[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/22506586/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/22538153/transformed.cor.cli.txt"

nPatients in clinical file=595, in cluster file=577, common to both=573
[1]  68 573
[1] "AMP PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            92                            481 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            92                            481 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          159                           414 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          159                           414 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         99                         474 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         99                         474 
[1] "AMP PEAK  4(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           49                           524 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           49                           524 
[1] "AMP PEAK  5(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           109                            464 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           109                            464 
[1] "AMP PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           525 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           525 
[1] "AMP PEAK  7(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         465 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         465 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          503                            70 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          503                            70 
[1] "AMP PEAK  9(7Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           461                            112 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           461                            112 
[1] "AMP PEAK 10(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          476                            97 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          476                            97 
[1] "AMP PEAK 11(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          469                           104 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          469                           104 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            69                            504 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            69                            504 
[1] "AMP PEAK 13(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          543 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          543 
[1] "AMP PEAK 14(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             84                             489 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             84                             489 
[1] "AMP PEAK 15(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           134                            439 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           134                            439 
[1] "AMP PEAK 16(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          93                          480 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          93                          480 
[1] "AMP PEAK 17(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          541 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          541 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          543 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          543 
[1] "AMP PEAK 19(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             537 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             537 
[1] "AMP PEAK 20(17P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            522 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            522 
[1] "AMP PEAK 21(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            84                            489 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            84                            489 
[1] "AMP PEAK 22(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           244                            329 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           244                            329 
[1] "AMP PEAK 23(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                         215                          358 
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                         215                          358 
[1] "AMP PEAK 24(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                            70                            503 
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                            70                            503 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            97                            476 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            97                            476 
[1] "DEL PEAK  2(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           132                            441 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           132                            441 
[1] "DEL PEAK  3(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           61                           512 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           61                           512 
[1] "DEL PEAK  4(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           48                           525 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           48                           525 
[1] "DEL PEAK  5(1Q42.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            50                            523 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            50                            523 
[1] "DEL PEAK  6(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         35                         538 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         35                         538 
[1] "DEL PEAK  7(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           526 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           526 
[1] "DEL PEAK  8(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           518 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           518 
[1] "DEL PEAK  9(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           54                           519 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           54                           519 
[1] "DEL PEAK 10(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            517 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            517 
[1] "DEL PEAK 11(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                         65                         508 
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                         65                         508 
[1] "DEL PEAK 12(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                           78                           495 
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                           78                           495 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           93                           480 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           93                           480 
[1] "DEL PEAK 14(5Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                         69                         504 
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                         69                         504 
[1] "DEL PEAK 15(6Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                          155                           418 
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                          155                           418 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        179                         394 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        179                         394 
[1] "DEL PEAK 17(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                           66                           507 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                           66                           507 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          419                           154 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          419                           154 
[1] "DEL PEAK 19(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                           79                           494 
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                           79                           494 
[1] "DEL PEAK 20(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           466                            107 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           466                            107 
[1] "DEL PEAK 21(10P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                         467                          106 
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                         467                          106 
[1] "DEL PEAK 22(10P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                            472                             101 
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                            472                             101 
[1] "DEL PEAK 23(10Q11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                            485                              88 
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                            485                              88 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            510                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            510                              63 
[1] "DEL PEAK 25(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           511                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           511                             62 
[1] "DEL PEAK 26(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           132                            441 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           132                            441 
[1] "DEL PEAK 27(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           105                            468 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           105                            468 
[1] "DEL PEAK 28(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            477 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            477 
[1] "DEL PEAK 29(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            72                            501 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            72                            501 
[1] "DEL PEAK 30(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          77                          496 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          77                          496 
[1] "DEL PEAK 31(12Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          79                          494 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          79                          494 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           240                            333 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           240                            333 
[1] "DEL PEAK 33(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           228                            345 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           228                            345 
[1] "DEL PEAK 34(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           176                            397 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           176                            397 
[1] "DEL PEAK 35(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           171                            402 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           171                            402 
[1] "DEL PEAK 36(15Q14) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         154                          419 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         154                          419 
[1] "DEL PEAK 37(16P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            92                            481 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            92                            481 
[1] "DEL PEAK 38(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           100                            473 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           100                            473 
[1] "DEL PEAK 39(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            98                            475 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            98                            475 
[1] "DEL PEAK 40(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            72                            501 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            72                            501 
[1] "DEL PEAK 41(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            82                            491 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            82                            491 
[1] "DEL PEAK 42(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                            100                             473 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                            100                             473 
[1] "DEL PEAK 43(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                            56                            517 
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                            56                            517 
[1] "DEL PEAK 44(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            212                             361 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            212                             361 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 573 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=378,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=90,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 573 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P36.21) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  1(1P36.21) MUTATED    11  81
  AMP PEAK  1(1P36.21) WILD-TYPE  86 392
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            92                            478 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                            81                            392 
$`AMP PEAK  1(1P36.21) MUTATED`
TCGA-06-5856 TCGA-06-6698 TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-12-5295 
        3.75         4.77        15.65        44.02        14.53        14.93 
TCGA-14-0783 TCGA-14-1034 TCGA-14-1452 TCGA-14-1454 TCGA-14-1794 TCGA-14-1823 
        6.21        15.95         7.10        30.18         0.99        17.85 
TCGA-14-1827 TCGA-14-2554 TCGA-14-3477 TCGA-16-1056 TCGA-19-1390 TCGA-19-1787 
        5.88        17.49         3.78        14.01        25.38        12.66 
TCGA-19-1791 TCGA-19-4065 TCGA-26-1440 TCGA-26-5132 TCGA-26-5136 TCGA-28-1752 
        0.13         7.04         9.73         9.40        18.97         8.48 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1987 TCGA-32-2638 TCGA-32-4210 TCGA-32-5222 
        4.77        15.39        14.86        25.18         3.72        19.23 
TCGA-41-2575 TCGA-41-6646 TCGA-74-6584 TCGA-76-4934 TCGA-06-0209 TCGA-02-0001 
        9.53        12.46         7.50         2.53         7.63        11.77 
TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 
       42.74        12.59         2.50        11.67        92.65        17.72 
TCGA-02-0269 TCGA-02-0332 TCGA-02-0451 TCGA-02-0456 TCGA-06-0130 TCGA-06-0133 
       10.75        25.71        16.21         3.35        12.95        14.30 
TCGA-06-0152 TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 TCGA-06-0188 
       12.33         4.47         4.18         3.65        27.22        44.58 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 
       38.96         7.40         7.66         0.53        24.16        13.64 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0649 TCGA-06-2557 
        4.70        35.11        12.62         5.75         2.10         1.08 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0386 TCGA-08-0520 TCGA-08-0531 TCGA-12-0619 
        9.80        29.23        18.02        10.75         7.56        34.92 
TCGA-12-0662 TCGA-12-0769 TCGA-12-0776 TCGA-12-0820 TCGA-12-0826 TCGA-12-1090 
       38.17        15.06         9.73        18.48        27.78         7.59 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        3.98         4.14         1.35         5.39         2.04        28.93 
TCGA-15-1449 TCGA-19-1386 TCGA-19-1388 TCGA-28-5207 TCGA-28-5216 TCGA-28-6450 
       13.28         9.07        12.95        11.28        13.64         5.42 
TCGA-32-2616 TCGA-76-6283 
        7.36         5.42 

$`AMP PEAK  1(1P36.21) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        6.15         4.57         5.23         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 
       14.60        17.72        15.35        21.73        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       34.92         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       23.05        13.78         3.25         2.89        16.50        26.33 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        1.15         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1829 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 
       17.79         7.63         7.17         7.96         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         4.57        10.29         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 
        6.41         8.61        14.27         3.39         3.65         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-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        7.13         9.37         8.88        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        16.77        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        0.66         6.74        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-4208 
       20.78        15.02        15.95         8.84        22.78        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        10.85         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9R 
        0.99         4.44        11.84         0.20        15.12         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-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-76-6282 TCGA-76-6285 
       36.85        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        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 TCGA-02-0006 
       36.20         5.92         6.28        20.55         4.73        18.35 
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-02-0024 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        53.10        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 
       18.31         6.87        14.73         3.22        15.09         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 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-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        65.00        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-02-0290 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-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        15.91         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        9.27        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       22.72        33.67        25.35        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       17.79        10.09         8.61        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 
        3.22         4.04        91.00        88.14        20.25        69.90 
TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       73.84        15.42        10.42         4.67         5.56         0.39 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        8.42         7.40        11.84        15.02         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       72.36         9.57         3.16         5.75         9.80        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        7.36        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 
        4.80         7.27        15.98        18.41        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       10.45         7.59        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 
       12.13         3.65        20.38        28.41        53.85        43.23 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
        7.63        14.93        14.86        91.76        24.79        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-14-0787 TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        2.24        11.24        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 
       19.10        53.19         3.91        26.07        16.37        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 
       21.90         0.66        10.75         5.95         4.64        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-76-6280 
       23.44        11.01         5.16        22.68        12.76        11.38 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                          0.13                           0.10 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                         92.65                         127.59 
  AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE 
                        11.475                         12.410 
[1] "0.1 - 92.7 (11.5)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.3"
D1V2, continuous
D1V3, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED    40  52
  AMP PEAK  1(1P36.21) WILD-TYPE 185 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     40   52
  AMP PEAK  1(1P36.21) WILD-TYPE  185  296
        clus
vv       AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           40                            185
  MALE                             52                            296
[1] 2 2
[1] FALSE
D1V4, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED    17  72
  AMP PEAK  1(1P36.21) WILD-TYPE  57 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED     17   72
  AMP PEAK  1(1P36.21) WILD-TYPE   57  403
     clus
vv    AMP PEAK  1(1P36.21) MUTATED AMP PEAK  1(1P36.21) WILD-TYPE
  NO                            17                             57
  YES                           72                            403
[1] 2 2
[1] FALSE
D1V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  1(1P36.21) MUTATED                               1
  AMP PEAK  1(1P36.21) WILD-TYPE                            29
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  1(1P36.21) MUTATED                     1
  AMP PEAK  1(1P36.21) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  1(1P36.21) MUTATED                                90
  AMP PEAK  1(1P36.21) WILD-TYPE                             435
D1V6, multiclass
                                 clus
vv                                AMP PEAK  1(1P36.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           90
                                 clus
vv                                AMP PEAK  1(1P36.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               29
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P36.21) MUTATED       0                         4    83
  AMP PEAK  1(1P36.21) WILD-TYPE    13                        46   404
D1V7, multiclass
                           clus
vv                          AMP PEAK  1(1P36.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               83
                           clus
vv                          AMP PEAK  1(1P36.21) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             46
  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"
D1V8, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.21) MUTATED     3  70
  AMP PEAK  1(1P36.21) WILD-TYPE   9 405
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.21) MUTATED      3   70
  AMP PEAK  1(1P36.21) WILD-TYPE    9  405
                        clus
vv                       AMP PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            405
[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    27 130
  AMP PEAK  2(1Q32.1) WILD-TYPE  70 343
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          157                           413 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                          130                           343 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5411 TCGA-06-5856 TCGA-06-6698 TCGA-06-6699 
        3.98        15.32         8.35         3.75         4.77         1.55 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-3649 
       26.79         3.12        15.35        21.73        15.65        15.22 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0865 TCGA-14-1401 TCGA-14-1452 TCGA-14-1454 
       14.53         6.21        16.50         3.75         7.10        30.18 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-16-0848 TCGA-19-0963 
       12.43         0.99        17.85         3.78        17.59        14.27 
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-26-1440 TCGA-27-1834 TCGA-27-2518 TCGA-27-2524 
       18.90        12.10         9.73        40.54        24.76         7.59 
TCGA-27-2528 TCGA-28-1750 TCGA-28-1752 TCGA-28-2509 TCGA-32-1970 TCGA-32-1979 
       15.78         8.35         8.48         4.77        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-4W-AA9S 
       19.23         8.94         0.99        15.12        12.46         1.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4934 TCGA-76-4935 TCGA-76-6662 
        4.34        14.33         7.50         2.53        36.85        34.45 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0007 TCGA-02-0014 TCGA-02-0024 TCGA-02-0028 
        7.63        11.77        23.18        82.59        53.10        90.58 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0071 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 
       12.59         2.50         5.49        65.00        11.67        92.65 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0330 TCGA-02-0333 TCGA-02-0422 TCGA-02-0430 
       17.72        10.75        15.91         4.37        14.50        10.55 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-06-0128 TCGA-06-0130 
       16.21         3.35        12.92        15.32        22.72        12.95 
TCGA-06-0133 TCGA-06-0143 TCGA-06-0145 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 
       14.30        11.74         2.33         8.61        12.33        13.94 
TCGA-06-0157 TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0177 TCGA-06-0182 
        3.19         3.42         5.85        19.66         4.18         3.65 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0210 
       73.84        44.58        38.96         7.40         7.66         7.40 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0240 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       24.16        13.64        20.42        72.36         4.70         9.57 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0750 TCGA-06-1084 TCGA-06-1087 TCGA-06-1804 
       35.11         5.75         0.92        23.93         4.04        13.61 
TCGA-06-2557 TCGA-06-2569 TCGA-08-0244 TCGA-08-0349 TCGA-08-0350 TCGA-08-0353 
        1.08         0.43        22.68         9.80        29.23         8.42 
TCGA-08-0357 TCGA-08-0386 TCGA-08-0514 TCGA-08-0524 TCGA-08-0531 TCGA-12-0619 
       37.58        18.02        11.08         7.27         7.56        34.92 
TCGA-12-0670 TCGA-12-0692 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0821 
       25.97         3.65        15.06        43.23         7.63        10.62 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1090 TCGA-12-1096 TCGA-12-1098 
       27.78        38.76        20.58         7.59         9.11         3.98 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        4.14         2.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-19-0962 
       19.30        13.78        19.10        13.28         3.91         0.66 
TCGA-19-1387 TCGA-26-6173 TCGA-28-5207 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 
        5.95         7.92        11.28        13.64         5.16        12.76 
TCGA-76-6283 
        5.42 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        1.48        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 
        8.32        12.85         4.77         4.96         1.87         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       14.60        17.72        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       44.02        26.93        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
       13.78         3.25         2.89        26.33        15.95         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         6.67         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 
        7.17        17.49         7.96         3.42        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
        8.61         3.39        25.38         3.65        12.66         3.25 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        4.87         7.53         0.16        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       17.19         8.02         4.73         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        24.23        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 
       14.04        11.51        18.08        16.77        16.08         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 
       14.40         0.20         2.53         9.21         7.63         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-32-1973 
        1.55         2.83         0.13         0.66         6.74        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-32-2638 TCGA-32-4208 
       12.23        20.78        15.02        15.95        25.18        21.14 
TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 
       12.59        10.85         0.85        13.35         9.53         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       11.84         0.20         4.08        25.58         3.45        20.91 
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-76-6191 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-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        4.83         5.03        23.90        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 
        6.28        20.55         4.73        18.35        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       20.71        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        6.54        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       26.43        28.70        25.05        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
       16.96         3.48        27.02        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0271 TCGA-02-0281 
       15.65        48.95        16.54        16.93        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-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       10.62         7.33        25.71        25.12        10.59        12.39 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-02-2485 TCGA-02-2486 
       47.11        11.34         9.27        16.80        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       33.67        25.35        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 
       10.29         2.20        20.09        17.79        10.09        19.46 
TCGA-06-0151 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       46.59        10.45        10.82         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       10.65         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 
       91.00        88.14        20.25        69.90        27.22        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0211 
       10.42         4.67         5.56         0.39         8.42        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0241 
        0.53        15.02         0.72        19.82        13.32        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       10.82         9.01         0.26         3.16        12.62         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        7.86         2.70         2.70        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 
       40.41        16.57        20.78        26.76         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       11.84        15.32        33.90        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0245 
       31.50         7.79         5.39       120.56         7.36        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 
       65.33         1.28        17.95        24.56        31.10        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        42.15        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 
       10.75         4.80        15.98        18.41        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 
       10.45         7.59        94.78         0.10        38.17        26.66 
TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0776 TCGA-12-0778 
       12.13        20.38        28.41        53.85         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0828 
       14.86        91.76        24.79        18.48        23.51         8.94 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
      127.59         5.82        33.21        15.98        12.23        15.85 
TCGA-12-1097 TCGA-14-0789 TCGA-14-1043 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 
       14.53        11.24         0.79        50.53        53.19        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
       16.37        11.77        21.90        10.75         9.07        12.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 
        4.64        31.33        14.86         5.49         1.58         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 
       31.27        23.44        11.01        22.68         5.42         7.36 
TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         3.75         1.61        17.72        26.30 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.13                          0.10 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        92.65                        127.59 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        11.74                         12.49 
[1] "0.1 - 92.7 (11.7)"  "0.1 - 127.6 (12.5)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    63  96
  AMP PEAK  2(1Q32.1) WILD-TYPE 162 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     63   96
  AMP PEAK  2(1Q32.1) WILD-TYPE  162  252
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          63                           162
  MALE                            96                           252
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    26 126
  AMP PEAK  2(1Q32.1) WILD-TYPE  48 349
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     26  126
  AMP PEAK  2(1Q32.1) WILD-TYPE   48  349
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           26                            48
  YES                         126                           349
[1] 2 2
[1] FALSE
D2V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  2(1Q32.1) MUTATED                               8
  AMP PEAK  2(1Q32.1) WILD-TYPE                            22
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  2(1Q32.1) MUTATED                     5
  AMP PEAK  2(1Q32.1) WILD-TYPE                  13
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  2(1Q32.1) MUTATED                               146
  AMP PEAK  2(1Q32.1) WILD-TYPE                             379
D2V6, multiclass
                                 clus
vv                                AMP PEAK  2(1Q32.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             8
  TREATED PRIMARY GBM                                       5
  UNTREATED PRIMARY (DE NOVO) GBM                         146
                                 clus
vv                                AMP PEAK  2(1Q32.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              22
  TREATED PRIMARY GBM                                        13
  UNTREATED PRIMARY (DE NOVO) GBM                           379
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED       3                        15   135
  AMP PEAK  2(1Q32.1) WILD-TYPE    10                        35   352
D2V7, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          15
  WHITE                                             135
                           clus
vv                          AMP PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            35
  WHITE                                               352
[1] 3 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     2 131
  AMP PEAK  2(1Q32.1) WILD-TYPE  10 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      2  131
  AMP PEAK  2(1Q32.1) WILD-TYPE   10  344
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         131
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(1Q44) MUTATED    17  82
  AMP PEAK  3(1Q44) WILD-TYPE  80 391
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         99                         471 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         82                         391 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-06-5856 TCGA-06-6698 TCGA-06-A5U0 TCGA-12-1598 TCGA-12-3653 TCGA-14-0783 
        3.75         4.77        26.79        15.65        14.53         6.21 
TCGA-14-0865 TCGA-14-1452 TCGA-14-1454 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 
       16.50         7.10        30.18         0.99        17.85         3.78 
TCGA-19-1786 TCGA-19-1791 TCGA-19-2625 TCGA-19-4065 TCGA-26-1440 TCGA-27-2524 
        7.17         0.13         4.08         7.04         9.73         7.59 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1987 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 
        4.77        15.39        14.86         8.84        22.78         3.72 
TCGA-32-4719 TCGA-32-5222 TCGA-41-5651 TCGA-74-6578 TCGA-74-6584 TCGA-76-4934 
       10.85        19.23        15.12        14.33         7.50         2.53 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0024 TCGA-02-0028 TCGA-02-0052 TCGA-02-0055 
        7.63        11.77        53.10        90.58        12.59         2.50 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 TCGA-02-0269 TCGA-02-0290 
       65.00        11.67        92.65        17.72        10.75        15.95 
TCGA-02-0330 TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 TCGA-02-2485 TCGA-06-0133 
       15.91        16.21         3.35        15.32        15.45        14.30 
TCGA-06-0152 TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 TCGA-06-0177 
       12.33         3.42         5.85        19.66         4.47         4.18 
TCGA-06-0182 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0216 
        3.65        44.58        38.96         7.40         7.66        24.16 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-1084 
       13.64        72.36         4.70        35.11         5.75        23.93 
TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-2561 TCGA-06-2569 TCGA-08-0349 
        4.04        11.84         1.08        17.65         0.43         9.80 
TCGA-08-0350 TCGA-08-0354 TCGA-08-0380 TCGA-08-0386 TCGA-08-0524 TCGA-08-0529 
       29.23        17.95        14.93        18.02         7.27        18.41 
TCGA-08-0531 TCGA-12-0619 TCGA-12-0657 TCGA-12-0773 TCGA-12-0826 TCGA-12-0827 
        7.56        34.92         0.10        43.23        27.78        38.76 
TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 
        7.59         3.98         4.14         1.35         5.39         2.04 
TCGA-14-0871 TCGA-15-0742 TCGA-15-1449 TCGA-19-0962 TCGA-26-6173 TCGA-28-5214 
       28.93        13.78        13.28         0.66         7.92        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-76-6283 
       13.64         5.16         5.42 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        6.15         4.57         5.23         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       17.72        15.35        21.73        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 
        0.95        23.05        13.78         3.25         2.89        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
       23.11         1.15         0.92        40.96         6.67        12.43 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39        25.38         3.65        12.66         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 
        9.67         4.87         1.08         7.53         0.16        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1443 TCGA-26-1799 
       17.79        28.54        10.03        13.87         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 
       11.51        24.76        18.08        16.77        16.08         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-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        0.66         6.74        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       20.78        15.02        15.95        25.18        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-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84         0.20        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-76-4925 
       25.58         3.45        20.91         4.34         8.22         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        6.28        20.55         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       20.12        42.74        24.59        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 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-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 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-02-0317 
       16.93        14.47         3.98        13.87        14.20        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73        10.62         7.33        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-02-2466 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 
       11.34         9.27        16.80        12.92        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        12.95        25.35        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       17.79        10.09         8.61        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       10.45         3.19        10.82         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       10.65         3.29        13.12         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       88.14        20.25        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 
       10.42         4.67         5.56         0.39         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
       11.84         0.53        15.02         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       20.42        48.69        10.82         9.01         0.26         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        3.16        12.62         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 
       20.78        26.76         6.84        26.79        15.32        13.61 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       33.90        12.49         4.93        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         5.98         4.37        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
      120.56         7.36        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 
        1.74         8.42        25.71        12.16        65.33         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
        8.42        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       12.23        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        4.80        15.98        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       94.78        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 
       23.51         8.94        20.58       127.59         5.82        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-14-0787 
       15.98        12.23        15.85         9.11        14.53         2.24 
TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       11.24        19.30         0.79        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 
        3.91        26.07        16.37        11.77        21.90        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
        9.07         5.95        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        5.49         1.58         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
       11.28        17.88        14.53        11.77        31.27        11.01 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 
       22.68        12.76         5.42         7.36        11.38         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        0.1                         0.1 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      92.65                      127.59 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      11.77                       12.39 
[1] "0.1 - 92.7 (11.8)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    45  54
  AMP PEAK  3(1Q44) WILD-TYPE 180 294
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     45   54
  AMP PEAK  3(1Q44) WILD-TYPE  180  294
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        45                         180
  MALE                          54                         294
[1] 2 2
[1] FALSE
D3V4, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    17  78
  AMP PEAK  3(1Q44) WILD-TYPE  57 397
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     17   78
  AMP PEAK  3(1Q44) WILD-TYPE   57  397
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         17                          57
  YES                        78                         397
[1] 2 2
[1] FALSE
D3V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  3(1Q44) MUTATED                               2                   3
  AMP PEAK  3(1Q44) WILD-TYPE                            28                  15
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  3(1Q44) MUTATED                                94
  AMP PEAK  3(1Q44) WILD-TYPE                             431
D3V6, multiclass
                                 clus
vv                                AMP PEAK  3(1Q44) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           2
  TREATED PRIMARY GBM                                     3
  UNTREATED PRIMARY (DE NOVO) GBM                        94
                                 clus
vv                                AMP PEAK  3(1Q44) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            28
  TREATED PRIMARY GBM                                      15
  UNTREATED PRIMARY (DE NOVO) GBM                         431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       2                         9    81
  AMP PEAK  3(1Q44) WILD-TYPE    11                        41   406
D3V7, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                            81
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                          41
  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"
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED     3  77
  AMP PEAK  3(1Q44) WILD-TYPE   9 398
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      3   77
  AMP PEAK  3(1Q44) WILD-TYPE    9  398
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        77                         398
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P24.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P24.3) MUTATED     9  39
  AMP PEAK  4(2P24.3) WILD-TYPE  88 434
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           48                           522 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                           39                           434 
$`AMP PEAK  4(2P24.3) MUTATED`
TCGA-06-6391 TCGA-06-5856 TCGA-12-3653 TCGA-14-0740 TCGA-14-1823 TCGA-14-3477 
        1.48         3.75        14.53        11.97        17.85         3.78 
TCGA-19-1786 TCGA-19-2629 TCGA-19-A60I TCGA-26-1439 TCGA-27-1834 TCGA-27-1836 
        7.17        24.23        17.79        13.87        40.54        30.05 
TCGA-32-4210 TCGA-41-2573 TCGA-74-6584 TCGA-02-0001 TCGA-02-0014 TCGA-02-0104 
        3.72         8.94         7.50        11.77        82.59        65.00 
TCGA-02-0113 TCGA-02-0258 TCGA-02-0281 TCGA-06-0133 TCGA-06-0151 TCGA-06-0192 
       92.65        16.54         3.98        14.30        46.59        38.96 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0649 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 
       24.16        19.82         2.10         6.84         4.04        15.32 
TCGA-06-2557 TCGA-06-2569 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 TCGA-08-0517 
        1.08         0.43         8.42        18.02         4.27        58.68 
TCGA-12-0619 TCGA-12-0773 TCGA-12-0778 TCGA-12-1099 TCGA-14-0817 TCGA-14-0871 
       34.92        43.23        14.93         4.14         5.39        28.93 
TCGA-16-0846 TCGA-16-0850 TCGA-19-0957 TCGA-26-1442 TCGA-26-5133 TCGA-28-5218 
        3.91        16.37        21.90        31.33        14.86         5.16 

