620 
[1] "0.1 - 73.8 (11.5)" "0.1 - 127.6 (9.6)"
[1] "hr=" "1.2"
D71V2, continuous
D71V3, binary
                             cls
clus                            0   1
  DEL PEAK 46(XQ23) MUTATED    44  62
  DEL PEAK 46(XQ23) WILD-TYPE 176 278
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 46(XQ23) MUTATED     44   62
  DEL PEAK 46(XQ23) WILD-TYPE  176  278
        clus
vv       DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE
  FEMALE                        44                         176
  MALE                          62                         278
[1] 2 2
[1] FALSE
D71V4, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 46(XQ23) MUTATED                               3                   2
  DEL PEAK 46(XQ23) WILD-TYPE                            14                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 46(XQ23) MUTATED                               101
  DEL PEAK 46(XQ23) WILD-TYPE                             424
D71V5, multiclass
                                 clus
vv                                DEL PEAK 46(XQ23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           3
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                       101
                                 clus
vv                                DEL PEAK 46(XQ23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            14
  TREATED PRIMARY GBM                                      16
  UNTREATED PRIMARY (DE NOVO) GBM                         424
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                             cls
clus                            0   1
  DEL PEAK 46(XQ23) MUTATED    76  30
  DEL PEAK 46(XQ23) WILD-TYPE 306 148
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 46(XQ23) MUTATED     76   30
  DEL PEAK 46(XQ23) WILD-TYPE  306  148
     clus
vv    DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE
  NO                         76                         306
  YES                        30                         148
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(XQ23) MUTATED       4                         9    88
  DEL PEAK 46(XQ23) WILD-TYPE     9                        30   397
D71V7, multiclass
                           clus
vv                          DEL PEAK 46(XQ23) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                            88
                           clus
vv                          DEL PEAK 46(XQ23) WILD-TYPE
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          30
  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"
D71V8, binary
                             cls
clus                            0   1
  DEL PEAK 46(XQ23) MUTATED     3  86
  DEL PEAK 46(XQ23) WILD-TYPE   9 376
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 46(XQ23) MUTATED      3   86
  DEL PEAK 46(XQ23) WILD-TYPE    9  376
                        clus
vv                       DEL PEAK 46(XQ23) MUTATED DEL PEAK 46(XQ23) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        86                         376
[1] 2 2
[1] FALSE