$`AMP PEAK  4(2P24.3) WILD-TYPE`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        3.98        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
       14.60        17.72        15.35        21.73        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       15.12         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 
        2.89        16.50        26.33        15.95         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39        25.38         3.65        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 
       16.80        14.96        28.54        10.03         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 
       16.60         9.86        24.23        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        18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1976 
        0.66         6.74         4.77        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23         0.85        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-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-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       27.02        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       48.95        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        3.98        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 
       27.22        44.58        15.42        10.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 
       40.41        16.57        20.78        26.76        23.93        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       11.84        13.61        33.90        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 
       31.50         7.79         5.39       120.56         7.36        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18       115.86         1.74        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        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-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 
       15.85         9.11        14.53         3.98         2.24        11.24 
TCGA-14-0813 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35         2.04        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-19-0955 TCGA-19-0962 
       19.10        53.19        13.28        26.07        11.77         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-5134 
       10.75         9.07         5.95        12.95         4.64         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       11.01        13.64        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                        92.65                        127.59 
  AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE 
                       14.695                        12.195 
[1] "0.4 - 92.7 (14.7)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED    22  27
  AMP PEAK  4(2P24.3) WILD-TYPE 203 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED     22   27
  AMP PEAK  4(2P24.3) WILD-TYPE  203  321
        clus
vv       AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  FEMALE                          22                           203
  MALE                            27                           321
[1] 2 2
[1] FALSE
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     6  41
  AMP PEAK  4(2P24.3) WILD-TYPE  68 434
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      6   41
  AMP PEAK  4(2P24.3) WILD-TYPE   68  434
     clus
vv    AMP PEAK  4(2P24.3) MUTATED AMP PEAK  4(2P24.3) WILD-TYPE
  NO                            6                            68
  YES                          41                           434
[1] 2 2
[1] FALSE
D4V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  4(2P24.3) MUTATED                               2
  AMP PEAK  4(2P24.3) WILD-TYPE                            28
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  4(2P24.3) MUTATED                     1
  AMP PEAK  4(2P24.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  4(2P24.3) MUTATED                                46
  AMP PEAK  4(2P24.3) WILD-TYPE                             479
D4V6, multiclass
                                 clus
vv                                AMP PEAK  4(2P24.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          46
                                 clus
vv                                AMP PEAK  4(2P24.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              28
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.3) MUTATED       1                         6    40
  AMP PEAK  4(2P24.3) WILD-TYPE    12                        44   447
D4V7, multiclass
                           clus
vv                          AMP PEAK  4(2P24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              40
                           clus
vv                          AMP PEAK  4(2P24.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.3) MUTATED     0  42
  AMP PEAK  4(2P24.3) WILD-TYPE  12 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.3) MUTATED      0   42
  AMP PEAK  4(2P24.3) WILD-TYPE   12  433
                        clus
vv                       AMP PEAK  4(2P24.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK  4(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           433
[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    18  91
  AMP PEAK  5(3Q26.33) WILD-TYPE  79 382
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           109                            461 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                            91                            382 
$`AMP PEAK  5(3Q26.33) MUTATED`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5416 TCGA-06-5856 TCGA-06-6695 TCGA-12-0615 
        1.48        11.74         6.71         3.75         8.32        15.35 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 
       15.65         6.77        59.77        44.02        15.12         6.21 
TCGA-14-0812 TCGA-14-1451 TCGA-14-1453 TCGA-14-1794 TCGA-14-1825 TCGA-14-1829 
        3.25        23.11         1.15         0.99         7.63         7.17 
TCGA-14-3477 TCGA-19-0963 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 
        3.78        14.27         3.65        24.23         7.04         9.73 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-2521 TCGA-28-1752 
        5.06        16.60        40.54        21.30        16.77         8.48 
TCGA-28-2506 TCGA-28-2509 TCGA-32-1991 TCGA-32-2632 TCGA-41-2575 TCGA-41-3915 
        6.74         4.77        16.93         8.84         9.53        11.84 
TCGA-41-4097 TCGA-74-6577 TCGA-74-6584 TCGA-76-4934 TCGA-76-6285 TCGA-02-0001 
        0.20         4.34         7.50         2.53         8.35        11.77 
TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0047 TCGA-02-0048 TCGA-02-0074 
       10.59        87.06        77.65        14.73         3.22        10.19 
TCGA-02-0106 TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0332 TCGA-06-0166 
       11.67         3.98         7.73        10.62        25.71         5.85 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0211 TCGA-06-0237 TCGA-06-0402 TCGA-06-0410 
       44.58        38.96        11.84        13.64         0.26         4.70 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 
        3.16        35.11        12.62         9.80         2.10        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-2557 TCGA-06-2563 
       26.40         7.86         7.17         4.04         1.08        30.64 
TCGA-06-6389 TCGA-06-6694 TCGA-08-0345 TCGA-08-0346 TCGA-08-0353 TCGA-08-0358 
        7.79         7.36         1.74         8.42         8.42        22.29 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0520 TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 
        0.72         4.27        10.75        15.98        12.99        34.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0822 
        0.10        38.17        12.13         9.73        14.93        23.51 
TCGA-12-0827 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1099 TCGA-14-0813 
       38.76        20.58       127.59         7.59         4.14         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-15-1449 TCGA-19-1388 TCGA-26-6174 TCGA-28-5207 
        5.39         2.04        13.28        12.95         2.33        11.28 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       31.27        11.01        13.64        22.68        12.76         5.42 
TCGA-76-6660 
        3.75 

$`AMP PEAK  5(3Q26.33) WILD-TYPE`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        15.32         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         6.15         4.57         5.23 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1092 
        1.87         3.12         2.56        14.60        17.72        21.73 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       25.68        14.73        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        0.95        23.05        13.78         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 
        1.97        17.79        17.85         5.88        17.49         7.96 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 
        9.14        21.24        13.97         6.41         8.61         3.39 
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-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03        13.87         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1832 TCGA-27-1833 TCGA-27-1836 
        8.88        18.97        19.33         9.86        24.23        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        0.66        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
       19.50         1.18         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02        15.95        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 
       13.35         8.94         0.99         4.44        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 
        4.08         1.45        25.58         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-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6286 
       36.85        16.70         3.29         2.70        17.06        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 
        5.92         6.28        20.55         7.63         4.73        18.35 
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0023 
       23.18        35.41        20.71        82.59        20.61        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0051 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-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       65.00        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-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 
       13.87        14.20        15.95        12.23         9.90         7.33 
TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.66         8.42         7.40         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 
        9.01        72.36         9.57         5.75         5.75        23.57 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       46.88         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79        11.84        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        17.65        12.56         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 
        4.37         0.43        31.50         5.39       120.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       37.84         4.18       115.86        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         1.28        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       37.58         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       13.97        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
       19.33         4.80         7.27        18.41         7.56        14.73 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       10.45         7.59        94.78        25.97        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 
       14.86        91.76        24.79        18.48        10.62        27.78 
TCGA-12-0828 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        8.94         5.82        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0871 
        9.11        14.53         3.98         2.24        11.24        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       19.30         0.79        13.78        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        3.91        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         9.07         5.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        5.49         1.58         7.92         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-32-2616 
       17.88        14.53        11.77        23.44         5.16         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         1.61        17.72        26.30 

  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                        127.59                         120.56 
  AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE 
                          9.73                          12.69 
[1] "0.1 - 127.6 (9.7)"  "0.1 - 120.6 (12.7)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    40  69
  AMP PEAK  5(3Q26.33) WILD-TYPE 185 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     40   69
  AMP PEAK  5(3Q26.33) WILD-TYPE  185  279
        clus
vv       AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  FEMALE                           40                            185
  MALE                             69                            279
[1] 2 2
[1] FALSE
D5V4, binary
                                cls
clus                               0   1
  AMP PEAK  5(3Q26.33) MUTATED    20  86
  AMP PEAK  5(3Q26.33) WILD-TYPE  54 389
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED     20   86
  AMP PEAK  5(3Q26.33) WILD-TYPE   54  389
     clus
vv    AMP PEAK  5(3Q26.33) MUTATED AMP PEAK  5(3Q26.33) WILD-TYPE
  NO                            20                             54
  YES                           86                            389
[1] 2 2
[1] FALSE
D5V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  5(3Q26.33) MUTATED                               1
  AMP PEAK  5(3Q26.33) WILD-TYPE                            29
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  5(3Q26.33) MUTATED                     0
  AMP PEAK  5(3Q26.33) WILD-TYPE                  18
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  5(3Q26.33) MUTATED                               108
  AMP PEAK  5(3Q26.33) WILD-TYPE                             417
D5V6, multiclass
                                 clus
vv                                AMP PEAK  5(3Q26.33) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              1
  TREATED PRIMARY GBM                                        0
  UNTREATED PRIMARY (DE NOVO) GBM                          108
                                 clus
vv                                AMP PEAK  5(3Q26.33) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               29
  TREATED PRIMARY GBM                                         18
  UNTREATED PRIMARY (DE NOVO) GBM                            417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3Q26.33) MUTATED       0                         7    94
  AMP PEAK  5(3Q26.33) WILD-TYPE    13                        43   393
D5V7, multiclass
                           clus
vv                          AMP PEAK  5(3Q26.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               94
                           clus
vv                          AMP PEAK  5(3Q26.33) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                393
[1] 3 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  83
  AMP PEAK  5(3Q26.33) WILD-TYPE  11 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.33) MUTATED      1   83
  AMP PEAK  5(3Q26.33) WILD-TYPE   11  392
                        clus
vv                       AMP PEAK  5(3Q26.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       AMP PEAK  5(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            392
[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     6  42
  AMP PEAK  6(4P16.3) WILD-TYPE  91 431
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           48                           522 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           42                           431 
$`AMP PEAK  6(4P16.3) MUTATED`
TCGA-19-A6J4 TCGA-06-6388 TCGA-06-6697 TCGA-12-3650 TCGA-14-1795 TCGA-14-1821 
        3.98         5.23        12.85        10.95         1.97        17.79 
TCGA-14-2554 TCGA-14-3477 TCGA-16-1056 TCGA-19-1392 TCGA-19-5947 TCGA-19-5958 
       17.49         3.78        14.01         3.65         6.64        14.07 
TCGA-26-1439 TCGA-27-1835 TCGA-27-2521 TCGA-28-2506 TCGA-32-1982 TCGA-32-1991 
       13.87        21.30        16.77         6.74         4.67        16.93 
TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-74-6578 TCGA-76-4925 TCGA-02-0011 
        9.53        11.84         0.20        14.33         4.80        20.71 
TCGA-02-0021 TCGA-02-0055 TCGA-02-0074 TCGA-02-0075 TCGA-02-0086 TCGA-02-0113 
       77.65         2.50        10.19        20.84         8.81        92.65 
TCGA-06-0125 TCGA-06-0130 TCGA-06-0157 TCGA-06-0195 TCGA-06-0409 TCGA-06-0410 
       47.61        12.95         3.19         7.40        72.36         4.70 
TCGA-06-0744 TCGA-06-0879 TCGA-08-0246 TCGA-08-0510 TCGA-08-0531 TCGA-12-0616 
       46.88        40.41         4.18         4.27         7.56        14.73 
TCGA-12-0691 TCGA-12-0820 TCGA-12-0826 TCGA-16-0846 TCGA-19-1387 TCGA-28-5215 
       12.13        18.48        27.78         3.91         5.95        11.01 

$`AMP PEAK  6(4P16.3) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        6.15         4.57         8.32         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       17.72        15.35        21.73        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3651 
        6.77        59.77        44.02        26.93        15.22        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 
        2.89        16.50        26.33        15.95         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-4157 
       17.85         7.63         5.88         7.17         7.96         3.42 
TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 
       17.59        29.03         4.57        10.29         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 
       13.97         6.41         8.61        14.27         3.39        25.38 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.04        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        22.49        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
       18.97        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       40.54        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
        1.55         2.83         0.13         0.66         4.77        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-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        0.99         4.44        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45        20.91         4.34         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        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
        5.92         6.28        20.55         7.63        11.77         4.73 
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-02-0016 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 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-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
       27.02        65.00        11.67        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 
       20.38         6.94         3.98        22.72        33.67        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        9.01         0.26         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 
       31.50         7.79         5.39       120.56         7.36        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0618 TCGA-12-0619 
        4.80         7.27        15.98        18.41        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       24.79        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.85         9.11        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
       11.24         1.35         5.39         2.04        28.93        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        0.79        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
       26.07        16.37        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07        12.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  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 
                       11.425                        12.360 
[1] "0.2 - 92.7 (11.4)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED    22  26
  AMP PEAK  6(4P16.3) WILD-TYPE 203 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED     22   26
  AMP PEAK  6(4P16.3) WILD-TYPE  203  322
        clus
vv       AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          22                           203
  MALE                            26                           322
[1] 2 2
[1] FALSE
D6V4, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED     5  41
  AMP PEAK  6(4P16.3) WILD-TYPE  69 434
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED      5   41
  AMP PEAK  6(4P16.3) WILD-TYPE   69  434
     clus
vv    AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  NO                            5                            69
  YES                          41                           434
[1] 2 2
[1] FALSE
D6V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  6(4P16.3) MUTATED                               1
  AMP PEAK  6(4P16.3) WILD-TYPE                            29
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  6(4P16.3) MUTATED                     1
  AMP PEAK  6(4P16.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  6(4P16.3) MUTATED                                46
  AMP PEAK  6(4P16.3) WILD-TYPE                             479
D6V6, multiclass
                                 clus
vv                                AMP PEAK  6(4P16.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             1
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          46
                                 clus
vv                                AMP PEAK  6(4P16.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              29
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4P16.3) MUTATED       0                         4    43
  AMP PEAK  6(4P16.3) WILD-TYPE    13                        46   444
D6V7, multiclass
                           clus
vv                          AMP PEAK  6(4P16.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              43
                           clus
vv                          AMP PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               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"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED     1  42
  AMP PEAK  6(4P16.3) WILD-TYPE  11 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED      1   42
  AMP PEAK  6(4P16.3) WILD-TYPE   11  433
                        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                           433
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(4Q12) MUTATED    19  89
  AMP PEAK  7(4Q12) WILD-TYPE  78 384
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        108                         462 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                         89                         384 
$`AMP PEAK  7(4Q12) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5856 TCGA-06-6695 TCGA-12-3646 TCGA-14-0740 
        3.98        11.74         3.75         8.32        44.02        11.97 
TCGA-14-0812 TCGA-14-0865 TCGA-14-1455 TCGA-14-1821 TCGA-14-1825 TCGA-14-1829 
        3.25        16.50         0.92        17.79         7.63         7.17 
TCGA-14-3477 TCGA-16-0848 TCGA-19-0960 TCGA-19-0963 TCGA-19-1390 TCGA-19-1392 
        3.78        17.59         8.61        14.27        25.38         3.65 
TCGA-19-2631 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
        7.00        17.79        10.03        13.87         9.40         8.88 
TCGA-27-1830 TCGA-27-1834 TCGA-28-2506 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        5.06        40.54         6.74        21.07         0.49         0.10 
TCGA-32-1991 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2575 TCGA-41-3915 
       16.93         3.72        12.59        19.23         9.53        11.84 
TCGA-41-4097 TCGA-4W-AA9R TCGA-74-6575 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 
        0.20         4.08        20.91         3.09         2.53        36.85 
TCGA-76-6193 TCGA-RR-A6KA TCGA-02-0014 TCGA-02-0024 TCGA-02-0055 TCGA-02-0069 
        2.70         6.28        82.59        53.10         2.50        28.70 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0113 TCGA-02-0281 TCGA-02-0285 
       10.19        20.84        27.25        92.65         3.98        13.87 
TCGA-02-0289 TCGA-02-0339 TCGA-02-0440 TCGA-02-0446 TCGA-02-2485 TCGA-06-0130 
       14.20        12.39        11.34         9.27        15.45        12.95 
TCGA-06-0138 TCGA-06-0143 TCGA-06-0155 TCGA-06-0166 TCGA-06-0171 TCGA-06-0173 
       24.23        11.74        10.45         5.85        13.12         4.47 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0192 TCGA-06-0195 TCGA-06-0210 TCGA-06-0211 
        3.22         4.18        38.96         7.40         7.40        11.84 
TCGA-06-0214 TCGA-06-0221 TCGA-06-0241 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       15.02        19.82        48.69         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0649 TCGA-06-0743 TCGA-06-0875 TCGA-06-0879 TCGA-06-1802 
        9.57         2.10        26.40        43.46        40.41        15.32 
TCGA-06-2559 TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0353 TCGA-08-0510 
        4.93        37.84         4.18        25.71         8.42         4.27 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0524 TCGA-08-0531 TCGA-12-0616 TCGA-12-0692 
       11.08        19.59         7.27         7.56        14.73         3.65 
TCGA-12-0828 TCGA-12-1096 TCGA-12-1097 TCGA-14-0817 TCGA-16-0846 TCGA-19-0957 
        8.94         9.11        14.53         5.39         3.91        21.90 
TCGA-19-1387 TCGA-19-1388 TCGA-26-5134 TCGA-28-5211 TCGA-28-5215 TCGA-28-5216 
        5.95        12.95         5.49        11.77        11.01        13.64 

$`AMP PEAK  7(4Q12) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        15.32         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-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        5.23        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.35        21.73        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       14.53        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
        6.21        23.05        13.78         2.89        26.33        15.95 
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-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15        30.18        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 
        0.99         1.97        17.85         5.88        17.49         7.96 
TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        3.42        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0964 TCGA-19-1786 TCGA-19-1787 
       21.24        13.97         6.41         3.39         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-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        24.23         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1443 
       14.07        16.80        14.96        28.54         9.73         7.13 
TCGA-26-1799 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        9.37        18.97        19.33        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        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-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-32-1970 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       15.39        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       14.86        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       22.78        25.18        21.14        19.86        10.85         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        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-6191 
        7.50         4.80         4.54         3.65         9.17        16.70 
TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        3.29        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KC 
       23.90        34.45        18.64        36.20         5.92        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       35.41        20.71        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        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-02-0290 TCGA-02-0317 TCGA-02-0321 
       17.72        10.75        14.47        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0451 
       25.12        10.59        14.50        10.55        47.11        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0119 
        3.35        16.80        12.92        15.32        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       33.67        25.35        14.30        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
       10.29         2.20         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 
        8.61        19.46        46.59        12.33        13.94         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       19.66         3.29         4.04        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       10.42         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        0.53        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       10.82         9.01         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80        23.57        14.20        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 
        2.70         2.70         0.92        46.19         7.17        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 
       11.84        13.61        33.90         1.08        12.49        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 
       22.68       115.86         1.74         8.42        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         1.28        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 
       15.35        13.97         0.72        12.56        42.15        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0618 
       19.33        10.75         4.80        15.98        18.41        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        26.66        12.13        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       38.76        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.98        12.23        15.85         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       11.24         1.35         2.04        28.93        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
       13.78        50.53        19.10        53.19        13.28        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 
       16.37        11.77         0.66        10.75         9.07         4.64 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       31.33        14.86         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 
        5.26        14.93        11.28        17.88        14.53        31.27 
TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       23.44         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                        0.1                         0.1 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      92.65                      127.59 
  AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE 
                      10.73                       12.62 
[1] "0.1 - 92.7 (10.7)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    38  70
  AMP PEAK  7(4Q12) WILD-TYPE 187 278
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     38   70
  AMP PEAK  7(4Q12) WILD-TYPE  187  278
        clus
vv       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  FEMALE                        38                         187
  MALE                          70                         278
[1] 2 2
[1] FALSE
D7V4, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED    20  84
  AMP PEAK  7(4Q12) WILD-TYPE  54 391
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED     20   84
  AMP PEAK  7(4Q12) WILD-TYPE   54  391
     clus
vv    AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  NO                         20                          54
  YES                        84                         391
[1] 2 2
[1] FALSE
D7V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  AMP PEAK  7(4Q12) MUTATED                               4                   2
  AMP PEAK  7(4Q12) WILD-TYPE                            26                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  7(4Q12) MUTATED                               102
  AMP PEAK  7(4Q12) WILD-TYPE                             423
D7V6, multiclass
                                 clus
vv                                AMP PEAK  7(4Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           4
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                       102
                                 clus
vv                                AMP PEAK  7(4Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            26
  TREATED PRIMARY GBM                                      16
  UNTREATED PRIMARY (DE NOVO) GBM                         423
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q12) MUTATED       1                        11    93
  AMP PEAK  7(4Q12) WILD-TYPE    12                        39   394
D7V7, multiclass
                           clus
vv                          AMP PEAK  7(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                            93
                           clus
vv                          AMP PEAK  7(4Q12) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          39
  WHITE                                             394
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK  7(4Q12) MUTATED     2  90
  AMP PEAK  7(4Q12) WILD-TYPE  10 385
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4Q12) MUTATED      2   90
  AMP PEAK  7(4Q12) WILD-TYPE   10  385
                        clus
vv                       AMP PEAK  7(4Q12) MUTATED AMP PEAK  7(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                        90                         385
[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    76 424
  AMP PEAK  8(7P11.2) WILD-TYPE  21  49
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          500                            70 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          424                            49 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        3.98        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 
        4.77         1.87         3.12         2.56        14.60        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       21.73        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       14.53        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 
        6.21        23.05        13.78         3.25         2.89        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         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-14-1823 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 
        5.88         7.17        17.49         7.96         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         4.57        10.29         9.14        21.24        13.97 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       14.27         3.39        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        9.73         7.13         9.37         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        1.55         0.13         0.66         6.74         4.77        15.39 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       15.95         8.84        25.18         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 
        9.17         2.53        36.85        16.70         3.29        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 
       11.77         4.73        18.35        23.18        10.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 
       87.06        77.65        20.12        42.74        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 
       14.14         3.62        10.72        18.31         6.87         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 
       15.09        12.59         6.54         2.50        19.86         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       20.84        27.25        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       92.65        15.65        48.95        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
        4.37        25.12        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       13.94        10.45         3.19        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00         4.18        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26        72.36         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        5.39       120.56         7.36        22.68        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
        0.72        12.56         4.27        11.08        19.33        10.75 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0819 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-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        2.24        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       19.30         0.79        13.78        19.10        13.28         3.91 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       12.95         4.64         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
        5.42         7.36        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-06-6391 TCGA-06-5416 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TL TCGA-14-0740 
        1.48         6.71         4.96        26.79        17.72        11.97 
TCGA-14-0865 TCGA-14-1821 TCGA-14-3477 TCGA-16-1056 TCGA-16-1460 TCGA-19-0960 
       16.50        17.79         3.78        14.01         6.41         8.61 
TCGA-19-2625 TCGA-19-5956 TCGA-27-2521 TCGA-28-1756 TCGA-32-1973 TCGA-32-2634 
        4.08        22.49        16.77         2.83        21.07        22.78 
TCGA-32-4208 TCGA-41-4097 TCGA-76-6193 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       21.14         0.20         2.70        35.41        20.71        82.59 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0028 TCGA-02-0039 TCGA-02-0047 TCGA-02-0058 
       53.10        24.59        90.58        10.52        14.73         8.35 
TCGA-02-0060 TCGA-02-0080 TCGA-02-0084 TCGA-02-0104 TCGA-02-0114 TCGA-02-0258 
        6.02        89.72        12.62        65.00        99.98        16.54 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2483 TCGA-06-0129 TCGA-06-0146 
       10.59        12.39        47.11        15.32        33.67        20.09 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0178 TCGA-06-0221 TCGA-06-0410 TCGA-06-1805 
       11.80        10.65        88.14        19.82         4.70        33.90 
TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 
        5.98         0.43        31.50         7.79       115.86        29.23 
TCGA-08-0351 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       65.33        42.15        19.59        58.68         4.80         7.27 
TCGA-12-0818 TCGA-12-0827 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 
       91.76        38.76        50.53        53.19        26.07        16.37 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-28-5216 
       31.33        14.86         5.49        13.64 

  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          0.1                           0.2 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                       127.59                        115.86 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                       11.805                        17.245 
[1] "0.1 - 127.6 (11.8)" "0.2 - 115.9 (17.2)"
[1] "hr=" "2.1"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED   193 310
  AMP PEAK  8(7P11.2) WILD-TYPE  32  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED    193  310
  AMP PEAK  8(7P11.2) WILD-TYPE   32   38
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                         193                            32
  MALE                           310                            38
[1] 2 2
[1] FALSE
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    69 413
  AMP PEAK  8(7P11.2) WILD-TYPE   5  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     69  413
  AMP PEAK  8(7P11.2) WILD-TYPE    5   62
     clus
vv    AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  NO                           69                             5
  YES                         413                            62
[1] 2 2
[1] FALSE
D8V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  8(7P11.2) MUTATED                              25
  AMP PEAK  8(7P11.2) WILD-TYPE                             5
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK  8(7P11.2) MUTATED                    13
  AMP PEAK  8(7P11.2) WILD-TYPE                   5
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  8(7P11.2) MUTATED                               465
  AMP PEAK  8(7P11.2) WILD-TYPE                              60
D8V6, multiclass
                                 clus
vv                                AMP PEAK  8(7P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            25
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         465
                                 clus
vv                                AMP PEAK  8(7P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               5
  TREATED PRIMARY GBM                                         5
  UNTREATED PRIMARY (DE NOVO) GBM                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P11.2) MUTATED      10                        44   427
  AMP PEAK  8(7P11.2) WILD-TYPE     3                         6    60
D8V7, multiclass
                           clus
vv                          AMP PEAK  8(7P11.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          44
  WHITE                                             427
                           clus
vv                          AMP PEAK  8(7P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED     8 415
  AMP PEAK  8(7P11.2) WILD-TYPE   4  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      8  415
  AMP PEAK  8(7P11.2) WILD-TYPE    4   60
                        clus
vv                       AMP PEAK  8(7P11.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         415
                        clus
vv                       AMP PEAK  8(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            60
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7Q11.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(7Q11.21) MUTATED    72 386
  AMP PEAK  9(7Q11.21) WILD-TYPE  25  87
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           458                            112 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           386                             87 
$`AMP PEAK  9(7Q11.21) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        15.32         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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 
        1.87         2.56        14.60        15.35        21.73        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
        2.04        15.12         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        3.25        26.33        15.95         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-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 
        0.92         6.67        12.43         0.99         1.97        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 
       17.59        29.03         4.57        10.29        21.24        13.97 
TCGA-19-0960 TCGA-19-0963 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        8.61        14.27        25.38         3.65         7.17        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 
        0.13         9.67         7.53         0.16        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.04         6.64        17.19        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-5132 TCGA-26-5135 
       10.03        13.87         9.73         7.13         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
       18.97        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 
       40.54        21.30        11.51        24.76        18.08         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-28-2509 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
        0.66         6.74         4.77        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-32-2615 TCGA-32-2632 TCGA-32-2638 
       16.93        12.23        20.78        15.95         8.84        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
        3.72        12.59        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44        11.84        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         7.50         4.80         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 
        9.17         2.53        36.85        16.70         3.29        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 
       11.77         4.73        18.35        23.18        10.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 
       87.06        77.65        20.12        42.74        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       14.14         3.62        10.72         6.87         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 
       12.59         6.54         2.50        19.86         9.57        19.73 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0085 
       25.05         5.49        10.19        20.84        27.25        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 
        8.81        57.76        16.96         3.48        27.02        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       17.65        23.18        92.65        15.65        48.95        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0430 TCGA-02-0440 
       15.91        25.71         4.37        25.12        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 
        9.27        16.21         3.35        16.80        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 
       22.72        12.95        25.35        14.30        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.20        10.29        11.74         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        46.59        12.33        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       10.82         9.44        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        69.90        73.84        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       24.16        13.64        13.32        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26        72.36         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40        46.88         7.86         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 TCGA-06-6390 TCGA-06-6694 TCGA-08-0244 
       30.64         5.95         4.37         5.39         7.36        22.68 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 
       12.56         4.27        19.33        10.75        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 
       94.78         0.10        38.17        25.97        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
        9.73        14.93        14.86        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       27.78         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 
        3.98         4.14         2.24        11.24         1.35         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
       28.93        19.30         0.79        13.78        19.10        13.28 
TCGA-16-0846 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
        3.91        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.95        12.95         4.64         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 
        7.30         5.26        14.93        11.28        17.88        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
        5.42         7.36        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`AMP PEAK  9(7Q11.21) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5416 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 
        1.48        11.74         6.71         4.96        26.79         3.12 
TCGA-06-A7TL TCGA-12-3652 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1456 
       17.72        34.92        11.97         2.89        16.50        40.96 
TCGA-14-1821 TCGA-14-3477 TCGA-16-1056 TCGA-16-1060 TCGA-16-1460 TCGA-19-0964 
       17.79         3.78        14.01         9.14         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        22.49 
TCGA-26-1799 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 TCGA-27-2523 TCGA-28-1756 
        9.37        30.05        14.04        16.77        16.08         2.83 
TCGA-32-1973 TCGA-32-2495 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 
       21.07        15.02        22.78        21.14        19.86        10.85 
TCGA-41-4097 TCGA-76-4926 TCGA-76-6193 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        0.20         4.54         2.70        35.41        20.71        82.59 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0028 TCGA-02-0039 TCGA-02-0043 TCGA-02-0047 
       53.10        24.59        90.58        10.52        18.31        14.73 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 
        8.35         6.02        26.43        28.70        89.72        22.72 
TCGA-02-0084 TCGA-02-0104 TCGA-02-0114 TCGA-02-0258 TCGA-02-0338 TCGA-02-0339 
       12.62        65.00        99.98        16.54        10.59        12.39 
TCGA-02-0422 TCGA-02-0432 TCGA-02-2483 TCGA-06-0127 TCGA-06-0129 TCGA-06-0137 
       14.50        47.11        15.32         3.98        33.67        26.70 
TCGA-06-0142 TCGA-06-0146 TCGA-06-0154 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        2.20        20.09        13.94        11.80         3.42        10.65 
TCGA-06-0178 TCGA-06-0187 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 TCGA-06-0410 
       88.14        27.22         0.72        19.82        20.42         4.70 
TCGA-06-0747 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
        2.70        33.90        16.64         5.98         0.43        31.50 
TCGA-06-6389 TCGA-06-6693 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 
        7.79       120.56        37.84         4.18       115.86        29.23 
TCGA-08-0351 TCGA-08-0353 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       65.33         8.42        42.15        11.08        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0688 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 
        4.80         7.27        26.66        91.76        24.79        38.76 
TCGA-14-0817 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-26-1442 
        5.39        50.53        53.19        26.07        16.37        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-28-5209 TCGA-28-5216 
       14.86         5.49        14.53        13.64 

  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                           0.1                            0.2 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                        127.59                         120.56 
  AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE 
                         11.77                          15.70 
[1] "0.1 - 127.6 (11.8)" "0.2 - 120.6 (15.7)"
[1] "hr=" "1.7"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED   175 286
  AMP PEAK  9(7Q11.21) WILD-TYPE  50  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED    175  286
  AMP PEAK  9(7Q11.21) WILD-TYPE   50   62
        clus
vv       AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  FEMALE                          175                             50
  MALE                            286                             62
[1] 2 2
[1] FALSE
D9V4, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED    63 377
  AMP PEAK  9(7Q11.21) WILD-TYPE  11  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED     63  377
  AMP PEAK  9(7Q11.21) WILD-TYPE   11   98
     clus
vv    AMP PEAK  9(7Q11.21) MUTATED AMP PEAK  9(7Q11.21) WILD-TYPE
  NO                            63                             11
  YES                          377                             98
[1] 2 2
[1] FALSE
D9V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK  9(7Q11.21) MUTATED                              22
  AMP PEAK  9(7Q11.21) WILD-TYPE                             8
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK  9(7Q11.21) MUTATED                    10
  AMP PEAK  9(7Q11.21) WILD-TYPE                   8
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK  9(7Q11.21) MUTATED                               429
  AMP PEAK  9(7Q11.21) WILD-TYPE                              96
D9V6, multiclass
                                 clus
vv                                AMP PEAK  9(7Q11.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             22
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          429
                                 clus
vv                                AMP PEAK  9(7Q11.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                8
  TREATED PRIMARY GBM                                          8
  UNTREATED PRIMARY (DE NOVO) GBM                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7Q11.21) MUTATED       8                        41   390
  AMP PEAK  9(7Q11.21) WILD-TYPE     5                         9    97
D9V7, multiclass
                           clus
vv                          AMP PEAK  9(7Q11.21) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           41
  WHITE                                              390
                           clus
vv                          AMP PEAK  9(7Q11.21) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(7Q11.21) MUTATED     7 379
  AMP PEAK  9(7Q11.21) WILD-TYPE   5  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(7Q11.21) MUTATED      7  379
  AMP PEAK  9(7Q11.21) WILD-TYPE    5   96
                        clus
vv                       AMP PEAK  9(7Q11.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          379
                        clus
vv                       AMP PEAK  9(7Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q21.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7Q21.2) MUTATED    72 401
  AMP PEAK 10(7Q21.2) WILD-TYPE  25  72
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          473                            97 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          401                            72 
$`AMP PEAK 10(7Q21.2) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        3.98        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 
        4.77         1.87         3.12         2.56        14.60        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
       21.73        15.65        25.68        14.73        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
       26.93        15.22        10.95        12.69        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        3.25        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         1.15        30.18         0.92 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 
        5.88         7.17        17.49         7.96         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       29.03         4.57        10.29        21.24        13.97         6.41 
TCGA-19-0963 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       14.27        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 
        0.13         9.67         7.53         0.16        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.04         6.64        17.19        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        14.07        16.80        14.96        17.79        28.54 
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-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        40.54        21.30        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 
       18.08        16.77        16.08         7.59         2.86         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        1.55         0.13         0.66         6.74         4.77        15.39 
TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49        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-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 
        8.84        25.18         3.72        12.59        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 
        6.28        20.55         7.63        11.77         4.73        18.35 
TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       10.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       12.16         2.83        14.14         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.86         9.57        19.73        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       20.84        89.72        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       92.65        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       25.71        25.12        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 
        2.70        20.38        47.61         6.94        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       10.29        11.74         2.33        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44         3.42        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        4.18        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16        19.82        13.64        13.32 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       48.69        10.82         9.01         0.26        72.36         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 
        4.04        26.79        11.84        15.32        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2567 TCGA-06-6390 TCGA-06-6694 TCGA-08-0244 TCGA-08-0345 TCGA-08-0346 
        4.37         5.39         7.36        22.68         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
       25.71        12.16         9.80         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       18.02        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       11.08        19.33        10.75        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 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-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82         7.59        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       14.53         3.98         4.14         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        5.39         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-19-0955 TCGA-19-0957 
       50.53        19.10        13.28         3.91        11.77        21.90 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        0.66        10.75         9.07         5.95        12.95         4.64 
TCGA-26-1442 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 
       31.33         1.58         7.92         2.33         7.30        14.93 
TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       11.28        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 
        5.16        22.68        12.76         5.42         7.36        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

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

  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                       127.59                        120.56 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                        11.90                         15.12 
[1] "0.1 - 127.6 (11.9)" "0.1 - 120.6 (15.1)"
[1] "hr=" "1.7"
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED   183 293
  AMP PEAK 10(7Q21.2) WILD-TYPE  42  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED    183  293
  AMP PEAK 10(7Q21.2) WILD-TYPE   42   55
        clus
vv       AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  FEMALE                         183                            42
  MALE                           293                            55
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED    64 393
  AMP PEAK 10(7Q21.2) WILD-TYPE  10  82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED     64  393
  AMP PEAK 10(7Q21.2) WILD-TYPE   10   82
     clus
vv    AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  NO                           64                            10
  YES                         393                            82
[1] 2 2
[1] FALSE
D10V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 10(7Q21.2) MUTATED                              24
  AMP PEAK 10(7Q21.2) WILD-TYPE                             6
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK 10(7Q21.2) MUTATED                    12
  AMP PEAK 10(7Q21.2) WILD-TYPE                   6
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 10(7Q21.2) MUTATED                               440
  AMP PEAK 10(7Q21.2) WILD-TYPE                              85
D10V6, multiclass
                                 clus
vv                                AMP PEAK 10(7Q21.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            24
  TREATED PRIMARY GBM                                      12
  UNTREATED PRIMARY (DE NOVO) GBM                         440
                                 clus
vv                                AMP PEAK 10(7Q21.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               6
  TREATED PRIMARY GBM                                         6
  UNTREATED PRIMARY (DE NOVO) GBM                            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q21.2) MUTATED       7                        42   405
  AMP PEAK 10(7Q21.2) WILD-TYPE     6                         8    82
D10V7, multiclass
                           clus
vv                          AMP PEAK 10(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          42
  WHITE                                             405
                           clus
vv                          AMP PEAK 10(7Q21.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q21.2) MUTATED     7 394
  AMP PEAK 10(7Q21.2) WILD-TYPE   5  81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED      7  394
  AMP PEAK 10(7Q21.2) WILD-TYPE    5   81
                        clus
vv                       AMP PEAK 10(7Q21.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         394
                        clus
vv                       AMP PEAK 10(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            81
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q31.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q31.2) MUTATED    74 392
  AMP PEAK 11(7Q31.2) WILD-TYPE  23  81
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          466                           104 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          392                            81 
$`AMP PEAK 11(7Q31.2) MUTATED`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        1.55         4.77         1.87         3.12         2.56        14.60 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
       21.73        15.65        25.68        14.73        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
       26.93        15.22        10.95        12.69        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        3.25        26.33        15.95         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         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 
        7.17        17.49         7.96         3.42        17.59        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0963 
        4.57        10.29        21.24        13.97         6.41        14.27 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 TCGA-19-2623 
       25.38         3.65         7.17        12.66         0.13         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
        7.59         2.86         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-32-1970 TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 
        6.74         4.77        15.39         0.49        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-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       20.78        15.02         8.84        25.18         3.72        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 
        2.53        36.85        16.70         3.29        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 
       36.20         5.92         6.28        20.55         7.63        11.77 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0015 TCGA-02-0016 
        4.73        18.35        10.59        35.41        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 
       77.65        20.12        53.10        42.74        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 
       14.14         3.62        10.72        18.31         6.87        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-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0422 
       10.62         7.33        15.91        25.71        25.12        14.50 
TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       10.55        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 
       12.92        15.45        20.32         2.70        20.38        47.61 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        6.94        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90         0.20        10.29        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 
       13.94        10.45         3.19         9.44        56.91         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00         4.18        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 
       11.84         0.53        15.02        24.16        19.82        13.64 
TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       13.32        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 TCGA-06-2569 TCGA-06-6390 TCGA-06-6694 
       30.64         5.95         4.37         0.43         5.39         7.36 
TCGA-08-0244 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       22.68         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
        1.28        17.95        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 
       12.56         4.27        19.33        10.75        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       94.78         0.10        38.17        25.97        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        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-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82         7.59        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       14.53         3.98         4.14         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        5.39         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       19.10        13.28         3.91        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 
       10.75         9.07         5.95        12.95         4.64        31.33 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        1.58         7.92         2.33         7.30        14.93        11.28 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

$`AMP PEAK 11(7Q31.2) WILD-TYPE`
TCGA-06-5416 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TL TCGA-12-0615 TCGA-12-1602 
        6.71         4.96        26.79        17.72        15.35         6.77 
TCGA-12-3652 TCGA-14-0736 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1402 
       34.92        15.12        11.97         2.89        16.50        32.05 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-16-1056 TCGA-16-1060 
        7.10         1.15        17.79         3.78        14.01         9.14 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        8.61         3.39         3.25         9.67         4.87         1.08 
TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 TCGA-27-1836 TCGA-27-2527 TCGA-27-2528 
        4.08         8.02        22.49        30.05        14.40        15.78 
TCGA-28-1756 TCGA-32-1973 TCGA-32-1977 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 
        2.83        21.07         0.10        15.95        22.78        21.14 
TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 TCGA-02-0007 TCGA-02-0011 
       19.86        10.85         0.20         2.70        23.18        20.71 
TCGA-02-0014 TCGA-02-0026 TCGA-02-0028 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 
       82.59        24.59        90.58        10.52        14.73         3.22 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0083 TCGA-02-0084 
        8.35         6.02        26.43        28.70        22.72        12.62 
TCGA-02-0104 TCGA-02-0114 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 
       65.00        99.98         4.37        10.59        12.39        47.11 
TCGA-02-2483 TCGA-06-0122 TCGA-06-0127 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 
       15.32         6.15         3.98        33.67         2.20        20.09 
TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0178 TCGA-06-0219 
       10.82        11.80         3.42        10.65        88.14         0.72 
TCGA-06-0240 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 TCGA-06-2570 TCGA-06-6389 
       20.42        33.90        16.64         5.98        31.50         7.79 
TCGA-06-6693 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
      120.56        37.84         4.18       115.86        29.23        65.33 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        8.42        24.56        42.15        11.08        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0691 TCGA-12-0827 TCGA-12-1091 TCGA-15-1444 
        4.80         7.27        12.13        38.76        33.21        50.53 
TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-26-5133 TCGA-26-5134 TCGA-28-2514 
       53.19        26.07        16.37        14.86         5.49         5.26 
TCGA-28-5208 TCGA-28-5220 
       17.88        12.76 

  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                       127.59                        120.56 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                       12.000                        14.795 
[1] "0.1 - 127.6 (12.0)" "0.1 - 120.6 (14.8)"
[1] "hr=" "1.5"
D11V2, continuous
D11V3, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   179 290
  AMP PEAK 11(7Q31.2) WILD-TYPE  46  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    179  290
  AMP PEAK 11(7Q31.2) WILD-TYPE   46   58
        clus
vv       AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  FEMALE                         179                            46
  MALE                           290                            58
[1] 2 2
[1] FALSE
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED    65 384
  AMP PEAK 11(7Q31.2) WILD-TYPE   9  91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED     65  384
  AMP PEAK 11(7Q31.2) WILD-TYPE    9   91
     clus
vv    AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  NO                           65                             9
  YES                         384                            91
[1] 2 2
[1] FALSE
D11V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 11(7Q31.2) MUTATED                              23
  AMP PEAK 11(7Q31.2) WILD-TYPE                             7
                               vv
clus                            TREATED PRIMARY GBM
  AMP PEAK 11(7Q31.2) MUTATED                    13
  AMP PEAK 11(7Q31.2) WILD-TYPE                   5
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 11(7Q31.2) MUTATED                               433
  AMP PEAK 11(7Q31.2) WILD-TYPE                              92
D11V6, multiclass
                                 clus
vv                                AMP PEAK 11(7Q31.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            23
  TREATED PRIMARY GBM                                      13
  UNTREATED PRIMARY (DE NOVO) GBM                         433
                                 clus
vv                                AMP PEAK 11(7Q31.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               7
  TREATED PRIMARY GBM                                         5
  UNTREATED PRIMARY (DE NOVO) GBM                            92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q31.2) MUTATED       7                        42   399
  AMP PEAK 11(7Q31.2) WILD-TYPE     6                         8    88
D11V7, multiclass
                           clus
vv                          AMP PEAK 11(7Q31.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          42
  WHITE                                             399
                           clus
vv                          AMP PEAK 11(7Q31.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED     7 389
  AMP PEAK 11(7Q31.2) WILD-TYPE   5  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED      7  389
  AMP PEAK 11(7Q31.2) WILD-TYPE    5   86
                        clus
vv                       AMP PEAK 11(7Q31.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         389
                        clus
vv                       AMP PEAK 11(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            86
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    12  57
  AMP PEAK 12(8Q24.21) WILD-TYPE  85 416
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            69                            501 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            57                            416 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-19-A6J4 TCGA-06-5856 TCGA-06-6701 TCGA-12-1092 TCGA-12-1598 TCGA-12-1602 
        3.98         3.75         4.96        21.73        15.65         6.77 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0865 TCGA-14-1453 TCGA-14-1456 TCGA-14-1825 
       44.02        14.53        16.50         1.15        40.96         7.63 
TCGA-14-3477 TCGA-19-1392 TCGA-19-2619 TCGA-19-A6J5 TCGA-27-1834 TCGA-27-2521 
        3.78         3.65         9.67        28.54        40.54        16.77 
TCGA-28-1746 TCGA-32-1976 TCGA-32-1978 TCGA-32-2632 TCGA-32-4210 TCGA-41-2573 
        0.20         0.49        15.85         8.84         3.72         8.94 
TCGA-41-4097 TCGA-41-5651 TCGA-06-0209 TCGA-02-0010 TCGA-02-0014 TCGA-02-0024 
        0.20        15.12         7.63        35.41        82.59        53.10 
TCGA-02-0037 TCGA-02-0055 TCGA-02-0074 TCGA-02-0075 TCGA-02-0084 TCGA-02-0104 
        3.62         2.50        10.19        20.84        12.62        65.00 
TCGA-02-0325 TCGA-02-2483 TCGA-06-0128 TCGA-06-0146 TCGA-06-0177 TCGA-06-0188 
       10.62        15.32        22.72        20.09         4.18        44.58 
TCGA-06-0192 TCGA-06-0211 TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 TCGA-06-2557 
       38.96        11.84        72.36        35.11        14.20         1.08 
TCGA-06-2569 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-08-0350 TCGA-08-0351 
        0.43         7.79       120.56         7.36        29.23        65.33 
TCGA-08-0516 TCGA-12-0616 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 TCGA-12-1099 
       19.59        14.73        91.76        24.79        38.76         4.14 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-19-1388 TCGA-26-5133 TCGA-28-5204 
        5.39         2.04        28.93        12.95        14.86        14.93 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.01         5.16        22.68 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77        26.79         1.87         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
       17.72        15.35        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
       13.78         3.25         2.89        26.33        15.95         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-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79        17.85         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
        9.14        21.24        13.97         6.41         8.61        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        3.39        25.38         7.17        12.66         3.25         0.13 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       14.96        17.79        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        24.23        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        18.08        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       14.40        15.78         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-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1979 
        6.74         4.77        15.39        21.07         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02        15.95        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R 
        9.53         0.99         4.44        11.84        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58         2.83        14.14        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        6.54        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 
       26.43        28.70        25.05         5.49        27.25        89.72 
TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       27.22        15.42        10.42         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        0.39         7.66         8.42         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       23.57        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-6390 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        4.37        31.50         5.39        22.68        37.84         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       18.41         7.56        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 
        7.63         9.73        14.93        14.86        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        27.78         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-1037 
       14.53         3.98         2.24        11.24         1.35        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        0.79        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        3.91        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5134 
       10.75         9.07         5.95         4.64        31.33         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 
        1.58         7.92         2.33         7.30         5.26        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       17.88        14.53        11.77        31.27        23.44        13.64 
TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       12.76         5.42         7.36        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        120.56                         127.59 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         14.53                          12.16 
[1] "0.2 - 120.6 (14.5)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    29  40
  AMP PEAK 12(8Q24.21) WILD-TYPE 196 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     29   40
  AMP PEAK 12(8Q24.21) WILD-TYPE  196  308
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           29                            196
  MALE                             40                            308
[1] 2 2
[1] FALSE
D12V4, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    10  52
  AMP PEAK 12(8Q24.21) WILD-TYPE  64 423
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     10   52
  AMP PEAK 12(8Q24.21) WILD-TYPE   64  423
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            10                             64
  YES                           52                            423
[1] 2 2
[1] FALSE
D12V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 12(8Q24.21) MUTATED                               2
  AMP PEAK 12(8Q24.21) WILD-TYPE                            28
                                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                                65
  AMP PEAK 12(8Q24.21) WILD-TYPE                             460
D12V6, multiclass
                                 clus
vv                                AMP PEAK 12(8Q24.21) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           65
                                 clus
vv                                AMP PEAK 12(8Q24.21) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               28
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            460
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       1                         9    59
  AMP PEAK 12(8Q24.21) WILD-TYPE    12                        41   428
D12V7, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               59
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                             41
  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"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED     1  58
  AMP PEAK 12(8Q24.21) WILD-TYPE  11 417
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      1   58
  AMP PEAK 12(8Q24.21) WILD-TYPE   11  417
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            417
[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  28
  AMP PEAK 13(11P13) WILD-TYPE  95 445
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          30                          540 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                          28                          445 
$`AMP PEAK 13(11P13) MUTATED`
TCGA-12-1598 TCGA-19-4065 TCGA-19-5958 TCGA-19-A60I TCGA-27-1838 TCGA-27-2521 
       15.65         7.04        14.07        17.79        11.51        16.77 
TCGA-27-2526 TCGA-02-0025 TCGA-02-0037 TCGA-02-0054 TCGA-02-0099 TCGA-02-0106 
        2.86        42.74         3.62         6.54         3.48        11.67 
TCGA-02-0115 TCGA-02-0258 TCGA-02-0290 TCGA-06-0130 TCGA-06-0160 TCGA-06-0221 
       15.65        16.54        15.95        12.95        11.80        19.82 
TCGA-06-0743 TCGA-06-1087 TCGA-06-2557 TCGA-08-0386 TCGA-08-0517 TCGA-12-0616 
       26.40         4.04         1.08        18.02        58.68        14.73 
TCGA-12-0670 TCGA-12-0826 TCGA-12-1093 TCGA-14-0871 TCGA-19-1388 TCGA-28-5207 
       25.97        27.78        15.98        28.93        12.95        11.28 

$`AMP PEAK 13(11P13) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 
        3.75         6.15         4.57         5.23         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96        26.79         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
        3.12         2.56        14.60        17.72        15.35        21.73 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       23.05        13.78         3.25         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         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 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
        9.14        21.24        13.97         6.41         8.61        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        3.39        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       14.96        28.54        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       14.04        24.76        18.08        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-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        6.74         4.77        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        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA 
       23.90        34.45        18.64        36.20         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
       20.55         7.63        11.77         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       10.59        35.41        20.71        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       77.65        20.12        53.10        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
        2.83        14.14        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        15.09        12.59         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0102 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-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       48.95        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       13.87        14.20        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        33.67        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
        9.44         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 
        7.79         5.39       120.56         7.36        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       14.93        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        11.08        19.59        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 
        7.27        15.98        18.41         7.56        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 
       10.45         7.59        94.78         0.10        38.17        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 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-12-1094 
       20.58       127.59         5.82         7.59        33.21        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.85         9.11        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 
       11.24         1.35         5.39         2.04        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
       26.07        16.37        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07         5.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                        1.08                         0.10 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       58.68                       127.59 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       15.19                        12.16 
[1] "1.1 - 58.7 (15.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED    12  18
  AMP PEAK 13(11P13) WILD-TYPE 213 330
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED     12   18
  AMP PEAK 13(11P13) WILD-TYPE  213  330
        clus
vv       AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  FEMALE                         12                          213
  MALE                           18                          330
[1] 2 2
[1] FALSE
D13V4, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     2  27
  AMP PEAK 13(11P13) WILD-TYPE  72 448
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      2   27
  AMP PEAK 13(11P13) WILD-TYPE   72  448
     clus
vv    AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  NO                           2                           72
  YES                         27                          448
[1] 2 2
[1] FALSE
D13V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 13(11P13) MUTATED                               2
  AMP PEAK 13(11P13) WILD-TYPE                            28
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 13(11P13) MUTATED                     1
  AMP PEAK 13(11P13) WILD-TYPE                  17
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 13(11P13) MUTATED                                27
  AMP PEAK 13(11P13) WILD-TYPE                             498
D13V6, multiclass
                                 clus
vv                                AMP PEAK 13(11P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 13(11P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             28
  TREATED PRIMARY GBM                                       17
  UNTREATED PRIMARY (DE NOVO) GBM                          498
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11P13) MUTATED       1                         2    27
  AMP PEAK 13(11P13) WILD-TYPE    12                        48   460
D13V7, multiclass
                           clus
vv                          AMP PEAK 13(11P13) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             27
                           clus
vv                          AMP PEAK 13(11P13) WILD-TYPE
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                           48
  WHITE                                              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"
D13V8, binary
                              cls
clus                             0   1
  AMP PEAK 13(11P13) MUTATED     1  27
  AMP PEAK 13(11P13) WILD-TYPE  11 448
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      1   27
  AMP PEAK 13(11P13) WILD-TYPE   11  448
                        clus
vv                       AMP PEAK 13(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         27
                        clus
vv                       AMP PEAK 13(11P13) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          448
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12P13.32) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 14(12P13.32) MUTATED    16  67
  AMP PEAK 14(12P13.32) WILD-TYPE  81 406
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             83                             487 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                             67                             406 
$`AMP PEAK 14(12P13.32) MUTATED`
TCGA-06-5415 TCGA-06-5856 TCGA-06-5859 TCGA-06-6699 TCGA-06-A7TK TCGA-06-A7TL 
        8.55         3.75         4.57         1.55        14.60        17.72 
TCGA-12-1602 TCGA-12-3653 TCGA-14-0740 TCGA-14-0790 TCGA-14-1396 TCGA-14-1453 
        6.77        14.53        11.97        13.78         1.12         1.15 
TCGA-14-1458 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-16-1460 TCGA-19-1786 
        6.67        17.79        17.85        17.49         6.41         7.17 
TCGA-19-1787 TCGA-19-5954 TCGA-26-1438 TCGA-26-5132 TCGA-27-1838 TCGA-28-1756 
       12.66        12.10        10.03         9.40        11.51         2.83 
TCGA-28-2506 TCGA-32-1979 TCGA-32-1991 TCGA-32-2615 TCGA-32-4208 TCGA-32-4210 
        6.74        19.50        16.93        15.95        21.14         3.72 
TCGA-32-5222 TCGA-74-6577 TCGA-76-4928 TCGA-02-0001 TCGA-02-0024 TCGA-02-0051 
       19.23         4.34         3.09        11.77        53.10        15.09 
TCGA-02-0054 TCGA-02-0070 TCGA-02-0074 TCGA-02-0084 TCGA-02-0087 TCGA-02-0266 
        6.54        25.05        10.19        12.62        57.76        17.72 
TCGA-02-0271 TCGA-02-0324 TCGA-02-2466 TCGA-06-0129 TCGA-06-0146 TCGA-06-0151 
       14.47         7.73        16.80        33.67        20.09        46.59 
TCGA-06-0157 TCGA-06-0162 TCGA-06-0164 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
        3.19         3.42        56.91         4.18        69.90        27.22 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0216 TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 
       44.58        38.96        24.16        19.82        13.32        72.36 
TCGA-06-0649 TCGA-06-0743 TCGA-06-1086 TCGA-06-1087 TCGA-06-2561 TCGA-06-6389 
        2.10        26.40         6.84         4.04        17.65         7.79 
TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 TCGA-08-0352 TCGA-08-0392 TCGA-08-0516 
        7.36        37.84         4.18         1.28         0.72        19.59 
TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-1090 TCGA-12-1098 
       12.13         9.73        14.93        18.48         7.59         3.98 
TCGA-15-1449 TCGA-16-0850 TCGA-26-1442 TCGA-28-5207 TCGA-28-5218 
       13.28        16.37        31.33        11.28         5.16 

$`AMP PEAK 14(12P13.32) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        4.54         8.81         8.98         6.71         2.73         6.15 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32        12.85         4.77         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-12-0615 TCGA-12-1092 
       26.79         1.87         3.12         2.56        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0812 
        2.04        15.12         0.95         6.21        23.05         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 
        2.89        16.50        26.33        15.95         1.38         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-14-1459 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-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 
        7.17         7.96         3.78         3.42        17.59        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 
        8.61        14.27         3.39        25.38         3.65         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
        8.02        18.90         4.73         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 
       16.80        14.96        17.79        28.54        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        7.13         9.37         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        24.76        18.08        16.77        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-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        0.66         4.77        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
       15.85         1.18         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 
       20.78        15.02         8.84        22.78        25.18        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        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 
        4.08         1.45        25.58         3.45        20.91        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.80         4.54         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       19.73        26.43        28.70         5.49        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 
       89.72        22.72        51.32         8.81        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 
       99.98        15.65        48.95        16.54        16.93        10.75 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        9.27        16.21         3.35        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 
        2.33        17.79        10.09         8.61        19.46        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 
       13.94        10.45        10.82         9.44        11.80        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.04        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.64        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         5.75         9.80        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       12.49         4.93        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6390 TCGA-06-6693 
        5.98         4.37         0.43        31.50         5.39       120.56 
TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       22.68       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       18.02        15.35        13.97        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
       43.23         7.63        14.86        91.76        24.79        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       14.53         4.14         2.24        11.24         1.35         5.39 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        2.04        28.93        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 
       19.10        53.19         3.91        26.07        11.77        21.90 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        0.66        10.75         9.07         5.95        12.95         4.64 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01        13.64        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        7.36        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                           0.72                            0.10 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                          72.36                          127.59 
  AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE 
                          12.62                           12.23 
[1] "0.7 - 72.4 (12.6)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED    33  51
  AMP PEAK 14(12P13.32) WILD-TYPE 192 297
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED     33   51
  AMP PEAK 14(12P13.32) WILD-TYPE  192  297
        clus
vv       AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  FEMALE                            33                             192
  MALE                              51                             297
[1] 2 2
[1] FALSE
D14V4, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED     7  73
  AMP PEAK 14(12P13.32) WILD-TYPE  67 402
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED      7   73
  AMP PEAK 14(12P13.32) WILD-TYPE   67  402
     clus
vv    AMP PEAK 14(12P13.32) MUTATED AMP PEAK 14(12P13.32) WILD-TYPE
  NO                              7                              67
  YES                            73                             402
[1] 2 2
[1] FALSE
D14V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 14(12P13.32) MUTATED                               3
  AMP PEAK 14(12P13.32) WILD-TYPE                            27
                                 vv
clus                              TREATED PRIMARY GBM
  AMP PEAK 14(12P13.32) MUTATED                     2
  AMP PEAK 14(12P13.32) WILD-TYPE                  16
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 14(12P13.32) MUTATED                                79
  AMP PEAK 14(12P13.32) WILD-TYPE                             446
D14V6, multiclass
                                 clus
vv                                AMP PEAK 14(12P13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               3
  TREATED PRIMARY GBM                                         2
  UNTREATED PRIMARY (DE NOVO) GBM                            79
                                 clus
vv                                AMP PEAK 14(12P13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                27
  TREATED PRIMARY GBM                                          16
  UNTREATED PRIMARY (DE NOVO) GBM                             446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12P13.32) MUTATED       3                         6    71
  AMP PEAK 14(12P13.32) WILD-TYPE    10                        44   416
D14V7, multiclass
                           clus
vv                          AMP PEAK 14(12P13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                71
                           clus
vv                          AMP PEAK 14(12P13.32) WILD-TYPE
  ASIAN                                                  10
  BLACK OR AFRICAN AMERICAN                              44
  WHITE                                                 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"
D14V8, binary
                                 cls
clus                                0   1
  AMP PEAK 14(12P13.32) MUTATED     2  68
  AMP PEAK 14(12P13.32) WILD-TYPE  10 407
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(12P13.32) MUTATED      2   68
  AMP PEAK 14(12P13.32) WILD-TYPE   10  407
                        clus
vv                       AMP PEAK 14(12P13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            68
                        clus
vv                       AMP PEAK 14(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             407
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(12Q14.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(12Q14.1) MUTATED    20 112
  AMP PEAK 15(12Q14.1) WILD-TYPE  77 361
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           132                            438 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           112                            361 
$`AMP PEAK 15(12Q14.1) MUTATED`
TCGA-06-6391 TCGA-06-5415 TCGA-06-5856 TCGA-06-5859 TCGA-06-6695 TCGA-06-A7TK 
        1.48         8.55         3.75         4.57         8.32        14.60 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3653 TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 
       15.65         6.77        14.53        13.78         1.12        58.78 
TCGA-14-1451 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-16-0848 TCGA-16-1056 
       23.11        17.79        17.85        17.49        17.59        14.01 
TCGA-19-0960 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 TCGA-19-2624 TCGA-19-5950 
        8.61         7.17        12.66         0.13         0.16        17.19 
TCGA-19-5960 TCGA-26-1438 TCGA-26-5135 TCGA-27-1833 TCGA-27-1835 TCGA-27-1838 
       14.96        10.03         8.88        24.23        21.30        11.51 
TCGA-27-2518 TCGA-27-2526 TCGA-28-1746 TCGA-28-2506 TCGA-32-1979 TCGA-32-2615 
       24.76         2.86         0.20         6.74        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        19.23         0.85         8.94         0.20 
TCGA-41-5651 TCGA-74-6577 TCGA-76-4928 TCGA-76-4935 TCGA-76-6193 TCGA-RR-A6KA 
       15.12         4.34         3.09        36.85         2.70         6.28 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0024 TCGA-02-0046 
        7.63        11.77         4.73        18.35        53.10         6.87 
TCGA-02-0051 TCGA-02-0054 TCGA-02-0060 TCGA-02-0070 TCGA-02-0074 TCGA-02-0099 
       15.09         6.54         6.02        25.05        10.19         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0266 TCGA-02-0271 TCGA-02-0324 TCGA-02-0332 
       27.02        17.65        17.72        14.47         7.73        25.71 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 TCGA-06-0138 TCGA-06-0145 
       15.45        20.32        22.72        33.67        24.23         2.33 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0157 TCGA-06-0162 TCGA-06-0164 TCGA-06-0173 
       46.59        12.33         3.19         3.42        56.91         4.47 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0182 TCGA-06-0188 TCGA-06-0192 TCGA-06-0214 
        3.22         4.18         3.65        44.58        38.96        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0402 TCGA-06-0409 
       24.16         0.72        19.82        13.32         0.26        72.36 
TCGA-06-0412 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0875 TCGA-06-1086 
        9.57         2.10        14.20        26.40        43.46         6.84 
TCGA-06-1087 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2569 
        4.04        33.90        12.49         4.93        17.65         0.43 
TCGA-06-2570 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 TCGA-08-0352 
       31.50         5.39         7.36        37.84         4.18         1.28 
TCGA-08-0380 TCGA-08-0518 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0657 
       14.93        19.33        14.73        12.99        10.45         0.10 
TCGA-12-0670 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-0826 
       25.97        12.13         9.73        14.93        18.48        27.78 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1098 TCGA-15-1444 TCGA-15-1449 TCGA-16-0846 
        5.82         7.59         3.98        50.53        13.28         3.91 
TCGA-16-0850 TCGA-19-0957 TCGA-28-5207 TCGA-28-5209 TCGA-28-5214 TCGA-28-5218 
       16.37        21.90        11.28        14.53        23.44         5.16 

$`AMP PEAK 15(12Q14.1) WILD-TYPE`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        3.98        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 
        8.81         8.98         6.71         2.73         6.15         5.23 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
        1.87         3.12         2.56        17.72        15.35        21.73 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.68        14.73        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0812 
       15.12        11.97         0.95         6.21        23.05         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 
        2.89        16.50        26.33        15.95         1.38         3.75 
TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       32.05         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 
        6.67        12.43         0.99         1.97         7.63         5.88 
TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 
        7.17         7.96         3.78         3.42        29.03         4.57 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0963 
       10.29         9.14        21.24        13.97         6.41        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 
        3.39        25.38         3.65         3.25         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1439 
       22.49        14.07        16.80        17.79        28.54        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5136 TCGA-26-A7UX 
        9.73         7.13         9.37         9.40        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
        5.06        16.60         9.86        40.54        30.05        14.04 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 
       18.08        16.77        16.08         7.59        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-28-2509 TCGA-32-1970 
        1.55         2.83         0.13         0.66         4.77        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 
        8.84        22.78        25.18         3.72        19.86        10.85 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 
       13.35         9.53         0.99         4.44        11.84        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 
        4.08         1.45        25.58         3.45        20.91        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.80         4.54         3.65         9.17 
TCGA-76-4934 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        2.53        16.70         3.29        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KC TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        5.92        20.55        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       10.72        10.52        18.31        14.73         3.22        12.59 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
        2.50        19.86         8.35         9.57        19.73        26.43 
TCGA-02-0069 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       28.70         5.49        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0104 
       12.62        51.32         8.81        57.76        16.96        65.00 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        10.75         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90        10.62         7.33        15.91 
TCGA-02-0333 TCGA-02-0337 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-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       12.92        15.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        6.94         3.98        12.95        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 
       11.90         0.20        10.29         2.20        11.74        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 
       17.79        10.09         8.61        19.46        13.94        10.45 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44        11.80        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        3.29        13.12         4.04        91.00        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       69.90        73.84        27.22        15.42        10.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       11.84         0.53        13.64        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        9.01         4.70         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        5.75         9.80        23.57        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        2.70         0.92        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       13.61         1.08        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 
        5.98         4.37         7.79       120.56        22.68       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       65.33         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       58.68        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0619 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0688 
        7.56        34.92         7.59        94.78        38.17        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 
        7.63        14.86        91.76        24.79        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1091 TCGA-12-1093 
       38.76         8.94        20.58       127.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 
       12.23        15.85         9.11        14.53         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
       11.24         1.35         5.39         2.04        28.93        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 TCGA-19-0955 
        0.79        13.78        19.10        53.19        26.07        11.77 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        0.66        10.75         9.07         5.95        12.95         4.64 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 
        7.30         5.26        14.93        17.88        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       11.01        13.64        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                         72.36                         127.59 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                        12.825                         12.160 
[1] "0.1 - 72.4 (12.8)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    57  77
  AMP PEAK 15(12Q14.1) WILD-TYPE 168 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     57   77
  AMP PEAK 15(12Q14.1) WILD-TYPE  168  271
        clus
vv       AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  FEMALE                           57                            168
  MALE                             77                            271
[1] 2 2
[1] FALSE
D15V4, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    21 108
  AMP PEAK 15(12Q14.1) WILD-TYPE  53 367
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     21  108
  AMP PEAK 15(12Q14.1) WILD-TYPE   53  367
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  NO                            21                             53
  YES                          108                            367
[1] 2 2
[1] FALSE
D15V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 15(12Q14.1) MUTATED                               5
  AMP PEAK 15(12Q14.1) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 15(12Q14.1) MUTATED                     3
  AMP PEAK 15(12Q14.1) WILD-TYPE                  15
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 15(12Q14.1) MUTATED                               126
  AMP PEAK 15(12Q14.1) WILD-TYPE                             399
D15V6, multiclass
                                 clus
vv                                AMP PEAK 15(12Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          126
                                 clus
vv                                AMP PEAK 15(12Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            399
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q14.1) MUTATED       4                        12   112
  AMP PEAK 15(12Q14.1) WILD-TYPE     9                        38   375
D15V7, multiclass
                           clus
vv                          AMP PEAK 15(12Q14.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              112
                           clus
vv                          AMP PEAK 15(12Q14.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             38
  WHITE                                                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"
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED     1 114
  AMP PEAK 15(12Q14.1) WILD-TYPE  11 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED      1  114
  AMP PEAK 15(12Q14.1) WILD-TYPE   11  361
                        clus
vv                       AMP PEAK 15(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       AMP PEAK 15(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            361
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12Q15) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(12Q15) MUTATED    13  79
  AMP PEAK 16(12Q15) WILD-TYPE  84 394
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          92                          478 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          79                          394 
$`AMP PEAK 16(12Q15) MUTATED`
TCGA-06-6391 TCGA-06-5415 TCGA-06-5856 TCGA-06-6695 TCGA-06-6700 TCGA-06-A7TK 
        1.48         8.55         3.75         8.32         4.77        14.60 
TCGA-12-1602 TCGA-12-3653 TCGA-14-0790 TCGA-14-1396 TCGA-14-1450 TCGA-14-1451 
        6.77        14.53        13.78         1.12        58.78        23.11 
TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-19-1786 TCGA-19-1787 TCGA-19-2624 
       17.79        17.85        17.49         7.17        12.66         0.16 
TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-27-2518 TCGA-27-2526 TCGA-28-2506 
       10.03         9.40         8.88        24.76         2.86         6.74 
TCGA-32-1978 TCGA-32-1979 TCGA-32-2615 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 
       15.85        19.50        15.95        21.14        12.59        19.23 
TCGA-41-2571 TCGA-74-6577 TCGA-74-6584 TCGA-06-0209 TCGA-02-0001 TCGA-02-0006 
        0.85         4.34         7.50         7.63        11.77        18.35 
TCGA-02-0024 TCGA-02-0039 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0060 
       53.10        10.52        15.09        12.59         6.54         6.02 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0099 TCGA-02-0102 TCGA-02-0271 
       25.05         5.49        10.19         3.48        27.02        14.47 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0330 TCGA-02-0337 TCGA-06-0138 TCGA-06-0140 
        9.90         7.73        15.91        25.12        24.23         0.20 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0162 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
       46.59        12.33         3.42        56.91         4.47         3.22 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0187 TCGA-06-0188 TCGA-06-0192 TCGA-06-0214 
        4.18         3.65        27.22        44.58        38.96        15.02 
TCGA-06-0216 TCGA-06-0409 TCGA-06-0648 TCGA-06-0686 TCGA-06-0743 TCGA-06-0939 
       24.16        72.36         9.80        14.20        26.40        26.76 
TCGA-06-1086 TCGA-06-1087 TCGA-06-2561 TCGA-06-2569 TCGA-06-6390 TCGA-08-0246 
        6.84         4.04        17.65         0.43         5.39         4.18 
TCGA-12-0616 TCGA-12-0670 TCGA-12-0691 TCGA-12-0772 TCGA-12-0778 TCGA-12-0826 
       14.73        25.97        12.13        53.85        14.93        27.78 
TCGA-12-1090 TCGA-12-1098 TCGA-15-1449 TCGA-19-0957 TCGA-28-5207 TCGA-28-5214 
        7.59         3.98        13.28        21.90        11.28        23.44 
TCGA-28-5218 TCGA-76-6660 
        5.16         3.75 

$`AMP PEAK 16(12Q15) WILD-TYPE`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        3.98        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.81         8.98         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 
        5.23        12.85         4.77         1.55         4.96        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
        1.87         3.12         2.56        17.72        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         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         6.67        12.43         0.99         1.97         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 
        5.88         7.17         7.96         3.78         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 
       13.97         6.41         8.61        14.27         3.39        25.38 
TCGA-19-1392 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        3.65         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
       22.49        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5136 TCGA-26-A7UX 
       13.87         9.73         7.13         9.37        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        11.51        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        0.13         0.66         4.77        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
        0.10         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.02         8.84        22.78        25.18 
TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
        3.72        19.86        10.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 
        4.08         1.45        25.58         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-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 
       18.64        36.20         5.92         6.28        20.55         4.73 
TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
       23.18        10.59        35.41        20.71        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       90.58         2.83        14.14         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        6.87        14.73         3.22         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 
        9.57        19.73        26.43        28.70        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       16.96        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-02-0281 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-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 
       10.62         7.33        25.71         4.37        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
       11.90        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0154 TCGA-06-0155 
       17.79        10.09         8.61        19.46        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 
        3.19        10.82         9.44        11.80        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       19.66         3.29        13.12         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       20.25        69.90        73.84        15.42        10.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       11.84         0.53         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 
       20.42        48.69        10.82         9.01         0.26         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        2.10        23.57        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.78        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         5.98         4.37        31.50         7.79 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
      120.56         7.36        22.68        37.84       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        18.41         7.56        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0692 
        7.59        94.78         0.10        38.17        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        43.23         7.63         9.73 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 
       38.76         8.94        20.58       127.59         5.82        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       15.98        12.23        15.85         9.11        14.53         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        2.24        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       19.30         0.79        13.78        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 
        3.91        26.07        16.37        11.77         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
        9.07         5.95        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
       14.93        17.88        14.53        11.77        31.27        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 
       13.64        22.68        12.76         5.42         7.36        11.38 
TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         1.61        17.72        26.30 

  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                        0.16                         0.10 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       72.36                       127.59 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       12.46                        12.23 
[1] "0.2 - 72.4 (12.5)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    32  61
  AMP PEAK 16(12Q15) WILD-TYPE 193 287
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     32   61
  AMP PEAK 16(12Q15) WILD-TYPE  193  287
        clus
vv       AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  FEMALE                         32                          193
  MALE                           61                          287
[1] 2 2
[1] FALSE
D16V4, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    12  76
  AMP PEAK 16(12Q15) WILD-TYPE  62 399
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     12   76
  AMP PEAK 16(12Q15) WILD-TYPE   62  399
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  NO                          12                           62
  YES                         76                          399
[1] 2 2
[1] FALSE
D16V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 16(12Q15) MUTATED                               4
  AMP PEAK 16(12Q15) WILD-TYPE                            26
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 16(12Q15) MUTATED                     2
  AMP PEAK 16(12Q15) WILD-TYPE                  16
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 16(12Q15) MUTATED                                87
  AMP PEAK 16(12Q15) WILD-TYPE                             438
D16V6, multiclass
                                 clus
vv                                AMP PEAK 16(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            4
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         87
                                 clus
vv                                AMP PEAK 16(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             26
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          438
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q15) MUTATED       3                         6    80
  AMP PEAK 16(12Q15) WILD-TYPE    10                        44   407
D16V7, multiclass
                           clus
vv                          AMP PEAK 16(12Q15) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             80
                           clus
vv                          AMP PEAK 16(12Q15) WILD-TYPE
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           44
  WHITE                                              407
[1] 3 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  79
  AMP PEAK 16(12Q15) WILD-TYPE  12 396
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED      0   79
  AMP PEAK 16(12Q15) WILD-TYPE   12  396
                        clus
vv                       AMP PEAK 16(12Q15) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         79
                        clus
vv                       AMP PEAK 16(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          396
[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  94 444
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          32                          538 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                          29                          444 
$`AMP PEAK 17(13Q34) MUTATED`
TCGA-19-A6J4 TCGA-06-5856 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-1453 
        3.98         3.75        21.73         6.77        14.53         1.15 
TCGA-14-4157 TCGA-16-1063 TCGA-19-1390 TCGA-19-1787 TCGA-28-1752 TCGA-32-1970 
        3.42        13.97        25.38        12.66         8.48        15.39 
TCGA-32-2615 TCGA-41-3392 TCGA-02-0001 TCGA-02-0024 TCGA-02-0025 TCGA-02-0114 
       15.95         0.99        11.77        53.10        42.74        99.98 
TCGA-02-0281 TCGA-02-0289 TCGA-02-0338 TCGA-06-0146 TCGA-06-0210 TCGA-06-0221 
        3.98        14.20        10.59        20.09         7.40        19.82 
TCGA-06-1087 TCGA-08-0386 TCGA-12-0769 TCGA-14-0817 TCGA-14-0871 TCGA-16-0849 
        4.04        18.02        15.06         5.39        28.93        26.07 
TCGA-19-1388 TCGA-28-5207 
       12.95        11.28 

$`AMP PEAK 17(13Q34) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.60        17.72        15.35        15.65        25.68        14.73 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       16.50        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.78        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        9.14        21.24         6.41         8.61        14.27         3.39 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65         7.17         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       17.79        28.54        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         8.35         7.63         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1973 TCGA-32-1976 
        0.13         0.66         6.74         4.77        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-32-2632 
       14.86        16.93        12.23        20.78        15.02         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        7.63         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       14.47        13.87        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
        3.65        20.38        28.41        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 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-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.85         9.11        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         2.04        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 
       50.53        19.10        53.19        13.28         3.91        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        4.64        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        2.33         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
       22.68        12.76         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                        0.99                         0.10 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                       99.98                       127.59 
  AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE 
                       13.46                        12.23 
[1] "1.0 - 100.0 (13.5)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED    10  22
  AMP PEAK 17(13Q34) WILD-TYPE 215 326
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED     10   22
  AMP PEAK 17(13Q34) WILD-TYPE  215  326
        clus
vv       AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  FEMALE                         10                          215
  MALE                           22                          326
[1] 2 2
[1] FALSE
D17V4, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED     5  26
  AMP PEAK 17(13Q34) WILD-TYPE  69 449
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED      5   26
  AMP PEAK 17(13Q34) WILD-TYPE   69  449
     clus
vv    AMP PEAK 17(13Q34) MUTATED AMP PEAK 17(13Q34) WILD-TYPE
  NO                           5                           69
  YES                         26                          449
[1] 2 2
[1] FALSE
D17V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 17(13Q34) MUTATED                               1
  AMP PEAK 17(13Q34) WILD-TYPE                            29
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 17(13Q34) MUTATED                     2
  AMP PEAK 17(13Q34) WILD-TYPE                  16
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 17(13Q34) MUTATED                                29
  AMP PEAK 17(13Q34) WILD-TYPE                             496
D17V6, multiclass
                                 clus
vv                                AMP PEAK 17(13Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            1
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         29
                                 clus
vv                                AMP PEAK 17(13Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             29
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          496
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(13Q34) MUTATED       0                         3    29
  AMP PEAK 17(13Q34) WILD-TYPE    13                        47   458
D17V7, multiclass
                           clus
vv                          AMP PEAK 17(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             29
                           clus
vv                          AMP PEAK 17(13Q34) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           47
  WHITE                                              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"
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(13Q34) MUTATED     0  26
  AMP PEAK 17(13Q34) WILD-TYPE  12 449
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(13Q34) MUTATED      0   26
  AMP PEAK 17(13Q34) WILD-TYPE   12  449
                        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                          449
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED     3  27
  AMP PEAK 18(13Q34) WILD-TYPE  94 446
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          30                          540 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          27                          446 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-19-A6J4 TCGA-12-1092 TCGA-12-1602 TCGA-12-3653 TCGA-14-1453 TCGA-14-4157 
        3.98        21.73         6.77        14.53         1.15         3.42 
TCGA-19-1390 TCGA-19-1787 TCGA-19-A60I TCGA-28-1752 TCGA-32-1970 TCGA-32-2615 
       25.38        12.66        17.79         8.48        15.39        15.95 
TCGA-41-3392 TCGA-02-0001 TCGA-02-0025 TCGA-02-0114 TCGA-02-0281 TCGA-02-0289 
        0.99        11.77        42.74        99.98         3.98        14.20 
TCGA-02-0338 TCGA-06-0221 TCGA-06-1087 TCGA-08-0354 TCGA-08-0386 TCGA-08-0389 
       10.59        19.82         4.04        17.95        18.02        15.35 
TCGA-12-0616 TCGA-12-0769 TCGA-14-0817 TCGA-14-0871 TCGA-19-1388 TCGA-28-5207 
       14.73        15.06         5.39        28.93        12.95        11.28 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 
        2.56        14.60        17.72        15.35        15.65        25.68 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       14.73        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 
        2.89        16.50        26.33        15.95         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.78        17.59        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       14.27         3.39         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       16.80        14.96        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
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-32-1973 
        2.83         0.13         0.66         6.74         4.77        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA 
       23.90        34.45        18.64        36.20         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
       20.55         7.63         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        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-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        92.65        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 
       17.72        10.75        14.47        13.87        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
        4.37        25.12        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 
        7.79         5.39       120.56         7.36        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 
        9.80        29.23        65.33         1.28         8.42        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        18.41         7.56        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 
       12.13         3.65        20.38        28.41        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 
        2.24        11.24         1.35         2.04        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
       26.07        16.37        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07         5.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.99                         0.10 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                       99.98                       127.59 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      14.365                       12.195 
[1] "1.0 - 100.0 (14.4)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    10  20
  AMP PEAK 18(13Q34) WILD-TYPE 215 328
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     10   20
  AMP PEAK 18(13Q34) WILD-TYPE  215  328
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         10                          215
  MALE                           20                          328
[1] 2 2
[1] FALSE
D18V4, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     4  25
  AMP PEAK 18(13Q34) WILD-TYPE  70 450
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      4   25
  AMP PEAK 18(13Q34) WILD-TYPE   70  450
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           4                           70
  YES                         25                          450
[1] 2 2
[1] FALSE
D18V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 18(13Q34) MUTATED                               2
  AMP PEAK 18(13Q34) WILD-TYPE                            28
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 18(13Q34) MUTATED                     1
  AMP PEAK 18(13Q34) WILD-TYPE                  17
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 18(13Q34) MUTATED                                27
  AMP PEAK 18(13Q34) WILD-TYPE                             498
D18V6, multiclass
                                 clus
vv                                AMP PEAK 18(13Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            2
  TREATED PRIMARY GBM                                      1
  UNTREATED PRIMARY (DE NOVO) GBM                         27
                                 clus
vv                                AMP PEAK 18(13Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             28
  TREATED PRIMARY GBM                                       17
  UNTREATED PRIMARY (DE NOVO) GBM                          498
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       0                         4    25
  AMP PEAK 18(13Q34) WILD-TYPE    13                        46   462
D18V7, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             25
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           46
  WHITE                                              462
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     0  24
  AMP PEAK 18(13Q34) WILD-TYPE  12 451
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      0   24
  AMP PEAK 18(13Q34) WILD-TYPE   12  451
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         24
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          451
[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  94 440
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             36                             534 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                             33                             440 
$`AMP PEAK 19(14Q32.33) MUTATED`
TCGA-06-5415 TCGA-12-1600 TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-19-2620 
        8.55        14.73        44.02        14.53        11.97         4.87 
TCGA-26-1439 TCGA-32-2495 TCGA-32-2632 TCGA-41-2575 TCGA-76-6286 TCGA-02-0059 
       13.87        15.02         8.84         9.53        20.98         9.57 
TCGA-02-0075 TCGA-02-0102 TCGA-06-0148 TCGA-06-0151 TCGA-06-0159 TCGA-06-0177 
       20.84        27.02        10.09        46.59         9.44         4.18 
TCGA-06-0195 TCGA-06-0237 TCGA-06-0397 TCGA-06-0414 TCGA-06-0747 TCGA-06-1087 
        7.40        13.64         9.01        35.11         2.70         4.04 
TCGA-06-2563 TCGA-06-2569 TCGA-08-0244 TCGA-08-0246 TCGA-08-0351 TCGA-08-0386 
       30.64         0.43        22.68         4.18        65.33        18.02 
TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-14-0867 TCGA-16-0846 TCGA-19-0962 
        4.27        11.08        34.92         2.04         3.91         0.66 

$`AMP PEAK 19(14Q32.33) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 
        2.56        14.60        17.72        15.35        21.73        15.65 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68         6.77        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       16.50        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
        7.96         3.78         3.42        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        8.61        14.27         3.39        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 
       12.66         3.25         0.13         9.67         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
       22.49        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
       18.97        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        6.74         4.77        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-32-2615 TCGA-32-2634 TCGA-32-2638 
       16.93        12.23        20.78        15.95        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 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-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
        5.92         6.28        20.55         7.63        11.77         4.73 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       18.35        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-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0060 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-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
        8.81        57.76        16.96         3.48        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       17.65        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 
        2.20        11.74         2.33        20.09        17.79         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       44.58        15.42        10.42        38.96         4.67         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       17.65        12.56         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0245 
       31.50         7.79         5.39       120.56         7.36        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       13.97         0.72        12.56        42.15        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        7.56        14.73        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 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-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.85         9.11        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       11.24         1.35         5.39        28.93        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
       13.78        50.53        19.10        53.19        13.28        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       16.37        11.77        21.90        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       12.95         4.64        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                           0.43                            0.10 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                          65.33                          127.59 
  AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE 
                         10.585                          12.360 
[1] "0.4 - 65.3 (10.6)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.2"
D19V2, continuous
D19V3, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED    12  24
  AMP PEAK 19(14Q32.33) WILD-TYPE 213 324
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED     12   24
  AMP PEAK 19(14Q32.33) WILD-TYPE  213  324
        clus
vv       AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  FEMALE                            12                             213
  MALE                              24                             324
[1] 2 2
[1] FALSE
D19V4, binary
                                 cls
clus                                0   1
  AMP PEAK 19(14Q32.33) MUTATED     4  30
  AMP PEAK 19(14Q32.33) WILD-TYPE  70 445
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED      4   30
  AMP PEAK 19(14Q32.33) WILD-TYPE   70  445
     clus
vv    AMP PEAK 19(14Q32.33) MUTATED AMP PEAK 19(14Q32.33) WILD-TYPE
  NO                              4                              70
  YES                            30                             445
[1] 2 2
[1] FALSE
D19V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 19(14Q32.33) MUTATED                               2
  AMP PEAK 19(14Q32.33) WILD-TYPE                            28
                                 vv
clus                              TREATED PRIMARY GBM
  AMP PEAK 19(14Q32.33) MUTATED                     2
  AMP PEAK 19(14Q32.33) WILD-TYPE                  16
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 19(14Q32.33) MUTATED                                32
  AMP PEAK 19(14Q32.33) WILD-TYPE                             493
D19V6, multiclass
                                 clus
vv                                AMP PEAK 19(14Q32.33) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               2
  TREATED PRIMARY GBM                                         2
  UNTREATED PRIMARY (DE NOVO) GBM                            32
                                 clus
vv                                AMP PEAK 19(14Q32.33) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                28
  TREATED PRIMARY GBM                                          16
  UNTREATED PRIMARY (DE NOVO) GBM                             493
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(14Q32.33) MUTATED       0                         2    34
  AMP PEAK 19(14Q32.33) WILD-TYPE    13                        48   453
D19V7, multiclass
                           clus
vv                          AMP PEAK 19(14Q32.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                34
                           clus
vv                          AMP PEAK 19(14Q32.33) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                              48
  WHITE                                                 453
[1] 3 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  12 441
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(14Q32.33) MUTATED      0   34
  AMP PEAK 19(14Q32.33) WILD-TYPE   12  441
                        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                             441
[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     4  47
  AMP PEAK 20(17P13.2) WILD-TYPE  93 426
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            51                            519 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                            47                            426 
$`AMP PEAK 20(17P13.2) MUTATED`
TCGA-19-A6J4 TCGA-06-A5U1 TCGA-12-1600 TCGA-12-1602 TCGA-14-0865 TCGA-19-1390 
        3.98         1.87        14.73         6.77        16.50        25.38 
TCGA-27-2521 TCGA-28-1746 TCGA-28-2506 TCGA-32-2615 TCGA-32-4210 TCGA-41-2575 
       16.77         0.20         6.74        15.95         3.72         9.53 
TCGA-41-4097 TCGA-RR-A6KA TCGA-02-0051 TCGA-02-0266 TCGA-02-0281 TCGA-02-2466 
        0.20         6.28        15.09        17.72         3.98        16.80 
TCGA-06-0151 TCGA-06-0166 TCGA-06-0173 TCGA-06-0195 TCGA-06-0216 TCGA-06-0409 
       46.59         5.85         4.47         7.40        24.16        72.36 
TCGA-06-0414 TCGA-06-0686 TCGA-06-0743 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 
       35.11        14.20        26.40         4.04        11.84         1.08 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 
       25.71        12.16        29.23        65.33         8.42        24.56 
TCGA-08-0356 TCGA-08-0375 TCGA-08-0389 TCGA-08-0392 TCGA-08-0510 TCGA-12-0821 
       31.10        12.23        15.35         0.72         4.27        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-1096 TCGA-14-0813 TCGA-15-1447 TCGA-16-0849 
       23.51        38.76         9.11         1.35        53.19        26.07 
TCGA-19-1388 TCGA-28-5207 TCGA-28-5218 
       12.95        11.28         5.16 

$`AMP PEAK 20(17P13.2) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96        26.79         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
       14.60        17.72        15.35        21.73        15.65        25.68 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        2.89        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
        7.96         3.78         3.42        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        8.61        14.27         3.39         3.65         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        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
       22.49        14.07        16.80        14.96        17.79        28.54 
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-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 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-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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02         8.84        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 
        8.94         0.99         4.44        11.84        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KC 
       23.90        34.45        18.64        36.20         5.92        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       20.12        53.10        42.74        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 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-02-0064 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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        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-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 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-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09         8.61        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 
       56.91        10.65        19.66         3.29        13.12         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80         2.10        23.57        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       26.79        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        7.36        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0349 TCGA-08-0352 TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 
        8.42         9.80         1.28        17.95        37.58        22.29 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 
        3.39        14.93        18.02        13.97        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0828 
       14.86        91.76        24.79        18.48        27.78         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         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       12.23        15.85        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       11.24         5.39         2.04        28.93        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 
       13.78        50.53        19.10        13.28         3.91        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        4.64        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        2.33         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       12.76         5.42         7.36        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                         72.36                         127.59 
  AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE 
                         12.23                          12.23 
[1] "0.2 - 72.4 (12.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    16  35
  AMP PEAK 20(17P13.2) WILD-TYPE 209 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     16   35
  AMP PEAK 20(17P13.2) WILD-TYPE  209  313
        clus
vv       AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  FEMALE                           16                            209
  MALE                             35                            313
[1] 2 2
[1] FALSE
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED    10  39
  AMP PEAK 20(17P13.2) WILD-TYPE  64 436
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED     10   39
  AMP PEAK 20(17P13.2) WILD-TYPE   64  436
     clus
vv    AMP PEAK 20(17P13.2) MUTATED AMP PEAK 20(17P13.2) WILD-TYPE
  NO                            10                             64
  YES                           39                            436
[1] 2 2
[1] FALSE
D20V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 20(17P13.2) MUTATED                               4
  AMP PEAK 20(17P13.2) WILD-TYPE                            26
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 20(17P13.2) MUTATED                     1
  AMP PEAK 20(17P13.2) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 20(17P13.2) MUTATED                                46
  AMP PEAK 20(17P13.2) WILD-TYPE                             479
D20V6, multiclass
                                 clus
vv                                AMP PEAK 20(17P13.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           46
                                 clus
vv                                AMP PEAK 20(17P13.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               26
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17P13.2) MUTATED       0                         5    42
  AMP PEAK 20(17P13.2) WILD-TYPE    13                        45   445
D20V7, multiclass
                           clus
vv                          AMP PEAK 20(17P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               42
                           clus
vv                          AMP PEAK 20(17P13.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             45
  WHITE                                                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"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(17P13.2) MUTATED     1  43
  AMP PEAK 20(17P13.2) WILD-TYPE  11 432
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17P13.2) MUTATED      1   43
  AMP PEAK 20(17P13.2) WILD-TYPE   11  432
                        clus
vv                       AMP PEAK 20(17P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 20(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            432
[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  77
  AMP PEAK 21(17Q25.1) WILD-TYPE  90 396
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            84                            486 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                            77                            396 
$`AMP PEAK 21(17Q25.1) MUTATED`
TCGA-19-A6J4 TCGA-06-6700 TCGA-06-A5U1 TCGA-12-1092 TCGA-12-1600 TCGA-12-1602 
        3.98         4.77         1.87        21.73        14.73         6.77 
TCGA-12-5301 TCGA-14-0865 TCGA-14-1453 TCGA-14-1794 TCGA-14-1827 TCGA-14-1829 
        2.04        16.50         1.15         0.99         5.88         7.17 
TCGA-14-3477 TCGA-16-1063 TCGA-19-1390 TCGA-19-1392 TCGA-19-A60I TCGA-27-1835 
        3.78        13.97        25.38         3.65        17.79        21.30 
TCGA-27-2521 TCGA-28-1746 TCGA-28-1757 TCGA-28-2506 TCGA-32-1991 TCGA-32-2495 
       16.77         0.20         0.13         6.74        16.93        15.02 
TCGA-32-2615 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-74-6573 TCGA-RR-A6KA 
       15.95         9.53        11.84         0.20         3.45         6.28 
TCGA-02-0003 TCGA-02-0047 TCGA-02-0051 TCGA-02-0104 TCGA-02-0106 TCGA-02-0266 
        4.73        14.73        15.09        65.00        11.67        17.72 
TCGA-02-0281 TCGA-02-0325 TCGA-02-0456 TCGA-02-2466 TCGA-06-0151 TCGA-06-0152 
        3.98        10.62         3.35        16.80        46.59        12.33 
TCGA-06-0166 TCGA-06-0173 TCGA-06-0188 TCGA-06-0195 TCGA-06-0216 TCGA-06-0237 
        5.85         4.47        44.58         7.40        24.16        13.64 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 
       72.36         4.70        35.11         2.10        14.20        26.40 
TCGA-06-0744 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 
       46.88        23.93         4.04        11.84         1.08         7.36 
TCGA-08-0346 TCGA-08-0350 TCGA-08-0353 TCGA-08-0510 TCGA-08-0514 TCGA-08-0531 
        8.42        29.23         8.42         4.27        11.08         7.56 
TCGA-12-0619 TCGA-12-0662 TCGA-12-0818 TCGA-12-0821 TCGA-12-0827 TCGA-12-1090 
       34.92        38.17        91.76        10.62        38.76         7.59 
TCGA-12-1096 TCGA-12-1098 TCGA-14-0813 TCGA-15-1449 TCGA-16-0846 TCGA-19-1388 
        9.11         3.98         1.35        13.28         3.91        12.95 
TCGA-28-5207 TCGA-28-5215 TCGA-28-5218 TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 
       11.28        11.01         5.16         7.36        11.38         3.75 

$`AMP PEAK 21(17Q25.1) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        1.55         4.96        26.79         3.12         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 
       17.72        15.35        15.65        25.68        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
       23.05        13.78         3.25         2.89        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-2554 TCGA-14-2555 
        1.97        17.79        17.85         7.63        17.49         7.96 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        9.14        21.24         6.41         8.61        14.27         3.39 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        40.54        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 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-28-2502 TCGA-28-2509 TCGA-32-1970 
        1.22         1.55         2.83         0.66         4.77        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2632 
        4.67        12.69        14.86        12.23        20.78         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 
       10.85        19.23         0.85        13.35         8.94         0.99 
TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 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        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 
        5.92        20.55         7.63        11.77        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       10.59        35.41        20.71        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       77.65        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 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-02-0058 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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       16.96         3.48        27.02        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-02-0271 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-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 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-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91        10.65        19.66         3.29        13.12 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        3.65        69.90        73.84        27.22        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       23.57         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
        6.84        26.79        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
        5.98         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
      120.56        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       25.71        12.16         9.80        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
        7.27        15.98        18.41        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        14.86        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 
       33.21        15.98        12.23        15.85        14.53         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
        2.24        11.24         5.39         2.04        28.93        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 
        0.79        13.78        50.53        19.10        53.19        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       16.37        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        5.95         4.64        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        7.92         2.33         7.30         5.26        14.93        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 
       14.53        11.77        31.27        23.44        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       12.76         5.42         5.42         1.61        17.72        26.30 

  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                          0.13                           0.10 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                         91.76                         127.59 
  AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE 
                         10.62                          12.59 
[1] "0.1 - 91.8 (10.6)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    27  57
  AMP PEAK 21(17Q25.1) WILD-TYPE 198 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     27   57
  AMP PEAK 21(17Q25.1) WILD-TYPE  198  291
        clus
vv       AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  FEMALE                           27                            198
  MALE                             57                            291
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED    15  65
  AMP PEAK 21(17Q25.1) WILD-TYPE  59 410
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED     15   65
  AMP PEAK 21(17Q25.1) WILD-TYPE   59  410
     clus
vv    AMP PEAK 21(17Q25.1) MUTATED AMP PEAK 21(17Q25.1) WILD-TYPE
  NO                            15                             59
  YES                           65                            410
[1] 2 2
[1] FALSE
D21V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 21(17Q25.1) MUTATED                               6
  AMP PEAK 21(17Q25.1) WILD-TYPE                            24
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 21(17Q25.1) MUTATED                     2
  AMP PEAK 21(17Q25.1) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 21(17Q25.1) MUTATED                                76
  AMP PEAK 21(17Q25.1) WILD-TYPE                             449
D21V6, multiclass
                                 clus
vv                                AMP PEAK 21(17Q25.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           76
                                 clus
vv                                AMP PEAK 21(17Q25.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(17Q25.1) MUTATED       0                        10    70
  AMP PEAK 21(17Q25.1) WILD-TYPE    13                        40   417
D21V7, multiclass
                           clus
vv                          AMP PEAK 21(17Q25.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               70
                           clus
vv                          AMP PEAK 21(17Q25.1) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             40
  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"
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(17Q25.1) MUTATED     2  70
  AMP PEAK 21(17Q25.1) WILD-TYPE  10 405
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(17Q25.1) MUTATED      2   70
  AMP PEAK 21(17Q25.1) WILD-TYPE   10  405
                        clus
vv                       AMP PEAK 21(17Q25.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK 21(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            405
[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    40 202
  AMP PEAK 22(19P13.3) WILD-TYPE  57 271
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           242                            328 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                           202                            271 
$`AMP PEAK 22(19P13.3) MUTATED`
TCGA-06-1806 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-6388 
       15.32         8.98         8.55         6.71         3.75         5.23 
TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        8.32         1.55         3.12        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        6.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0866 TCGA-14-1034 
       14.53         6.21        23.05        13.78        26.33        15.95 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 TCGA-14-1823 TCGA-14-1829 
       32.05        58.78         7.10        30.18        17.85         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 
       17.49         7.96         3.42        17.59        10.29        14.01 
TCGA-16-1062 TCGA-16-1063 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
       21.24        13.97        25.38         3.65         7.17         3.25 
TCGA-19-2620 TCGA-19-2629 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 
        4.87        24.23        17.19         8.02         4.73         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1799 TCGA-27-1833 
       14.07        16.80        17.79        28.54         9.37        24.23 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 TCGA-28-1746 
       24.76        16.77        16.08         7.59        15.78         0.20 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 TCGA-28-2506 
        9.21         7.63         8.48         1.22         0.66         6.74 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
       15.39         0.10        15.85        19.50         4.67        14.86 
TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 
       15.02         8.84        25.18        21.14        12.59        19.23 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R 
       13.35         9.53         4.44        11.84        15.12         4.08 
TCGA-4W-AA9T TCGA-74-6578 TCGA-76-4925 TCGA-76-4934 TCGA-76-6656 TCGA-76-6661 
       25.58        14.33         4.80         2.53         4.83        23.90 
TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0007 
       18.64        36.20         6.28        20.55         7.63        23.18 
TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       10.59        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0028 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0051 TCGA-02-0054 
       90.58         3.62        10.72        18.31        15.09         6.54 
TCGA-02-0057 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.86        19.73        26.43        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0080 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 
       20.84        89.72        27.02        11.67        23.18        92.65 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 TCGA-02-2466 
       13.87        14.20        15.95         4.37        10.55        16.80 
TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       15.45         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0137 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        3.98        33.67        26.70         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 TCGA-06-0174 
        3.19        10.82         9.44        56.91         4.47         3.22 
TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 
        4.04         4.18        20.25        73.84        10.42        38.96 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0211 TCGA-06-0216 TCGA-06-0221 
        0.39         7.66         8.42        11.84        24.16        19.82 
TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       13.64        10.82         0.26        72.36         4.70        35.11 
TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0879 
        5.75        23.57        26.40        46.88         2.70        40.41 
TCGA-06-1086 TCGA-06-1802 TCGA-06-2563 TCGA-06-2565 TCGA-06-2570 TCGA-06-6693 
        6.84        15.32        30.64        16.64        31.50       120.56 
TCGA-08-0246 TCGA-08-0347 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
        4.18        25.71         1.28         8.42        24.56        31.10 
TCGA-08-0357 TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       37.58        12.23        18.02        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 
        4.27        11.08        19.33        18.41         7.56        94.78 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
        0.10        25.97        26.66        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 
       53.85        14.93        14.86        24.79        18.48        27.78 
TCGA-12-0829 TCGA-12-1094 TCGA-12-1099 TCGA-14-0789 TCGA-14-0817 TCGA-14-0867 
       20.58        12.23         4.14        11.24         5.39         2.04 
TCGA-15-1446 TCGA-16-0846 TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-26-5139 
       19.10         3.91        11.77         9.07        12.95         1.58 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5215 
        7.30         5.26        17.88        14.53        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 
       13.64         5.16         5.42        11.38         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`AMP PEAK 22(19P13.3) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6697 TCGA-06-6698 
        8.81         2.73         6.15         4.57        12.85         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96        26.79         1.87         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 
       17.72        15.35        21.73        59.77        44.02        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0812 
        3.22         2.04        15.12        11.97         0.95         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 
        2.89        16.50         1.38         1.12         3.75        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 TCGA-16-1045 
        1.97        17.79         7.63         5.88         3.78        29.03 
TCGA-16-1047 TCGA-16-1060 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        4.57         9.14         6.41         8.61        14.27         3.39 
TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
       12.66         0.13         9.67         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 
        4.08         7.00         7.04         6.64        18.90        12.10 
TCGA-19-5956 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       22.49        14.96        10.03        13.87         9.73         7.13 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2519 TCGA-27-2526 TCGA-27-2527 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 
       18.08         2.86        14.40         2.53         8.35         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2509 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
        2.83         0.13         4.77        21.07         0.49         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 
       12.69        16.93        12.23        20.78        15.95        22.78 
TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 
        3.72        19.86        10.85         0.85         8.94         0.99 
TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        12.46         1.45         3.45        20.91         4.34 
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-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-OX-A56R TCGA-02-0001 TCGA-02-0003 
       20.98         5.03        34.45         5.92        11.77         4.73 
TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       18.35        35.41        20.71        53.10        42.74        24.59 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 
       12.16         2.83        14.14        10.52         6.87        14.73 
TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        3.22        12.59         2.50         8.35         9.57         6.02 
TCGA-02-0069 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       28.70        27.25        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 
       57.76        16.96         3.48        65.00        17.65        99.98 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.47         3.98        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 
       12.92        15.32        20.32        22.72        12.95        25.35 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.30        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0149 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 
       11.74         8.61        11.80         3.42        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 
       19.66         3.29        13.12        91.00        88.14         3.65 
TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 
       69.90        27.22        44.58        15.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 
        5.56         7.40         0.53        15.02         0.72        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       20.42        48.69         9.01         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 
        5.75         9.80         2.10        14.20         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 
        0.92        43.46        46.19         7.17        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
       26.76        23.93         4.04        26.79        11.84        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-6389 TCGA-06-6390 
        5.95         5.98         4.37         0.43         7.79         5.39 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        7.36        22.68        37.84       115.86         1.74         8.42 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 TCGA-08-0358 
       12.16         9.80        29.23        65.33        17.95        22.29 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
        3.39        14.93        15.35        42.15        19.59        58.68 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-12-0616 TCGA-12-0618 
       10.75         4.80         7.27        15.98        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 
       34.92        10.45         7.59        38.17        12.13         3.65 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 
       43.23         7.63         9.73        91.76        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       38.76         8.94       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 
       15.98        15.85         9.11        14.53         3.98         2.24 
TCGA-14-0813 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35        28.93        19.30         0.79        13.78        50.53 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 TCGA-19-0962 
       53.19        13.28        26.07        16.37        21.90         0.66 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
       10.75         5.95         4.64        31.33        14.86         5.49 
TCGA-26-6173 TCGA-26-6174 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 
        7.92         2.33        14.93        11.28        11.77        31.27 
TCGA-28-5219 TCGA-28-5220 TCGA-32-2616 TCGA-76-6283 
       22.68        12.76         7.36         5.42 

  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                          0.10                           0.13 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                        120.56                         127.59 
  AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE 
                        14.265                         11.065 
[1] "0.1 - 120.6 (14.3)" "0.1 - 127.6 (11.1)"
[1] "hr=" "1.2"
D22V2, continuous
D22V3, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED    95 149
  AMP PEAK 22(19P13.3) WILD-TYPE 130 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED     95  149
  AMP PEAK 22(19P13.3) WILD-TYPE  130  199
        clus
vv       AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  FEMALE                           95                            130
  MALE                            149                            199
[1] 2 2
[1] FALSE
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(19P13.3) MUTATED    27 206
  AMP PEAK 22(19P13.3) WILD-TYPE  47 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED     27  206
  AMP PEAK 22(19P13.3) WILD-TYPE   47  269
     clus
vv    AMP PEAK 22(19P13.3) MUTATED AMP PEAK 22(19P13.3) WILD-TYPE
  NO                            27                             47
  YES                          206                            269
[1] 2 2
[1] FALSE
D22V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 22(19P13.3) MUTATED                              13
  AMP PEAK 22(19P13.3) WILD-TYPE                            17
                                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                               221
  AMP PEAK 22(19P13.3) WILD-TYPE                             304
D22V6, multiclass
                                 clus
vv                                AMP PEAK 22(19P13.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             13
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          221
                                 clus
vv                                AMP PEAK 22(19P13.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               17
  TREATED PRIMARY GBM                                          8
  UNTREATED PRIMARY (DE NOVO) GBM                            304
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(19P13.3) MUTATED       8                        21   209
  AMP PEAK 22(19P13.3) WILD-TYPE     5                        29   278
D22V7, multiclass
                           clus
vv                          AMP PEAK 22(19P13.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           21
  WHITE                                              209
                           clus
vv                          AMP PEAK 22(19P13.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             29
  WHITE                                                278
[1] 3 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     6 202
  AMP PEAK 22(19P13.3) WILD-TYPE   6 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.3) MUTATED      6  202
  AMP PEAK 22(19P13.3) WILD-TYPE    6  273
                        clus
vv                       AMP PEAK 22(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          202
                        clus
vv                       AMP PEAK 22(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(19Q12) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 23(19Q12) MUTATED    36 178
  AMP PEAK 23(19Q12) WILD-TYPE  61 295
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                         214                          356 
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                         178                          295 
$`AMP PEAK 23(19Q12) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 
        3.98        15.32         8.98         8.55         6.71         5.23 
TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        8.32         1.55         3.12        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        6.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-14-0790 TCGA-14-0866 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 
       14.53        13.78        26.33        15.95        32.05        58.78 
TCGA-14-1454 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-16-0848 
       30.18        17.85         7.17        17.49         7.96        17.59 
TCGA-16-1055 TCGA-16-1062 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 
       10.29        21.24         3.65         7.17         3.25         4.87 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 TCGA-19-A6J5 TCGA-26-1799 
       17.19         8.02         4.73         1.78        28.54         9.37 
TCGA-27-1833 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2528 
       24.23        24.76        18.08        16.77         7.59        15.78 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 TCGA-28-2506 
        9.21         7.63         8.48         1.22         0.66         6.74 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
       15.39         0.10        15.85        19.50         4.67        14.86 
TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-5222 TCGA-41-2572 
       15.02         8.84        25.18        21.14        19.23        13.35 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6578 TCGA-76-4934 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 
       25.58        14.33         2.53         4.83        23.90        18.64 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 
        6.28        20.55         7.63        23.18        10.59        20.61 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       77.65        20.12        42.74         3.62        10.72        18.31 
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-02-0080 TCGA-02-0089 TCGA-02-0102 TCGA-02-0106 
       10.19        20.84        89.72        16.96        27.02        11.67 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       23.18        92.65        48.95        16.93        17.72        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 TCGA-02-2485 
       13.87        14.20        15.95         4.37        10.55        15.45 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       26.70         2.33        17.79        10.09        19.46        46.59 
TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 
       12.33        10.45         3.19        10.82         9.44        56.91 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.47         3.22         4.18        20.25         3.65        73.84 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0211 
       10.42        38.96         0.39         7.66         8.42        11.84 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       24.16        13.64        10.82         0.26        72.36         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.11         5.75        23.57        26.40        46.88         2.70 
TCGA-06-0879 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-2563 TCGA-06-2565 
       40.41         6.84         4.04        15.32        30.64        16.64 
TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 
        4.18        25.71         9.80         1.28        24.56        31.10 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       12.23        18.02        13.97        12.56         4.27        11.08 
TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0670 
       19.33         7.27        15.98        18.41         7.56        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0778 
       26.66        20.38        28.41        15.06        53.85        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 TCGA-12-1095 
       14.86        24.79        27.78        20.58        12.23        15.85 
TCGA-12-1099 TCGA-14-0789 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-15-1446 
        4.14        11.24         5.39         2.04        28.93        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-19-0955 TCGA-19-1386 TCGA-26-5139 TCGA-28-2513 
       13.28         3.91        11.77         9.07         1.58         7.30 
TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        5.26        17.88        14.53        23.44        13.64         5.16 
TCGA-76-6280 TCGA-76-6660 TCGA-81-5911 TCGA-87-5896 
       11.38         3.75        17.72        26.30 

$`AMP PEAK 23(19Q12) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6697 TCGA-06-6698 
        2.73         3.75         6.15         4.57        12.85         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96        26.79         1.87         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 
       17.72        15.35        21.73        59.77        44.02        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-1395 TCGA-14-1396 
       23.05         3.25         2.89        16.50         1.38         1.12 
TCGA-14-1401 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
        3.75        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 
        5.88         3.78         3.42        29.03         4.57        14.01 
TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        9.14        13.97         6.41         8.61        14.27         3.39 
TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 
       25.38        12.66         0.13         9.67         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       18.90        12.10        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-5132 
       17.79        10.03        13.87         9.73         7.13         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2523 
       40.54        21.30        30.05        14.04        11.51        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 
        2.86        14.40         0.20         2.53         8.35         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2509 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
        2.83         0.13         4.77        21.07         0.49         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 
       12.69        16.93        12.23        20.78        15.95        22.78 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 
        3.72        12.59        19.86        10.85         0.85         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        9.53         0.99        12.46         3.45        20.91         4.34 
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-76-6282 
        9.17        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-76-6664 TCGA-OX-A56R 
        8.35        20.98         5.03        34.45        36.20         5.92 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        18.35        35.41        20.71        82.59 
TCGA-02-0016 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       87.06        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       14.14        10.52         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 
       12.59         2.50         8.35         9.57         6.02        28.70 
TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0258 
        3.48        65.00        17.65        99.98        15.65        16.54 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.47         3.98        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 
       16.80        12.92        15.32        20.32        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        14.30        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 TCGA-06-0154 
       10.29         2.20        11.74        20.09         8.61        13.94 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 
       13.12         4.04        91.00        88.14        69.90        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 
       44.58        15.42         4.67         7.40         5.56         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 
       48.69         9.01         9.57         3.16        12.62         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
        9.80         2.10        14.20         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       43.46        46.19         7.17        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       23.93        26.79        11.84        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 
       12.49         4.93        17.65        12.56         5.95         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        7.36        22.68        37.84       115.86         1.74         8.42 
TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0357 
       12.16        29.23        65.33         8.42        17.95        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       22.29         3.39        14.93        15.35         0.72        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-12-0616 TCGA-12-0618 
       19.59        58.68        10.75         4.80        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 
       12.13         3.65        43.23         7.63         9.73        91.76 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 
       18.48        10.62        23.51        38.76         8.94       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1096 TCGA-12-1097 
        5.82         7.59        33.21        15.98         9.11        14.53 
TCGA-12-1098 TCGA-14-0787 TCGA-14-0813 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        3.98         2.24         1.35        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 TCGA-19-0962 
       50.53        53.19        26.07        16.37        21.90         0.66 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         5.95        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-6173 TCGA-26-6174 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 
        5.49         7.92         2.33        14.93        11.28        11.77 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       31.27        11.01        22.68        12.76         5.42         7.36 
TCGA-76-6283 TCGA-81-5910 
        5.42         1.61 

  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                       92.65                       127.59 
  AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE 
                      13.920                       11.785 
[1] "0.1 - 92.7 (13.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D23V2, continuous
D23V3, binary
                              cls
clus                             0   1
  AMP PEAK 23(19Q12) MUTATED    87 128
  AMP PEAK 23(19Q12) WILD-TYPE 138 220
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(19Q12) MUTATED     87  128
  AMP PEAK 23(19Q12) WILD-TYPE  138  220
        clus
vv       AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE
  FEMALE                         87                          138
  MALE                          128                          220
[1] 2 2
[1] FALSE
D23V4, binary
                              cls
clus                             0   1
  AMP PEAK 23(19Q12) MUTATED    21 182
  AMP PEAK 23(19Q12) WILD-TYPE  53 293
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(19Q12) MUTATED     21  182
  AMP PEAK 23(19Q12) WILD-TYPE   53  293
     clus
vv    AMP PEAK 23(19Q12) MUTATED AMP PEAK 23(19Q12) WILD-TYPE
  NO                          21                           53
  YES                        182                          293
[1] 2 2
[1] FALSE
D23V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 23(19Q12) MUTATED                              14
  AMP PEAK 23(19Q12) WILD-TYPE                            16
                              vv
clus                           TREATED PRIMARY GBM
  AMP PEAK 23(19Q12) MUTATED                     8
  AMP PEAK 23(19Q12) WILD-TYPE                  10
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 23(19Q12) MUTATED                               193
  AMP PEAK 23(19Q12) WILD-TYPE                             332
D23V6, multiclass
                                 clus
vv                                AMP PEAK 23(19Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           14
  TREATED PRIMARY GBM                                      8
  UNTREATED PRIMARY (DE NOVO) GBM                        193
                                 clus
vv                                AMP PEAK 23(19Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             16
  TREATED PRIMARY GBM                                       10
  UNTREATED PRIMARY (DE NOVO) GBM                          332
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(19Q12) MUTATED       6                        20   181
  AMP PEAK 23(19Q12) WILD-TYPE     7                        30   306
D23V7, multiclass
                           clus
vv                          AMP PEAK 23(19Q12) MUTATED
  ASIAN                                              6
  BLACK OR AFRICAN AMERICAN                         20
  WHITE                                            181
                           clus
vv                          AMP PEAK 23(19Q12) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           30
  WHITE                                              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"
D23V8, binary
                              cls
clus                             0   1
  AMP PEAK 23(19Q12) MUTATED     6 180
  AMP PEAK 23(19Q12) WILD-TYPE   6 295
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(19Q12) MUTATED      6  180
  AMP PEAK 23(19Q12) WILD-TYPE    6  295
                        clus
vv                       AMP PEAK 23(19Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        180
                        clus
vv                       AMP PEAK 23(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          295
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(21Q21.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(21Q21.1) MUTATED     9  61
  AMP PEAK 24(21Q21.1) WILD-TYPE  88 412
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                            70                            500 
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                            61                            412 
$`AMP PEAK 24(21Q21.1) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5856 TCGA-06-6698 TCGA-12-1602 TCGA-12-3646 
        3.98        15.32         3.75         4.77         6.77        44.02 
TCGA-14-1034 TCGA-14-1454 TCGA-19-1392 TCGA-19-1787 TCGA-19-5954 TCGA-27-1832 
       15.95        30.18         3.65        12.66        12.10         9.86 
TCGA-27-2526 TCGA-27-2527 TCGA-28-2506 TCGA-28-2509 TCGA-32-2615 TCGA-32-2632 
        2.86        14.40         6.74         4.77        15.95         8.84 
TCGA-32-2634 TCGA-32-4210 TCGA-41-2575 TCGA-41-3915 TCGA-4W-AA9S TCGA-76-6657 
       22.78         3.72         9.53        11.84         1.45         5.03 
TCGA-02-0001 TCGA-02-0006 TCGA-02-0025 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
       11.77        18.35        42.74         2.50         9.57        28.70 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0113 TCGA-02-0333 TCGA-02-0337 
       20.84        27.25        89.72        92.65         4.37        25.12 
TCGA-06-0130 TCGA-06-0140 TCGA-06-0149 TCGA-06-0151 TCGA-06-0159 TCGA-06-0164 
       12.95         0.20         8.61        46.59         9.44        56.91 
TCGA-06-0168 TCGA-06-0176 TCGA-06-0177 TCGA-06-0188 TCGA-06-0189 TCGA-06-0197 
       19.66        91.00         4.18        44.58        15.42         5.56 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0644 TCGA-06-0743 TCGA-06-1086 TCGA-06-1087 
       24.16        13.64        12.62        26.40         6.84         4.04 
TCGA-06-2565 TCGA-06-2567 TCGA-08-0246 TCGA-08-0386 TCGA-08-0510 TCGA-12-0619 
       16.64         4.37         4.18        18.02         4.27        34.92 
TCGA-12-0822 TCGA-12-1095 TCGA-14-0867 TCGA-14-0871 TCGA-16-0846 TCGA-28-5207 
       23.51        15.85         2.04        28.93         3.91        11.28 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-76-6283 
       11.01        13.64         5.16         5.42 

$`AMP PEAK 24(21Q21.1) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32        12.85         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       15.35        21.73        15.65        25.68        14.73        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
        6.21        23.05        13.78         3.25         2.89        16.50 
TCGA-14-0866 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       26.33         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.67 
TCGA-14-1459 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-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       17.59        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       21.24        13.97         6.41         8.61        14.27         3.39 
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        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 
       24.76        18.08        16.77        16.08         7.59        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-32-1970 
        1.22         1.55         2.83         0.13         0.66        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-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       15.02        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       19.23         0.85        13.35         8.94         0.99         4.44 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.08        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        4.83        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 
        6.28        20.55         7.63         4.73        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         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-02-0074 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       10.19        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
       15.91        25.71        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 
       25.35        14.30        26.70        24.23        11.90        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
       11.80         3.42        10.65         5.85         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.47         3.22         4.04        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       69.90        73.84        27.22        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        7.40         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        35.11         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 
       16.57        20.78        26.76        23.93        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2569 
       17.65        12.56        30.64         5.95         5.98         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 
       31.50         7.79         5.39       120.56         7.36        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        18.48        10.62        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       15.98        12.23         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-1037 TCGA-14-1043 
        2.24        11.24         1.35         5.39        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
       13.78        50.53        19.10        53.19        13.28        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       16.37        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        5.95        12.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 
       17.88        14.53        11.77        31.27        23.44        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42         7.36        11.38         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                           0.2                            0.1 
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                         92.65                         127.59 
  AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE 
                         11.97                          12.28 
[1] "0.2 - 92.7 (12.0)"  "0.1 - 127.6 (12.3)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                                cls
clus                               0   1
  AMP PEAK 24(21Q21.1) MUTATED    28  42
  AMP PEAK 24(21Q21.1) WILD-TYPE 197 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(21Q21.1) MUTATED     28   42
  AMP PEAK 24(21Q21.1) WILD-TYPE  197  306
        clus
vv       AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE
  FEMALE                           28                            197
  MALE                             42                            306
[1] 2 2
[1] FALSE
D24V4, binary
                                cls
clus                               0   1
  AMP PEAK 24(21Q21.1) MUTATED    10  56
  AMP PEAK 24(21Q21.1) WILD-TYPE  64 419
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(21Q21.1) MUTATED     10   56
  AMP PEAK 24(21Q21.1) WILD-TYPE   64  419
     clus
vv    AMP PEAK 24(21Q21.1) MUTATED AMP PEAK 24(21Q21.1) WILD-TYPE
  NO                            10                             64
  YES                           56                            419
[1] 2 2
[1] FALSE
D24V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  AMP PEAK 24(21Q21.1) MUTATED                               7
  AMP PEAK 24(21Q21.1) WILD-TYPE                            23
                                vv
clus                             TREATED PRIMARY GBM
  AMP PEAK 24(21Q21.1) MUTATED                     1
  AMP PEAK 24(21Q21.1) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  AMP PEAK 24(21Q21.1) MUTATED                                62
  AMP PEAK 24(21Q21.1) WILD-TYPE                             463
D24V6, multiclass
                                 clus
vv                                AMP PEAK 24(21Q21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              7
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           62
                                 clus
vv                                AMP PEAK 24(21Q21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(21Q21.1) MUTATED       4                         4    61
  AMP PEAK 24(21Q21.1) WILD-TYPE     9                        46   426
D24V7, multiclass
                           clus
vv                          AMP PEAK 24(21Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               61
                           clus
vv                          AMP PEAK 24(21Q21.1) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             46
  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"
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(21Q21.1) MUTATED     0  62
  AMP PEAK 24(21Q21.1) WILD-TYPE  12 413
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(21Q21.1) MUTATED      0   62
  AMP PEAK 24(21Q21.1) WILD-TYPE   12  413
                        clus
vv                       AMP PEAK 24(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK 24(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            413
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED    15  81
  DEL PEAK  1(1P36.32) WILD-TYPE  82 392
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            96                            474 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            81                            392 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-06-5411 TCGA-06-5859 TCGA-12-3649 TCGA-12-3651 TCGA-12-3653 TCGA-14-0786 
        8.35         4.57        15.22        12.69        14.53        23.05 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 TCGA-14-1453 TCGA-14-1458 TCGA-14-1821 
        2.89        16.50         1.12         1.15         6.67        17.79 
TCGA-16-1056 TCGA-19-0963 TCGA-19-2619 TCGA-19-2629 TCGA-19-5947 TCGA-19-5950 
       14.01        14.27         9.67        24.23         6.64        17.19 
TCGA-19-5958 TCGA-27-1833 TCGA-27-2521 TCGA-27-2524 TCGA-28-1747 TCGA-28-1750 
       14.07        24.23        16.77         7.59         2.53         8.35 
TCGA-28-1752 TCGA-28-1756 TCGA-28-2502 TCGA-32-1977 TCGA-32-2638 TCGA-32-4208 
        8.48         2.83         0.66         0.10        25.18        21.14 
TCGA-41-2575 TCGA-41-4097 TCGA-74-6575 TCGA-76-4931 TCGA-76-6285 TCGA-76-6286 
        9.53         0.20        20.91         9.17         8.35        20.98 
TCGA-76-6657 TCGA-OX-A56R TCGA-02-0015 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
        5.03         5.92        20.61        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0028 TCGA-02-0051 TCGA-02-0064 TCGA-02-0069 TCGA-02-0114 
       24.59        90.58        15.09        19.73        28.70        99.98 
TCGA-02-0115 TCGA-02-0281 TCGA-02-0446 TCGA-02-2483 TCGA-06-0126 TCGA-06-0162 
       15.65         3.98         9.27        15.32         6.94         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0171 TCGA-06-0175 TCGA-06-0184 TCGA-06-0195 
       56.91         5.85        13.12         4.04        69.90         7.40 
TCGA-06-0208 TCGA-06-0402 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 
        8.42         0.26        26.40         7.86         2.70         7.17 
TCGA-06-0879 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-2562 
       40.41        23.93         4.04        11.84        15.32        12.56 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
      120.56        22.68       115.86        15.35        13.97         0.72 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0517 TCGA-08-0520 TCGA-08-0531 TCGA-12-0688 
        4.27        11.08        58.68        10.75         7.56        26.66 
TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-14-0787 TCGA-15-1449 
       18.48        15.98        12.23        15.85         2.24        13.28 
TCGA-19-0962 TCGA-19-1387 TCGA-28-5211 TCGA-28-6450 TCGA-76-6660 TCGA-87-5896 
        0.66         5.95        11.77         5.42         3.75        26.30 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        6.15         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
       14.60        17.72        15.35        21.73        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 
       14.73         6.77        59.77        44.02        26.93        10.95 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 
        0.95         6.21        13.78         3.25        26.33        15.95 
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-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92        40.96        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.78         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 
        9.14        21.24        13.97         6.41         8.61         3.39 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-4065 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        7.04         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       22.49        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       13.87         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
       18.97        19.33         5.06        16.60         9.86        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1749 
       16.08         2.86        14.40        15.78         0.20         9.21 
TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2506 TCGA-28-2509 
        7.63         1.22         1.55         0.13         6.74         4.77 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39        21.07         0.49        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-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 
       15.02        15.95         8.84        22.78         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84        15.12        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        1.45        25.58         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 
        7.50         4.80         4.54         3.09         3.65         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6656 
       36.85        16.70         3.29         2.70        17.06         4.83 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC 
       23.90        34.45        18.64        36.20         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0027 
       35.41        20.71        82.59        87.06        77.65        12.16 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73         3.22        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0068 TCGA-02-0070 
       19.86         8.35         9.57         6.02        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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0116 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-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 
        2.70         6.15        20.38        47.61         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
       11.80        10.65        19.66         3.29         4.47         3.22 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
       91.00         4.18        88.14        20.25         3.65        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        5.56         0.39         7.66         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 
       20.42        48.69        10.82         9.01        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 
        9.80         2.10        23.57        14.20        46.88         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        0.92        43.46        46.19        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        6.84        26.79        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        17.65        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 
        4.37         0.43        31.50         7.79         5.39         7.36 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0518 
       14.93        18.02        12.56        42.15        19.59        19.33 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 
        4.80         7.27        15.98        18.41        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0789 TCGA-14-0813 
        9.11        14.53         3.98         4.14        11.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        5.39         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10        53.19         3.91        26.07        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 
       11.77        21.90        10.75         9.07        12.95         4.64 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 
       12.76         7.36        11.38         5.42         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 
                        120.56                         127.59 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        12.625                         12.230 
[1] "0.1 - 120.6 (12.6)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    28  69
  DEL PEAK  1(1P36.32) WILD-TYPE 197 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     28   69
  DEL PEAK  1(1P36.32) WILD-TYPE  197  279
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           28                            197
  MALE                             69                            279
[1] 2 2
[1] FALSE
D25V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    14  79
  DEL PEAK  1(1P36.32) WILD-TYPE  60 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     14   79
  DEL PEAK  1(1P36.32) WILD-TYPE   60  396
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            14                             60
  YES                           79                            396
[1] 2 2
[1] FALSE
D25V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  1(1P36.32) MUTATED                               2
  DEL PEAK  1(1P36.32) WILD-TYPE                            28
                                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
D25V6, multiclass
                                 clus
vv                                DEL PEAK  1(1P36.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        4
  UNTREATED PRIMARY (DE NOVO) GBM                           91
                                 clus
vv                                DEL PEAK  1(1P36.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               28
  TREATED PRIMARY GBM                                         14
  UNTREATED PRIMARY (DE NOVO) GBM                            434
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       5                         6    84
  DEL PEAK  1(1P36.32) WILD-TYPE     8                        44   403
D25V7, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               84
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             44
  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"
D25V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     1  82
  DEL PEAK  1(1P36.32) WILD-TYPE  11 393
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      1   82
  DEL PEAK  1(1P36.32) WILD-TYPE   11  393
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            393
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  2(1P36.23) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.23) MUTATED    19 112
  DEL PEAK  2(1P36.23) WILD-TYPE  78 361
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           131                            439 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           112                            361 
$`DEL PEAK  2(1P36.23) MUTATED`
TCGA-06-5411 TCGA-06-5414 TCGA-06-5415 TCGA-06-5859 TCGA-12-1599 TCGA-12-3649 
        8.35         8.98         8.55         4.57        25.68        15.22 
TCGA-12-3652 TCGA-14-0736 TCGA-14-0786 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
       34.92        15.12        23.05         2.89        16.50         1.12 
TCGA-14-1458 TCGA-14-1827 TCGA-14-1829 TCGA-16-1045 TCGA-16-1056 TCGA-19-0963 
        6.67         5.88         7.17        29.03        14.01        14.27 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2629 TCGA-19-5947 TCGA-19-5950 TCGA-19-5959 
        9.67         4.87        24.23         6.64        17.19        16.80 
TCGA-26-1439 TCGA-27-1833 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 
       13.87        24.23        16.77         7.59         8.35         8.48 
TCGA-28-2502 TCGA-32-1977 TCGA-32-1978 TCGA-32-2634 TCGA-32-2638 TCGA-32-5222 
        0.66         0.10        15.85        22.78        25.18        19.23 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-4W-AA9S TCGA-74-6575 
       13.35         9.53         4.44         0.20         1.45        20.91 
TCGA-76-4928 TCGA-76-4931 TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 
        3.09         9.17        16.70         8.35        20.98         5.03 
TCGA-76-6661 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0015 TCGA-02-0023 
       23.90         5.92         6.28        20.55        20.61        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0051 TCGA-02-0064 TCGA-02-0068 
       53.10        42.74        90.58        15.09        19.73        26.43 
TCGA-02-0069 TCGA-02-0106 TCGA-02-0115 TCGA-02-0281 TCGA-02-0285 TCGA-02-0290 
       28.70        11.67        15.65         3.98        13.87        15.95 
TCGA-02-0446 TCGA-02-2483 TCGA-06-0124 TCGA-06-0137 TCGA-06-0158 TCGA-06-0162 
        9.27        15.32        20.38        26.70        10.82         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 
       56.91         5.85        19.66         3.29        13.12         4.04 
TCGA-06-0184 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0208 TCGA-06-0219 
       69.90        10.42        38.96         7.40         8.42         0.72 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 
       26.40         7.86         2.70         7.17        40.41        20.78 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2562 
       23.93         4.04        11.84        15.32        13.61        12.56 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0375 TCGA-08-0386 
      120.56        22.68       115.86         1.74        12.23        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
       15.35        13.97         0.72         4.27        11.08        19.33 
TCGA-08-0520 TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 TCGA-12-0769 
       10.75         7.56        94.78        25.97        26.66        15.06 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0820 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        9.73        14.93        18.48        15.98        12.23        15.85 
TCGA-12-1097 TCGA-14-0787 TCGA-19-0962 TCGA-19-1386 TCGA-19-1387 TCGA-26-6173 
       14.53         2.24         0.66         9.07         5.95         7.92 
TCGA-28-5211 TCGA-28-6450 TCGA-76-6660 TCGA-81-5910 TCGA-87-5896 
       11.77         5.42         3.75         1.61        26.30 

$`DEL PEAK  2(1P36.23) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         4.54 
TCGA-06-5413 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.81         6.71         2.73         3.75         6.15         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       15.35        21.73        15.65        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 
       44.02        26.93        10.95        12.69        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0790 
        3.22         2.04        11.97         0.95         6.21        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
        3.25        26.33        15.95         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-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
       40.96        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 
        7.63        17.49         7.96         3.78         3.42        17.59 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        4.57        10.29         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        8.61         3.39        25.38         3.65         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        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        22.49        14.07        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
       18.97        19.33         5.06        16.60         9.86        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 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-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1979 
        6.74         4.77        15.39        21.07         0.49        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-32-2632 TCGA-32-4208 TCGA-32-4210 
       20.78        15.02        15.95         8.84        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 
       12.59        19.86        10.85         0.85         8.94         0.99 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 
       11.84        15.12        12.46         4.08        25.58         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        3.65         2.53        36.85         3.29         2.70        17.06 
TCGA-76-6656 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0001 
        4.83        34.45        18.64        36.20         7.63        11.77 
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-02-0016 TCGA-02-0021 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 
       82.59        87.06        77.65        24.59        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
        8.35         9.57         6.02        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        92.65        99.98        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0289 TCGA-02-0317 
       16.93        17.72        10.75        14.47        14.20        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       47.11        11.34        16.21         3.35        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 
       15.45        20.32         2.70         6.15        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 
       46.59        12.33        13.94        10.45         3.19         9.44 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 
       11.80        10.65         4.47         3.22        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       88.14        20.25         3.65        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0210 
       15.42         4.67         5.56         0.39         7.66         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 
       11.84         0.53        15.02        24.16        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0744 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0881 
       46.88         2.70         0.92        43.46        46.19        16.57 
TCGA-06-0939 TCGA-06-1086 TCGA-06-1800 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.76         6.84        26.79        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        17.65        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 
        4.37         0.43        31.50         7.79         5.39         7.36 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       37.84         4.18         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0509 
       31.10        37.58        22.29         3.39        14.93        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       42.15        19.59        58.68         4.80         7.27        15.98 
TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       18.41        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
        0.10        38.17        12.13         3.65        20.38        28.41 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       53.85        43.23         7.63        14.86        91.76        24.79 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 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-12-1096 TCGA-12-1098 
      127.59         5.82         7.59        33.21         9.11         3.98 
TCGA-12-1099 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        4.14        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       19.30         0.79        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 
       13.28         3.91        26.07        16.37        11.77        21.90 
TCGA-19-1385 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
       10.75        12.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        1.58         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       17.88        14.53        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         7.36        11.38         5.42 
TCGA-81-5911 
       17.72 

  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE 
                         13.61                          12.13 
[1] "0.1 - 120.6 (13.6)" "0.1 - 127.6 (12.1)"
[1] "hr=" "1"  
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    39  93
  DEL PEAK  2(1P36.23) WILD-TYPE 186 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     39   93
  DEL PEAK  2(1P36.23) WILD-TYPE  186  255
        clus
vv       DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  FEMALE                           39                            186
  MALE                             93                            255
[1] 2 2
[1] FALSE
D26V4, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED    18 110
  DEL PEAK  2(1P36.23) WILD-TYPE  56 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED     18  110
  DEL PEAK  2(1P36.23) WILD-TYPE   56  365
     clus
vv    DEL PEAK  2(1P36.23) MUTATED DEL PEAK  2(1P36.23) WILD-TYPE
  NO                            18                             56
  YES                          110                            365
[1] 2 2
[1] FALSE
D26V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  2(1P36.23) MUTATED                               5
  DEL PEAK  2(1P36.23) WILD-TYPE                            25
                                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                               124
  DEL PEAK  2(1P36.23) WILD-TYPE                             401
D26V6, multiclass
                                 clus
vv                                DEL PEAK  2(1P36.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                          124
                                 clus
vv                                DEL PEAK  2(1P36.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            401
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.23) MUTATED       5                        11   112
  DEL PEAK  2(1P36.23) WILD-TYPE     8                        39   375
D26V7, multiclass
                           clus
vv                          DEL PEAK  2(1P36.23) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              112
                           clus
vv                          DEL PEAK  2(1P36.23) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                375
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.23) MUTATED     1 111
  DEL PEAK  2(1P36.23) WILD-TYPE  11 364
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.23) MUTATED      1  111
  DEL PEAK  2(1P36.23) WILD-TYPE   11  364
                        clus
vv                       DEL PEAK  2(1P36.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       DEL PEAK  2(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            364
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  3(1P32.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P32.3) MUTATED     9  52
  DEL PEAK  3(1P32.3) WILD-TYPE  88 421
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           61                           509 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                           52                           421 
$`DEL PEAK  3(1P32.3) MUTATED`
TCGA-06-5411 TCGA-12-1092 TCGA-12-3649 TCGA-14-1452 TCGA-14-1455 TCGA-14-1458 
        8.35        21.73        15.22         7.10         0.92         6.67 
TCGA-14-1795 TCGA-16-1045 TCGA-19-1390 TCGA-19-2619 TCGA-19-2629 TCGA-19-5958 
        1.97        29.03        25.38         9.67        24.23        14.07 
TCGA-26-1440 TCGA-26-1799 TCGA-27-2521 TCGA-27-2527 TCGA-41-4097 TCGA-74-6575 
        9.73         9.37        16.77        14.40         0.20        20.91 
TCGA-76-4931 TCGA-76-6282 TCGA-OX-A56R TCGA-02-0028 TCGA-02-0059 TCGA-02-0074 
        9.17        17.06         5.92        90.58         9.57        10.19 
TCGA-02-0115 TCGA-02-0269 TCGA-02-0281 TCGA-02-0333 TCGA-02-0446 TCGA-02-2483 
       15.65        10.75         3.98         4.37         9.27        15.32 
TCGA-02-2486 TCGA-06-0188 TCGA-06-0194 TCGA-06-0241 TCGA-06-0410 TCGA-06-0646 
       20.32        44.58         4.67        48.69         4.70         5.75 
TCGA-06-0649 TCGA-06-0743 TCGA-06-0749 TCGA-06-0750 TCGA-06-1802 TCGA-06-2561 
        2.10        26.40         2.70         0.92        15.32        17.65 
TCGA-06-2567 TCGA-08-0244 TCGA-08-0344 TCGA-08-0390 TCGA-08-0392 TCGA-08-0510 
        4.37        22.68       115.86        13.97         0.72         4.27 
TCGA-08-0529 TCGA-12-0654 TCGA-12-0773 TCGA-12-0776 TCGA-14-0813 TCGA-19-1387 
       18.41         7.59        43.23         9.73         1.35         5.95 
TCGA-26-5134 TCGA-28-2514 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 
        5.49         5.26        31.27        11.01        13.64        12.76 
TCGA-76-6660 
        3.75 

$`DEL PEAK  3(1P32.3) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 
        2.56        14.60        17.72        15.35        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3650 
       14.73         6.77        59.77        44.02        26.93        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
       15.12        11.97         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 
        1.12         3.75        32.05        58.78        23.11         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 
       30.18        40.96        12.43         0.99        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        3.42        17.59         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       21.24        13.97         6.41         8.61        14.27         3.39 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        3.65         7.17        12.66         3.25         0.13         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        22.49        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1443 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       10.03        13.87         7.13         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         7.59         2.86        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        2.83         0.13         0.66         6.74         4.77        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-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 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-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       34.45        18.64        36.20         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        24.59        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       65.00        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 
       48.95        16.54        16.93        17.72        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91        25.71        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        47.11        11.34        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       16.80        12.92        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 
        0.72        19.82        13.64        13.32        20.42        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26        72.36         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
       12.62         5.75         9.80        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        7.86         2.70        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.79        11.84        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       14.93        18.02        15.35        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98         7.56        14.73        12.99        34.92        10.45 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 
        9.11        14.53         3.98         4.14         2.24        11.24 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        5.39         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
       50.53        19.10        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       16.37        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5139 TCGA-26-6173 
       12.95         4.64        31.33        14.86         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        2.33         7.30        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 
       11.77        23.44         5.16        22.68         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         1.61        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 
                       115.86                        127.59 
  DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE 
                         9.73                         12.43 
[1] "0.2 - 115.9 (9.7)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED    18  43
  DEL PEAK  3(1P32.3) WILD-TYPE 207 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     18   43
  DEL PEAK  3(1P32.3) WILD-TYPE  207  305
        clus
vv       DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  FEMALE                          18                           207
  MALE                            43                           305
[1] 2 2
[1] FALSE
D27V4, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED    10  49
  DEL PEAK  3(1P32.3) WILD-TYPE  64 426
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED     10   49
  DEL PEAK  3(1P32.3) WILD-TYPE   64  426
     clus
vv    DEL PEAK  3(1P32.3) MUTATED DEL PEAK  3(1P32.3) WILD-TYPE
  NO                           10                            64
  YES                          49                           426
[1] 2 2
[1] FALSE
D27V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  3(1P32.3) MUTATED                               2
  DEL PEAK  3(1P32.3) WILD-TYPE                            28
                               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
D27V6, multiclass
                                 clus
vv                                DEL PEAK  3(1P32.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          57
                                 clus
vv                                DEL PEAK  3(1P32.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              28
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P32.3) MUTATED       3                         4    52
  DEL PEAK  3(1P32.3) WILD-TYPE    10                        46   435
D27V7, multiclass
                           clus
vv                          DEL PEAK  3(1P32.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              52
                           clus
vv                          DEL PEAK  3(1P32.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P32.3) MUTATED     1  49
  DEL PEAK  3(1P32.3) WILD-TYPE  11 426
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P32.3) MUTATED      1   49
  DEL PEAK  3(1P32.3) WILD-TYPE   11  426
                        clus
vv                       DEL PEAK  3(1P32.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          49
                        clus
vv                       DEL PEAK  3(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           426
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  4(1P22.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(1P22.1) MUTATED     7  41
  DEL PEAK  4(1P22.1) WILD-TYPE  90 432
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           48                           522 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                           41                           432 
$`DEL PEAK  4(1P22.1) MUTATED`
TCGA-06-5411 TCGA-06-A5U1 TCGA-12-0615 TCGA-12-3652 TCGA-14-1452 TCGA-16-1047 
        8.35         1.87        15.35        34.92         7.10         4.57 
TCGA-16-1055 TCGA-16-1062 TCGA-19-0964 TCGA-19-1390 TCGA-19-2619 TCGA-19-2629 
       10.29        21.24         3.39        25.38         9.67        24.23 
TCGA-19-5953 TCGA-19-5959 TCGA-26-1440 TCGA-27-1837 TCGA-28-2502 TCGA-32-4719 
        4.73        16.80         9.73        14.04         0.66        10.85 
TCGA-41-5651 TCGA-74-6575 TCGA-76-6285 TCGA-02-0015 TCGA-02-0024 TCGA-02-0027 
       15.12        20.91         8.35        20.61        53.10        12.16 
TCGA-02-0028 TCGA-02-0038 TCGA-02-0043 TCGA-02-0083 TCGA-02-0451 TCGA-06-0122 
       90.58        10.72        18.31        22.72        16.21         6.15 
TCGA-06-0133 TCGA-06-0169 TCGA-06-0175 TCGA-06-1802 TCGA-06-2565 TCGA-08-0244 
       14.30         3.29         4.04        15.32        16.64        22.68 
TCGA-08-0344 TCGA-08-0347 TCGA-08-0348 TCGA-08-0392 TCGA-08-0510 TCGA-12-0691 
      115.86        25.71        12.16         0.72         4.27        12.13 
TCGA-12-0819 TCGA-12-0827 TCGA-19-1387 TCGA-28-5208 TCGA-28-5213 TCGA-76-6660 
       24.79        38.76         5.95        17.88        31.27         3.75 

$`DEL PEAK  4(1P22.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96        26.79         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.60        17.72        21.73        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 
        2.89        16.50        26.33        15.95         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         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1056 
        7.96         3.78         3.42        17.59        29.03        14.01 
TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-1392 
        9.14        13.97         6.41         8.61        14.27         3.65 
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-19-4065 TCGA-19-5947 
        7.53         0.16         4.08         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
       17.19         8.02        18.90        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.07        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        11.51        24.76        18.08        16.77        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-28-2506 TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 
        2.83         0.13         6.74         4.77        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        9.53         0.99         4.44        11.84         0.20        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 
        4.08         1.45        25.58         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       20.71        82.59        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0039 TCGA-02-0046 
       24.59         2.83        14.14         3.62        10.52         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       89.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 
       14.50        10.55        47.11        11.34         9.27         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 
       56.91        10.65         5.85        19.66        13.12         4.47 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.22        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
        4.04        26.79        11.84        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
        5.98         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
      120.56         7.36        37.84         4.18         1.74         8.42 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 
       14.93        18.02        15.35        13.97        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        26.66         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0820 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-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        2.24        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       19.30         0.79        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 
       13.28         3.91        26.07        16.37        11.77        21.90 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 
        0.66        10.75         9.07        12.95         4.64        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 
        5.26        14.93        11.28        14.53        11.77        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.36        11.38         5.42         1.61        17.72        26.30 

  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                         0.66                          0.10 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                       115.86                        127.59 
  DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE 
                        14.17                         12.23 
[1] "0.7 - 115.9 (14.2)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED    18  30
  DEL PEAK  4(1P22.1) WILD-TYPE 207 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED     18   30
  DEL PEAK  4(1P22.1) WILD-TYPE  207  318
        clus
vv       DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  FEMALE                          18                           207
  MALE                            30                           318
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(1P22.1) MUTATED     6  39
  DEL PEAK  4(1P22.1) WILD-TYPE  68 436
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED      6   39
  DEL PEAK  4(1P22.1) WILD-TYPE   68  436
     clus
vv    DEL PEAK  4(1P22.1) MUTATED DEL PEAK  4(1P22.1) WILD-TYPE
  NO                            6                            68
  YES                          39                           436
[1] 2 2
[1] FALSE
D28V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  4(1P22.1) MUTATED                               2
  DEL PEAK  4(1P22.1) WILD-TYPE                            28
                               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
D28V6, multiclass
                                 clus
vv                                DEL PEAK  4(1P22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       4
  UNTREATED PRIMARY (DE NOVO) GBM                          42
                                 clus
vv                                DEL PEAK  4(1P22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              28
  TREATED PRIMARY GBM                                        14
  UNTREATED PRIMARY (DE NOVO) GBM                           483
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1P22.1) MUTATED       1                         4    40
  DEL PEAK  4(1P22.1) WILD-TYPE    12                        46   447
D28V7, multiclass
                           clus
vv                          DEL PEAK  4(1P22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              40
                           clus
vv                          DEL PEAK  4(1P22.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               447
[1] 3 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  4(1P22.1) MUTATED     1  41
  DEL PEAK  4(1P22.1) WILD-TYPE  11 434
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1P22.1) MUTATED      1   41
  DEL PEAK  4(1P22.1) WILD-TYPE   11  434
                        clus
vv                       DEL PEAK  4(1P22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  4(1P22.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           434
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  5(1Q42.11) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(1Q42.11) MUTATED     9  41
  DEL PEAK  5(1Q42.11) WILD-TYPE  88 432
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            50                            520 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                            41                            432 
$`DEL PEAK  5(1Q42.11) MUTATED`
TCGA-06-1806 TCGA-06-5411 TCGA-12-1599 TCGA-14-0740 TCGA-14-0790 TCGA-14-0812 
       15.32         8.35        25.68        11.97        13.78         3.25 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1450 TCGA-19-1390 TCGA-19-2619 TCGA-19-2629 
       15.95         1.38        58.78        25.38         9.67        24.23 
TCGA-19-A6J5 TCGA-27-2524 TCGA-28-2502 TCGA-32-1977 TCGA-32-1986 TCGA-32-1987 
       28.54         7.59         0.66         0.10        12.69        14.86 
TCGA-74-6575 TCGA-74-6577 TCGA-76-6193 TCGA-RR-A6KA TCGA-02-0084 TCGA-02-0099 
       20.91         4.34         2.70         6.28        12.62         3.48 
TCGA-02-0106 TCGA-02-0281 TCGA-02-0333 TCGA-02-0446 TCGA-02-2466 TCGA-06-0126 
       11.67         3.98         4.37         9.27        16.80         6.94 
TCGA-06-0190 TCGA-06-0238 TCGA-06-0402 TCGA-06-1084 TCGA-06-1802 TCGA-06-2558 
       10.42        13.32         0.26        23.93        15.32        12.49 
TCGA-06-6390 TCGA-08-0246 TCGA-08-0392 TCGA-08-0510 TCGA-12-0620 TCGA-12-0656 
        5.39         4.18         0.72         4.27        10.45        94.78 
TCGA-12-0776 TCGA-14-0817 TCGA-19-0957 TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 
        9.73         5.39        21.90         0.66         5.95        12.95 
TCGA-26-5133 TCGA-76-6660 
       14.86         3.75 

$`DEL PEAK  5(1Q42.11) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 
        1.48         3.98        11.74         3.55         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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1600 
       14.60        17.72        15.35        21.73        15.65        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0862 TCGA-14-0865 
       15.12         0.95         6.21        23.05         2.89        16.50 
TCGA-14-0866 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 
       26.33         1.12         3.75        32.05        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 
        7.17        17.49         7.96         3.78         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 
       13.97         6.41         8.61        14.27         3.39         3.65 
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-19-4065 TCGA-19-5947 
        7.53         0.16         4.08         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-26-1438 
       22.49        14.07        16.80        14.96        17.79        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       13.87         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
       18.97        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39        21.07         0.49        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
        4.67        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6578 
       12.46         4.08         1.45        25.58         3.45        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 
        9.17         2.53        36.85        16.70         3.29        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 
       18.64        36.20         5.92        20.55         7.63        11.77 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 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-02-0102 
       22.72        51.32         8.81        57.76        16.96        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       65.00        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-02-0285 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-02-0338 
       10.62         7.33        15.91        25.71        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-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        6.15        20.38        47.61         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       44.58        15.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 
       15.02        24.16         0.72        19.82        13.64        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 
       40.41        16.57        20.78        26.76         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 
       26.79        11.84        13.61        33.90         1.08         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 
        4.37         0.43        31.50         7.79       120.56         7.36 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       12.23        14.93        18.02        15.35        13.97        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
        4.80         7.27        15.98        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       12.99        34.92         7.59         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-0871 
        4.14         2.24        11.24         1.35         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
       19.30         0.79        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-1385 
       13.28         3.91        26.07        16.37        11.77        10.75 
TCGA-19-1386 TCGA-19-1389 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        9.07         4.64        31.33         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 
        5.16        22.68        12.76         5.42         7.36        11.38 
TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         1.61        17.72        26.30 

  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                         94.78                         127.59 
  DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE 
                        10.075                         12.445 
[1] "0.1 - 94.8 (10.1)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED    19  31
  DEL PEAK  5(1Q42.11) WILD-TYPE 206 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED     19   31
  DEL PEAK  5(1Q42.11) WILD-TYPE  206  317
        clus
vv       DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  FEMALE                           19                            206
  MALE                             31                            317
[1] 2 2
[1] FALSE
D29V4, binary
                                cls
clus                               0   1
  DEL PEAK  5(1Q42.11) MUTATED     8  38
  DEL PEAK  5(1Q42.11) WILD-TYPE  66 437
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED      8   38
  DEL PEAK  5(1Q42.11) WILD-TYPE   66  437
     clus
vv    DEL PEAK  5(1Q42.11) MUTATED DEL PEAK  5(1Q42.11) WILD-TYPE
  NO                             8                             66
  YES                           38                            437
[1] 2 2
[1] FALSE
D29V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  5(1Q42.11) MUTATED                               4
  DEL PEAK  5(1Q42.11) WILD-TYPE                            26
                                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
D29V6, multiclass
                                 clus
vv                                DEL PEAK  5(1Q42.11) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           45
                                 clus
vv                                DEL PEAK  5(1Q42.11) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               26
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            480
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(1Q42.11) MUTATED       0                         6    40
  DEL PEAK  5(1Q42.11) WILD-TYPE    13                        44   447
D29V7, multiclass
                           clus
vv                          DEL PEAK  5(1Q42.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               40
                           clus
vv                          DEL PEAK  5(1Q42.11) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                             44
  WHITE                                                447
[1] 3 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  5(1Q42.11) MUTATED     2  38
  DEL PEAK  5(1Q42.11) WILD-TYPE  10 437
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(1Q42.11) MUTATED      2   38
  DEL PEAK  5(1Q42.11) WILD-TYPE   10  437
                        clus
vv                       DEL PEAK  5(1Q42.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       DEL PEAK  5(1Q42.11) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            437
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  6(1Q44) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  6(1Q44) MUTATED     8  27
  DEL PEAK  6(1Q44) WILD-TYPE  89 446
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         35                         535 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                         27                         446 
$`DEL PEAK  6(1Q44) MUTATED`
TCGA-06-1806 TCGA-06-5411 TCGA-12-3648 TCGA-14-0740 TCGA-14-0812 TCGA-14-1034 
       15.32         8.35        26.93        11.97         3.25        15.95 
TCGA-14-1395 TCGA-14-1456 TCGA-19-1390 TCGA-19-2619 TCGA-19-A6J5 TCGA-32-1986 
        1.38        40.96        25.38         9.67        28.54        12.69 
TCGA-74-6575 TCGA-74-6577 TCGA-76-4925 TCGA-76-6193 TCGA-02-0026 TCGA-02-0084 
       20.91         4.34         4.80         2.70        24.59        12.62 
TCGA-02-0333 TCGA-02-2466 TCGA-02-2485 TCGA-06-0145 TCGA-06-0149 TCGA-06-2558 
        4.37        16.80        15.45         2.33         8.61        12.49 
TCGA-08-0386 TCGA-08-0392 TCGA-08-0510 TCGA-12-0776 TCGA-12-0780 TCGA-19-0962 
       18.02         0.72         4.27         9.73        14.86         0.66 
TCGA-19-1387 TCGA-19-1388 TCGA-26-5133 TCGA-28-5215 TCGA-76-6660 
        5.95        12.95        14.86        11.01         3.75 

$`DEL PEAK  6(1Q44) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 
        1.48         3.98        11.74         3.55         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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
       14.60        17.72        15.35        21.73        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 
       14.73         6.77        59.77        44.02        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 
       15.12         0.95         6.21        23.05        13.78         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       16.50        26.33         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       23.11         7.10         1.15        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 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-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       17.59        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       21.24        13.97         6.41         8.61        14.27         3.39 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
        3.65         7.17        12.66         3.25         0.13         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       17.79        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        16.77        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-32-1970 TCGA-32-1973 
        0.13         0.66         6.74         4.77        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6578 
       12.46         4.08         1.45        25.58         3.45        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         7.50         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 
        2.53        36.85        16.70         3.29        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 
       36.20         5.92         6.28        20.55         7.63        11.77 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 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-02-0085 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-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0337 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-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       11.74        20.09        17.79        10.09        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 
       11.84        15.32        13.61        33.90         1.08         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        7.36        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       14.53         3.98         4.14         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        5.39         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
       50.53        19.10        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 
       16.37        11.77        21.90        10.75         9.07         4.64 
TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       31.33         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 
        5.42         7.36        11.38         5.42         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                       0.66                        0.10 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                      40.96                      127.59 
  DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE 
                      11.97                       12.23 
[1] "0.7 - 41.0 (12.0)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D30V2, continuous
D30V3, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED    13  22
  DEL PEAK  6(1Q44) WILD-TYPE 212 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED     13   22
  DEL PEAK  6(1Q44) WILD-TYPE  212  326
        clus
vv       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  FEMALE                        13                         212
  MALE                          22                         326
[1] 2 2
[1] FALSE
D30V4, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED     6  27
  DEL PEAK  6(1Q44) WILD-TYPE  68 448
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED      6   27
  DEL PEAK  6(1Q44) WILD-TYPE   68  448
     clus
vv    DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  NO                          6                          68
  YES                        27                         448
[1] 2 2
[1] FALSE
D30V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK  6(1Q44) MUTATED                               3                   1
  DEL PEAK  6(1Q44) WILD-TYPE                            27                  17
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK  6(1Q44) MUTATED                                31
  DEL PEAK  6(1Q44) WILD-TYPE                             494
D30V6, multiclass
                                 clus
vv                                DEL PEAK  6(1Q44) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           3
  TREATED PRIMARY GBM                                     1
  UNTREATED PRIMARY (DE NOVO) GBM                        31
                                 clus
vv                                DEL PEAK  6(1Q44) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            27
  TREATED PRIMARY GBM                                      17
  UNTREATED PRIMARY (DE NOVO) GBM                         494
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(1Q44) MUTATED       0                         3    28
  DEL PEAK  6(1Q44) WILD-TYPE    13                        47   459
D30V7, multiclass
                           clus
vv                          DEL PEAK  6(1Q44) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            28
                           clus
vv                          DEL PEAK  6(1Q44) WILD-TYPE
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                          47
  WHITE                                             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"
D30V8, binary
                             cls
clus                            0   1
  DEL PEAK  6(1Q44) MUTATED     1  25
  DEL PEAK  6(1Q44) WILD-TYPE  11 450
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(1Q44) MUTATED      1   25
  DEL PEAK  6(1Q44) WILD-TYPE   11  450
                        clus
vv                       DEL PEAK  6(1Q44) MUTATED DEL PEAK  6(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        25                         450
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  7(2Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q22.1) MUTATED     5  42
  DEL PEAK  7(2Q22.1) WILD-TYPE  92 431
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           47                           523 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                           42                           431 
$`DEL PEAK  7(2Q22.1) MUTATED`
TCGA-06-5416 TCGA-06-5856 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-12-0615 TCGA-12-1598 
        6.71         3.75         1.87         3.12        15.35        15.65 
TCGA-12-1600 TCGA-12-3646 TCGA-14-0736 TCGA-14-0783 TCGA-14-0812 TCGA-19-1390 
       14.73        44.02        15.12         6.21         3.25        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-26-A7UX TCGA-28-2509 TCGA-32-1978 
        3.65         4.08        22.49        19.33         4.77        15.85 
TCGA-32-2615 TCGA-4W-AA9R TCGA-76-4934 TCGA-76-6191 TCGA-02-0024 TCGA-02-0059 
       15.95         4.08         2.53        16.70        53.10         9.57 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0289 TCGA-02-0338 TCGA-02-2466 TCGA-06-0152 
       10.19        20.84        14.20        10.59        16.80        12.33 
TCGA-06-0182 TCGA-06-0188 TCGA-06-0414 TCGA-06-0649 TCGA-06-0749 TCGA-06-1087 
        3.65        44.58        35.11         2.10         2.70         4.04 
TCGA-06-6390 TCGA-06-6694 TCGA-12-0821 TCGA-12-0826 TCGA-12-1099 TCGA-14-0867 
        5.39         7.36        10.62        27.78         4.14         2.04 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 TCGA-28-5215 
       50.53        53.19        16.37        12.95        11.01 

$`DEL PEAK  7(2Q22.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
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-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.77         4.96        26.79         2.56        14.60        17.72 
TCGA-12-1092 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       21.73        25.68         6.77        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 
        2.04        11.97         0.95        23.05        13.78         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       16.50        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
        7.96         3.78         3.42        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        8.61        14.27         3.39         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-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 
        7.13         9.37         9.40         8.88        18.97         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        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-32-1970 TCGA-32-1973 
        2.83         0.13         0.66         6.74        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-32-2632 
       14.86        16.93        12.23        20.78        15.02         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 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-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
        9.17        36.85         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        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 
       36.20         5.92         6.28        20.55         7.63        11.77 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 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-02-0060 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-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 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-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       13.87        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0339 
        7.33        15.91        25.71         4.37        25.12        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       88.14        20.25        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 
        4.37         0.43        31.50         7.79       120.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
        9.11        14.53         3.98         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 
        5.39        28.93        19.30         0.79        13.78        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       13.28         3.91        26.07        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         9.07         5.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        13.64         5.16        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        7.36        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                         1.87                          0.10 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                        53.19                        127.59 
  DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE 
                        11.01                         12.23 
[1] "1.9 - 53.2 (11.0)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    21  26
  DEL PEAK  7(2Q22.1) WILD-TYPE 204 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     21   26
  DEL PEAK  7(2Q22.1) WILD-TYPE  204  322
        clus
vv       DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  FEMALE                          21                           204
  MALE                            26                           322
[1] 2 2
[1] FALSE
D31V4, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.1) MUTATED    10  35
  DEL PEAK  7(2Q22.1) WILD-TYPE  64 440
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED     10   35
  DEL PEAK  7(2Q22.1) WILD-TYPE   64  440
     clus
vv    DEL PEAK  7(2Q22.1) MUTATED DEL PEAK  7(2Q22.1) WILD-TYPE
  NO                           10                            64
  YES                          35                           440
[1] 2 2
[1] FALSE
D31V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  7(2Q22.1) MUTATED                               5
  DEL PEAK  7(2Q22.1) WILD-TYPE                            25
                               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
D31V6, multiclass
                                 clus
vv                                DEL PEAK  7(2Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             5
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          40
                                 clus
vv                                DEL PEAK  7(2Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              25
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           485
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(2Q22.1) MUTATED       0                         7    40
  DEL PEAK  7(2Q22.1) WILD-TYPE    13                        43   447
D31V7, multiclass
                           clus
vv                          DEL PEAK  7(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              40
                           clus
vv                          DEL PEAK  7(2Q22.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            43
  WHITE                                               447
[1] 3 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  7(2Q22.1) MUTATED     0  39
  DEL PEAK  7(2Q22.1) WILD-TYPE  12 436
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.1) MUTATED      0   39
  DEL PEAK  7(2Q22.1) WILD-TYPE   12  436
                        clus
vv                       DEL PEAK  7(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       DEL PEAK  7(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           436
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  8(2Q37.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(2Q37.1) MUTATED     6  49
  DEL PEAK  8(2Q37.1) WILD-TYPE  91 424
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           55                           515 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                           49                           424 
$`DEL PEAK  8(2Q37.1) MUTATED`
TCGA-06-5416 TCGA-06-5856 TCGA-06-A6S0 TCGA-12-1600 TCGA-12-3646 TCGA-12-5301 
        6.71         3.75         3.12        14.73        44.02         2.04 
TCGA-14-0783 TCGA-14-0812 TCGA-14-1821 TCGA-14-4157 TCGA-16-1047 TCGA-19-1390 
        6.21         3.25        17.79         3.42         4.57        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-27-2521 TCGA-28-1750 TCGA-28-2509 
        3.65         4.08        22.49        16.77         8.35         4.77 
TCGA-32-1978 TCGA-32-2495 TCGA-32-2615 TCGA-41-3393 TCGA-41-6646 TCGA-4W-AA9R 
       15.85        15.02        15.95         4.44        12.46         4.08 
TCGA-76-4934 TCGA-76-6657 TCGA-02-0025 TCGA-02-0059 TCGA-02-0074 TCGA-02-0075 
        2.53         5.03        42.74         9.57        10.19        20.84 
TCGA-02-0080 TCGA-02-0084 TCGA-02-0104 TCGA-02-0338 TCGA-06-0152 TCGA-06-0182 
       89.72        12.62        65.00        10.59        12.33         3.65 
TCGA-06-0188 TCGA-06-0221 TCGA-06-0414 TCGA-06-0649 TCGA-06-2562 TCGA-06-6694 
       44.58        19.82        35.11         2.10        12.56         7.36 
TCGA-08-0351 TCGA-08-0355 TCGA-08-0512 TCGA-12-0703 TCGA-12-0826 TCGA-12-1099 
       65.33        24.56        42.15        20.38        27.78         4.14 
TCGA-14-0867 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 TCGA-28-5215 
        2.04        50.53        53.19        16.37        12.95        11.01 
TCGA-76-6280 
       11.38 

$`DEL PEAK  8(2Q37.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
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-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96        26.79         1.87         2.56        14.60 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       17.72        15.35        21.73        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22        15.12        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       23.05        13.78         2.89        16.50        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 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-16-0848 TCGA-16-1045 
        7.17        17.49         7.96         3.78        17.59        29.03 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        8.61        14.27         3.39         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-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        18.08        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 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-32-1970 TCGA-32-1973 TCGA-32-1976 
        0.13         0.66         6.74        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-32-2494 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       16.93        12.23        20.78         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3915 
        0.85        13.35         8.94         9.53         0.99        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        0.20        15.12         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 
        2.70        17.06         8.35        20.98         4.83        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         8.35         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 
       25.05         5.49        27.25        22.72        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
       57.76        16.96         3.48        27.02        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        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-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0339 
        7.33        15.91        25.71         4.37        25.12        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        4.18        88.14        20.25        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       12.49         4.93        17.65        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
        5.98         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
      120.56        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 
        8.42        25.71        12.16         9.80        29.23         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
        8.42        17.95        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 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-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       14.53         3.98         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
       28.93        19.30         0.79        13.78        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
        3.91        26.07        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07         5.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                         2.04                          0.10 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                        89.72                        127.59 
  DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE 
                        12.46                         12.23 
[1] "2.0 - 89.7 (12.5)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    26  29
  DEL PEAK  8(2Q37.1) WILD-TYPE 199 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     26   29
  DEL PEAK  8(2Q37.1) WILD-TYPE  199  319
        clus
vv       DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  FEMALE                          26                           199
  MALE                            29                           319
[1] 2 2
[1] FALSE
D32V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED    10  42
  DEL PEAK  8(2Q37.1) WILD-TYPE  64 433
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED     10   42
  DEL PEAK  8(2Q37.1) WILD-TYPE   64  433
     clus
vv    DEL PEAK  8(2Q37.1) MUTATED DEL PEAK  8(2Q37.1) WILD-TYPE
  NO                           10                            64
  YES                          42                           433
[1] 2 2
[1] FALSE
D32V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  8(2Q37.1) MUTATED                               3
  DEL PEAK  8(2Q37.1) WILD-TYPE                            27
                               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
D32V6, multiclass
                                 clus
vv                                DEL PEAK  8(2Q37.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          51
                                 clus
vv                                DEL PEAK  8(2Q37.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           474
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(2Q37.1) MUTATED       0                         4    50
  DEL PEAK  8(2Q37.1) WILD-TYPE    13                        46   437
D32V7, multiclass
                           clus
vv                          DEL PEAK  8(2Q37.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              50
                           clus
vv                          DEL PEAK  8(2Q37.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               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"
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.1) MUTATED     1  46
  DEL PEAK  8(2Q37.1) WILD-TYPE  11 429
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.1) MUTATED      1   46
  DEL PEAK  8(2Q37.1) WILD-TYPE   11  429
                        clus
vv                       DEL PEAK  8(2Q37.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  8(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           429
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  9(3P21.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P21.1) MUTATED    12  42
  DEL PEAK  9(3P21.1) WILD-TYPE  85 431
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           54                           516 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                           42                           431 
$`DEL PEAK  9(3P21.1) MUTATED`
TCGA-06-1806 TCGA-06-5416 TCGA-06-5859 TCGA-06-A7TL TCGA-12-3653 TCGA-14-0862 
       15.32         6.71         4.57        17.72        14.53         2.89 
TCGA-14-1458 TCGA-14-1823 TCGA-14-3477 TCGA-16-1047 TCGA-19-0964 TCGA-19-2625 
        6.67        17.85         3.78         4.57         3.39         4.08 
TCGA-26-1439 TCGA-26-1440 TCGA-28-1752 TCGA-28-1756 TCGA-32-1991 TCGA-32-2615 
       13.87         9.73         8.48         2.83        16.93        15.95 
TCGA-76-4929 TCGA-02-0014 TCGA-02-0015 TCGA-02-0055 TCGA-02-0083 TCGA-02-0084 
        3.65        82.59        20.61         2.50        22.72        12.62 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0114 TCGA-02-0266 TCGA-02-0330 
       65.00        11.67        92.65        99.98        17.72        15.91 
TCGA-02-0432 TCGA-02-2486 TCGA-06-0128 TCGA-06-0152 TCGA-06-0214 TCGA-06-0216 
       47.11        20.32        22.72        12.33        15.02        24.16 
TCGA-06-0221 TCGA-06-0409 TCGA-06-0745 TCGA-06-0878 TCGA-06-1087 TCGA-06-6390 
       19.82        72.36         7.86         7.17         4.04         5.39 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 TCGA-08-0517 
       37.84         4.18        18.02        13.97        19.59        58.68 
TCGA-12-0776 TCGA-12-0826 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-19-1388 
        9.73        27.78        53.19        13.28        26.07        12.95 

$`DEL PEAK  9(3P21.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96        26.79         1.87         3.12         2.56        14.60 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.35        21.73        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0865 
        0.95         6.21        23.05        13.78         3.25        16.50 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       26.33        15.95         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-16-0848 
        5.88         7.17        17.49         7.96         3.42        17.59 
TCGA-16-1045 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        6.41         8.61        14.27        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
       22.49        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       10.03         7.13         9.37         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        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-32-1970 
        1.55         0.13         0.66         6.74         4.77        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        14.86        12.23        20.78        15.02 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA 
       23.90        34.45        18.64        36.20         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
       20.55         7.63        11.77         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       10.59        35.41        20.71        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         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-02-0071 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-02-0085 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-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       17.65        23.18        15.65        48.95        16.54        16.93 
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-02-0332 
       12.23         9.90         7.73        10.62         7.33        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0440 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-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.32        15.45         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        7.40        11.84         0.53         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 
       20.42        48.69        10.82         9.01         0.26         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0879 
        2.70         2.70         0.92        43.46        46.19        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
       16.57        20.78        26.76        23.93         6.84        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 
        5.98         4.37         0.43        31.50         7.79       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        7.36        22.68       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       12.23        14.93        15.35         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       42.15        11.08        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        2.24        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 
       19.30         0.79        13.78        50.53        19.10         3.91 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       16.37        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        5.95         4.64        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                          2.5                           0.1 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                        99.98                        127.59 
  DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE 
                       14.775                        12.035 
[1] "2.5 - 100.0 (14.8)" "0.1 - 127.6 (12.0)"
[1] "hr=" "1.4"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED    22  32
  DEL PEAK  9(3P21.1) WILD-TYPE 203 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED     22   32
  DEL PEAK  9(3P21.1) WILD-TYPE  203  316
        clus
vv       DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  FEMALE                          22                           203
  MALE                            32                           316
[1] 2 2
[1] FALSE
D33V4, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P21.1) MUTATED     4  48
  DEL PEAK  9(3P21.1) WILD-TYPE  70 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED      4   48
  DEL PEAK  9(3P21.1) WILD-TYPE   70  427
     clus
vv    DEL PEAK  9(3P21.1) MUTATED DEL PEAK  9(3P21.1) WILD-TYPE
  NO                            4                            70
  YES                          48                           427
[1] 2 2
[1] FALSE
D33V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK  9(3P21.1) MUTATED                               2
  DEL PEAK  9(3P21.1) WILD-TYPE                            28
                               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
D33V6, multiclass
                                 clus
vv                                DEL PEAK  9(3P21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             2
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          49
                                 clus
vv                                DEL PEAK  9(3P21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              28
  TREATED PRIMARY GBM                                        15
  UNTREATED PRIMARY (DE NOVO) GBM                           476
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P21.1) MUTATED       0                         6    46
  DEL PEAK  9(3P21.1) WILD-TYPE    13                        44   441
D33V7, multiclass
                           clus
vv                          DEL PEAK  9(3P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              46
                           clus
vv                          DEL PEAK  9(3P21.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               441
[1] 3 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  9(3P21.1) MUTATED     2  47
  DEL PEAK  9(3P21.1) WILD-TYPE  10 428
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P21.1) MUTATED      2   47
  DEL PEAK  9(3P21.1) WILD-TYPE   10  428
                        clus
vv                       DEL PEAK  9(3P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK  9(3P21.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           428
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 10(3Q13.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(3Q13.31) MUTATED     8  48
  DEL PEAK 10(3Q13.31) WILD-TYPE  89 425
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            56                            514 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                            48                            425 
$`DEL PEAK 10(3Q13.31) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5859 TCGA-06-A5U1 TCGA-12-1600 TCGA-12-3651 
        3.98        15.32         4.57         1.87        14.73        12.69 
TCGA-12-3653 TCGA-14-0812 TCGA-14-1458 TCGA-14-1823 TCGA-19-2621 TCGA-26-1439 
       14.53         3.25         6.67        17.85         1.08        13.87 
TCGA-28-1752 TCGA-28-1757 TCGA-32-1973 TCGA-32-2615 TCGA-76-4929 TCGA-02-0001 
        8.48         0.13        21.07        15.95         3.65        11.77 
TCGA-02-0021 TCGA-02-0054 TCGA-02-0055 TCGA-02-0060 TCGA-02-0069 TCGA-02-0084 
       77.65         6.54         2.50         6.02        28.70        12.62 
TCGA-02-0113 TCGA-02-0330 TCGA-02-0332 TCGA-02-2466 TCGA-06-0128 TCGA-06-0152 
       92.65        15.91        25.71        16.80        22.72        12.33 
TCGA-06-0182 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0409 
        3.65        15.02        24.16         0.72        19.82        72.36 
TCGA-06-2569 TCGA-06-6389 TCGA-06-6390 TCGA-08-0245 TCGA-08-0246 TCGA-08-0386 
        0.43         7.79         5.39        37.84         4.18        18.02 
TCGA-08-0390 TCGA-08-0516 TCGA-12-0691 TCGA-12-0773 TCGA-12-0776 TCGA-12-0826 
       13.97        19.59        12.13        43.23         9.73        27.78 
TCGA-12-1089 TCGA-12-1093 TCGA-14-0871 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 
        5.82        15.98        28.93        53.19        13.28        12.95 
TCGA-28-5220 TCGA-76-6280 
       12.76        11.38 

$`DEL PEAK 10(3Q13.31) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.96        26.79         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 
       15.35        21.73        15.65        25.68         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 
       44.02        26.93        15.22        10.95        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       23.05        13.78         2.89        16.50        26.33        15.95 
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-16-0848 TCGA-16-1045 
       17.49         7.96         3.78         3.42        17.59        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 
        6.41         8.61        14.27         3.39        25.38         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03         9.73         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        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-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        4.77        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.09         9.17         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 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        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 
        5.92         6.28        20.55         7.63         4.73        18.35 
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-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
       19.86         8.35         9.57        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-02-0104 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-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.73        10.62         7.33         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-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       88.14        20.25        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0344 
        4.37        31.50       120.56         7.36        22.68       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
        0.72        12.56         4.27        42.15        11.08        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       94.78         0.10        38.17        25.97        26.66         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 
       20.38        28.41        15.06        53.85         7.63        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1091 
       38.76         8.94        20.58       127.59         7.59        33.21 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 
        2.24        11.24         1.35         5.39         2.04        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0849 
        0.79        13.78        50.53        19.10         3.91        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       16.37        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        5.95         4.64        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 TCGA-76-6283 
       13.64         5.16        22.68         5.42         7.36         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE 
                        13.115                         12.130 
[1] "0.1 - 92.7 (13.1)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1"  
D34V2, continuous
D34V3, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED    24  32
  DEL PEAK 10(3Q13.31) WILD-TYPE 201 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED     24   32
  DEL PEAK 10(3Q13.31) WILD-TYPE  201  316
        clus
vv       DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  FEMALE                           24                            201
  MALE                             32                            316
[1] 2 2
[1] FALSE
D34V4, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED     6  45
  DEL PEAK 10(3Q13.31) WILD-TYPE  68 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED      6   45
  DEL PEAK 10(3Q13.31) WILD-TYPE   68  430
     clus
vv    DEL PEAK 10(3Q13.31) MUTATED DEL PEAK 10(3Q13.31) WILD-TYPE
  NO                             6                             68
  YES                           45                            430
[1] 2 2
[1] FALSE
D34V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 10(3Q13.31) MUTATED                               3
  DEL PEAK 10(3Q13.31) WILD-TYPE                            27
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 10(3Q13.31) MUTATED                     2
  DEL PEAK 10(3Q13.31) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 10(3Q13.31) MUTATED                                51
  DEL PEAK 10(3Q13.31) WILD-TYPE                             474
D34V6, multiclass
                                 clus
vv                                DEL PEAK 10(3Q13.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           51
                                 clus
vv                                DEL PEAK 10(3Q13.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            474
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q13.31) MUTATED       2                         6    48
  DEL PEAK 10(3Q13.31) WILD-TYPE    11                        44   439
D34V7, multiclass
                           clus
vv                          DEL PEAK 10(3Q13.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               48
                           clus
vv                          DEL PEAK 10(3Q13.31) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             44
  WHITE                                                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"
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q13.31) MUTATED     2  47
  DEL PEAK 10(3Q13.31) WILD-TYPE  10 428
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q13.31) MUTATED      2   47
  DEL PEAK 10(3Q13.31) WILD-TYPE   10  428
                        clus
vv                       DEL PEAK 10(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 10(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            428
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 11(3Q29) MUTATION ANALYSIS
D35V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(3Q29) MUTATED     8  57
  DEL PEAK 11(3Q29) WILD-TYPE  89 416
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                         65                         505 
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                         57                         416 
$`DEL PEAK 11(3Q29) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5415 TCGA-06-5859 TCGA-12-3652 TCGA-12-3653 
        3.98        15.32         8.55         4.57        34.92        14.53 
TCGA-12-5295 TCGA-14-0812 TCGA-14-1821 TCGA-14-1823 TCGA-14-4157 TCGA-19-1390 
       14.93         3.25        17.79        17.85         3.42        25.38 
TCGA-19-2631 TCGA-19-5956 TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-27-2523 
        7.00        22.49        13.87         5.06        16.77        16.08 
TCGA-27-2528 TCGA-32-2615 TCGA-41-2575 TCGA-74-6581 TCGA-74-6584 TCGA-76-4929 
       15.78        15.95         9.53         8.22         7.50         3.65 
TCGA-02-0010 TCGA-02-0021 TCGA-02-0026 TCGA-02-0055 TCGA-02-0084 TCGA-02-0113 
       35.41        77.65        24.59         2.50        12.62        92.65 
TCGA-02-0330 TCGA-02-0332 TCGA-06-0128 TCGA-06-0145 TCGA-06-0152 TCGA-06-0158 
       15.91        25.71        22.72         2.33        12.33        10.82 
TCGA-06-0159 TCGA-06-0175 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        9.44         4.04        15.02        24.16         0.72        19.82 
TCGA-06-0409 TCGA-06-0745 TCGA-06-2563 TCGA-06-2565 TCGA-06-6390 TCGA-06-6693 
       72.36         7.86        30.64        16.64         5.39       120.56 
TCGA-08-0246 TCGA-08-0351 TCGA-08-0386 TCGA-08-0392 TCGA-08-0516 TCGA-08-0531 
        4.18        65.33        18.02         0.72        19.59         7.56 
TCGA-12-0662 TCGA-12-0776 TCGA-12-0826 TCGA-12-0829 TCGA-12-1091 TCGA-12-1098 
       38.17         9.73        27.78        20.58        33.21         3.98 
TCGA-14-0871 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-28-5220 
       28.93        53.19        13.28        12.95        12.76 

$`DEL PEAK 11(3Q29) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.98         6.71         2.73         3.75         6.15         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       15.35        21.73        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-5299 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-14-0790 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       23.05        13.78         2.89        16.50        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         0.99         1.97         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
       17.49         7.96         3.78        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        8.61        14.27         3.39         3.65         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-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        24.23         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       16.80        14.96        17.79        28.54        10.03         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 
       14.04        11.51        24.76        18.08         7.59         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       14.40         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        6.74         4.77        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-32-2632 TCGA-32-2634 
       16.93        12.23        20.78        15.02         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       19.23         0.85        13.35         8.94         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
       11.84         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 
       25.58         3.45        20.91         4.34        14.33         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        36.85        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-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 
        6.28        20.55         7.63        11.77         4.73        18.35 
TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       23.18        10.59        20.71        82.59        20.61        87.06 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        42.74        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         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-02-0071 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-02-0114 
       27.02        65.00        11.67        17.65        23.18        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-02-0333 TCGA-02-0337 
        9.90         7.73        10.62         7.33         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
       11.74        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 TCGA-06-0162 
       46.59        13.94        10.45         3.19        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 
        7.66         8.42         7.40        11.84         0.53        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       46.88         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95         5.98         4.37         0.43        31.50         7.79 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        7.36        22.68        37.84       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 
       25.71        12.16         9.80        29.23         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       12.23        14.93        15.35        13.97        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        11.08        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
        7.27        15.98        18.41        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       10.45         7.59        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 
       18.48        10.62        23.51        38.76         8.94       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82         7.59        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       14.53         4.14         2.24        11.24         1.35         5.39 
TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        2.04        19.30         0.79        13.78        50.53        19.10 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        3.91        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         9.07         5.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 
       23.44        11.01        13.64         5.16        22.68         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        7.36        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                       0.72                        0.10 
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                     120.56                      127.59 
  DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE 
                      15.02                       11.90 
[1] "0.7 - 120.6 (15.0)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                             cls
clus                            0   1
  DEL PEAK 11(3Q29) MUTATED    25  40
  DEL PEAK 11(3Q29) WILD-TYPE 200 308
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(3Q29) MUTATED     25   40
  DEL PEAK 11(3Q29) WILD-TYPE  200  308
        clus
vv       DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE
  FEMALE                        25                         200
  MALE                          40                         308
[1] 2 2
[1] FALSE
D35V4, binary
                             cls
clus                            0   1
  DEL PEAK 11(3Q29) MUTATED     8  54
  DEL PEAK 11(3Q29) WILD-TYPE  66 421
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(3Q29) MUTATED      8   54
  DEL PEAK 11(3Q29) WILD-TYPE   66  421
     clus
vv    DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE
  NO                          8                          66
  YES                        54                         421
[1] 2 2
[1] FALSE
D35V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 11(3Q29) MUTATED                               3                   2
  DEL PEAK 11(3Q29) WILD-TYPE                            27                  16
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 11(3Q29) MUTATED                                60
  DEL PEAK 11(3Q29) WILD-TYPE                             465
D35V6, multiclass
                                 clus
vv                                DEL PEAK 11(3Q29) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           3
  TREATED PRIMARY GBM                                     2
  UNTREATED PRIMARY (DE NOVO) GBM                        60
                                 clus
vv                                DEL PEAK 11(3Q29) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            27
  TREATED PRIMARY GBM                                      16
  UNTREATED PRIMARY (DE NOVO) GBM                         465
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(3Q29) MUTATED       1                         5    57
  DEL PEAK 11(3Q29) WILD-TYPE    12                        45   430
D35V7, multiclass
                           clus
vv                          DEL PEAK 11(3Q29) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            57
                           clus
vv                          DEL PEAK 11(3Q29) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          45
  WHITE                                             430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                             cls
clus                            0   1
  DEL PEAK 11(3Q29) MUTATED     1  54
  DEL PEAK 11(3Q29) WILD-TYPE  11 421
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(3Q29) MUTATED      1   54
  DEL PEAK 11(3Q29) WILD-TYPE   11  421
                        clus
vv                       DEL PEAK 11(3Q29) MUTATED DEL PEAK 11(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                        54                         421
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 12(4P16.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4P16.3) MUTATED    10  68
  DEL PEAK 12(4P16.3) WILD-TYPE  87 405
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                           78                           492 
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                           68                           405 
$`DEL PEAK 12(4P16.3) MUTATED`
TCGA-06-5416 TCGA-06-A6S0 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        6.71         3.12        15.65        59.77        44.02        26.93 
TCGA-12-3653 TCGA-14-1454 TCGA-14-1458 TCGA-14-1821 TCGA-14-1823 TCGA-16-0848 
       14.53        30.18         6.67        17.79        17.85        17.59 
TCGA-19-2629 TCGA-19-4065 TCGA-27-1830 TCGA-27-1837 TCGA-27-1838 TCGA-28-2509 
       24.23         7.04         5.06        14.04        11.51         4.77 
TCGA-32-1978 TCGA-32-2632 TCGA-32-4210 TCGA-4W-AA9R TCGA-76-4925 TCGA-76-4928 
       15.85         8.84         3.72         4.08         4.80         3.09 
TCGA-76-4934 TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0025 
        2.53        35.41        82.59        20.61        87.06        42.74 
TCGA-02-0051 TCGA-02-0054 TCGA-02-0069 TCGA-02-0079 TCGA-02-0266 TCGA-02-2483 
       15.09         6.54        28.70        27.25        17.72        15.32 
TCGA-02-2485 TCGA-06-0138 TCGA-06-0152 TCGA-06-0166 TCGA-06-0173 TCGA-06-0174 
       15.45        24.23        12.33         5.85         4.47         3.22 
TCGA-06-0175 TCGA-06-0177 TCGA-06-0192 TCGA-06-0216 TCGA-06-0414 TCGA-06-0645 
        4.04         4.18        38.96        24.16        35.11         5.75 
TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 TCGA-06-2557 TCGA-06-6693 TCGA-08-0245 
       46.88         4.04        26.79         1.08       120.56        37.84 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0355 
        1.74         8.42        12.16        29.23        65.33        24.56 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0516 TCGA-08-0525 TCGA-12-0619 
        3.39        14.93        18.02        19.59        15.98        34.92 
TCGA-12-0620 TCGA-12-0662 TCGA-12-0827 TCGA-14-0867 TCGA-15-1449 TCGA-16-0849 
       10.45        38.17        38.76         2.04        13.28        26.07 
TCGA-19-1388 TCGA-28-2514 TCGA-28-5207 TCGA-28-5211 TCGA-28-5214 TCGA-76-6283 
       12.95         5.26        11.28        11.77        23.44         5.42 

$`DEL PEAK 12(4P16.3) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 
        1.55         4.77         4.96        26.79         1.87         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 
       14.60        17.72        15.35        21.73        25.68        14.73 
TCGA-12-1602 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
        6.77        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       23.05        13.78         3.25         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
       23.11         7.10         1.15         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        0.99         1.97         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.78         3.42        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       14.27         3.39        25.38         3.65         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-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16         4.08         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        9.73         7.13         9.37         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
       19.33        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       30.05        24.76        18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1976 
        0.13         0.66         6.74        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-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       16.93        12.23        20.78        15.02        15.95        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18        21.14        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        4.54         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA 
       23.90        34.45        18.64        36.20         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
       20.55         7.63        11.77         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0011 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 
       10.59        20.71        77.65        20.12        53.10        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       10.52        18.31         6.87        14.73         3.22        12.59 
TCGA-02-0055 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-02-0070 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-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 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-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       16.80        12.92        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        14.30        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        46.59        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       19.66         3.29        13.12        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        8.42         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
       12.62         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       23.93         6.84        11.84        15.32        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
       16.64         5.98         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6694 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 
        5.39         7.36        22.68         4.18       115.86        25.71 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 
        9.80         1.28         8.42        17.95        31.10        37.58 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       22.29        12.23        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        4.27        42.15        11.08        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        4.80         7.27        18.41         7.56        14.73        12.99 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        27.78         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       15.85         9.11        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       11.24         1.35         5.39        28.93        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0850 
       13.78        50.53        19.10        53.19         3.91        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        4.64        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 
        2.33         7.30        14.93        17.88        14.53        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.36        11.38         3.75         1.61        17.72        26.30 

  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                         1.08                          0.10 
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                       120.56                        127.59 
  DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE 
                       15.205                        11.935 
[1] "1.1 - 120.6 (15.2)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.2"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P16.3) MUTATED    26  52
  DEL PEAK 12(4P16.3) WILD-TYPE 199 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P16.3) MUTATED     26   52
  DEL PEAK 12(4P16.3) WILD-TYPE  199  296
        clus
vv       DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE
  FEMALE                          26                           199
  MALE                            52                           296
[1] 2 2
[1] FALSE
D36V4, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P16.3) MUTATED     9  65
  DEL PEAK 12(4P16.3) WILD-TYPE  65 410
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P16.3) MUTATED      9   65
  DEL PEAK 12(4P16.3) WILD-TYPE   65  410
     clus
vv    DEL PEAK 12(4P16.3) MUTATED DEL PEAK 12(4P16.3) WILD-TYPE
  NO                            9                            65
  YES                          65                           410
[1] 2 2
[1] FALSE
D36V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 12(4P16.3) MUTATED                               3
  DEL PEAK 12(4P16.3) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 12(4P16.3) MUTATED                     1
  DEL PEAK 12(4P16.3) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 12(4P16.3) MUTATED                                74
  DEL PEAK 12(4P16.3) WILD-TYPE                             451
D36V6, multiclass
                                 clus
vv                                DEL PEAK 12(4P16.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          74
                                 clus
vv                                DEL PEAK 12(4P16.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           451
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4P16.3) MUTATED       3                         6    64
  DEL PEAK 12(4P16.3) WILD-TYPE    10                        44   423
D36V7, multiclass
                           clus
vv                          DEL PEAK 12(4P16.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              64
                           clus
vv                          DEL PEAK 12(4P16.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               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"
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P16.3) MUTATED     2  62
  DEL PEAK 12(4P16.3) WILD-TYPE  10 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P16.3) MUTATED      2   62
  DEL PEAK 12(4P16.3) WILD-TYPE   10  413
                        clus
vv                       DEL PEAK 12(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 12(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           413
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q34.3) MUTATED    20  73
  DEL PEAK 13(4Q34.3) WILD-TYPE  77 400
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           93                           477 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           73                           400 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-A5U0 TCGA-12-1598 TCGA-12-3644 
        6.71         3.75         4.57        26.79        15.65        59.77 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-0862 TCGA-14-1453 
       44.02        14.53        15.12        11.97         2.89         1.15 
TCGA-14-1454 TCGA-14-1458 TCGA-14-1821 TCGA-14-1823 TCGA-16-0848 TCGA-16-1045 
       30.18         6.67        17.79        17.85        17.59        29.03 
TCGA-19-1390 TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-A7UX TCGA-27-1838 
       25.38        24.23         7.04        28.54        19.33        11.51 
TCGA-27-2518 TCGA-28-1749 TCGA-28-1756 TCGA-32-1973 TCGA-32-2491 TCGA-32-2632 
       24.76         9.21         2.83        21.07        12.23         8.84 
TCGA-32-2634 TCGA-32-4208 TCGA-41-5651 TCGA-4W-AA9R TCGA-76-4934 TCGA-76-6285 
       22.78        21.14        15.12         4.08         2.53         8.35 
TCGA-76-6286 TCGA-OX-A56R TCGA-02-0024 TCGA-02-0026 TCGA-02-0054 TCGA-02-0064 
       20.98         5.92        53.10        24.59         6.54        19.73 
TCGA-02-0079 TCGA-02-0432 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0129 
       27.25        47.11        16.80        15.32        15.45        33.67 
TCGA-06-0138 TCGA-06-0152 TCGA-06-0166 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
       24.23        12.33         5.85         3.22         4.04         4.18 
TCGA-06-0192 TCGA-06-0216 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0744 
       38.96        24.16        35.11        12.62         5.75        46.88 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2569 
        4.04        26.79        13.61        33.90         1.08         0.43 
TCGA-06-6389 TCGA-06-6390 TCGA-08-0246 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 
        7.79         5.39         4.18        29.23        65.33        17.95 
TCGA-08-0356 TCGA-08-0358 TCGA-08-0386 TCGA-12-0619 TCGA-12-0691 TCGA-12-0769 
       31.10        22.29        18.02        34.92        12.13        15.06 
TCGA-12-0827 TCGA-12-1098 TCGA-14-0787 TCGA-14-0813 TCGA-14-0867 TCGA-15-0742 
       38.76         3.98         2.24         1.35         2.04        13.78 
TCGA-15-1447 TCGA-15-1449 TCGA-19-1387 TCGA-19-1388 TCGA-26-1442 TCGA-28-2514 
       53.19        13.28         5.95        12.95        31.33         5.26 
TCGA-28-5214 TCGA-28-5220 TCGA-76-6283 
       23.44        12.76         5.42 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.96         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 
       15.35        21.73        25.68        14.73         6.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
        2.04         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       16.50        26.33        15.95         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1455 TCGA-14-1456 
       32.05        58.78        23.11         7.10         0.92        40.96 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         0.99         1.97         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-1047 TCGA-16-1055 
       17.49         7.96         3.78         3.42         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       14.96        17.79        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 
        9.37         9.40         8.88        18.97         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         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-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-32-2494 TCGA-32-2495 
        4.67        12.69        14.86        16.93        20.78        15.02 
TCGA-32-2615 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       15.95        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        11.84         0.20        12.46         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29         2.70        17.06         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC 
       23.90        34.45        18.64        36.20         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       20.12        42.74        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        20.84        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
       25.12        10.59        12.39        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 
        9.27        16.21         3.35        12.92        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       12.95        25.35        14.30        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0176 
       10.65        19.66         3.29        13.12         4.47        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       44.58        15.42        10.42         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        9.57         3.16         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 TCGA-06-2558 
       26.76        23.93         6.84        11.84        15.32        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 
        5.98         4.37        31.50       120.56         7.36        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0357 TCGA-08-0359 
        9.80         1.28         8.42        24.56        37.58         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       15.98        12.23        15.85         9.11        14.53         4.14 
TCGA-14-0789 TCGA-14-0817 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-1444 
       11.24         5.39        28.93        19.30         0.79        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 
       19.10         3.91        26.07        16.37        11.77        21.90 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 
        0.66        10.75         9.07         4.64        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        1.58         7.92         2.33         7.30        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       17.88        14.53        11.77        31.27        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 
        5.16        22.68         5.42         7.36        11.38         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                        65.33                        127.59 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                        15.12                         11.80 
[1] "0.4 - 65.3 (15.1)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED    28  65
  DEL PEAK 13(4Q34.3) WILD-TYPE 197 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     28   65
  DEL PEAK 13(4Q34.3) WILD-TYPE  197  283
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          28                           197
  MALE                            65                           283
[1] 2 2
[1] FALSE
D37V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED    16  73
  DEL PEAK 13(4Q34.3) WILD-TYPE  58 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     16   73
  DEL PEAK 13(4Q34.3) WILD-TYPE   58  402
     clus
vv    DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  NO                           16                            58
  YES                          73                           402
[1] 2 2
[1] FALSE
D37V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 13(4Q34.3) MUTATED                               6
  DEL PEAK 13(4Q34.3) WILD-TYPE                            24
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 13(4Q34.3) MUTATED                     2
  DEL PEAK 13(4Q34.3) WILD-TYPE                  16
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 13(4Q34.3) MUTATED                                85
  DEL PEAK 13(4Q34.3) WILD-TYPE                             440
D37V6, multiclass
                                 clus
vv                                DEL PEAK 13(4Q34.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             6
  TREATED PRIMARY GBM                                       2
  UNTREATED PRIMARY (DE NOVO) GBM                          85
                                 clus
vv                                DEL PEAK 13(4Q34.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              24
  TREATED PRIMARY GBM                                        16
  UNTREATED PRIMARY (DE NOVO) GBM                           440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q34.3) MUTATED       4                        11    78
  DEL PEAK 13(4Q34.3) WILD-TYPE     9                        39   409
D37V7, multiclass
                           clus
vv                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              78
                           clus
vv                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            39
  WHITE                                               409
[1] 3 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 13(4Q34.3) MUTATED     2  75
  DEL PEAK 13(4Q34.3) WILD-TYPE  10 400
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      2   75
  DEL PEAK 13(4Q34.3) WILD-TYPE   10  400
                        clus
vv                       DEL PEAK 13(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK 13(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           400
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 14(5Q34) MUTATION ANALYSIS
D38V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(5Q34) MUTATED    16  52
  DEL PEAK 14(5Q34) WILD-TYPE  81 421
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                         68                         502 
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                         52                         421 
$`DEL PEAK 14(5Q34) MUTATED`
TCGA-06-A5U0 TCGA-06-A7TL TCGA-12-1600 TCGA-12-3653 TCGA-14-0740 TCGA-14-0865 
       26.79        17.72        14.73        14.53        11.97        16.50 
TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-16-1045 TCGA-19-0960 TCGA-19-1786 
        1.15        17.79         3.78        29.03         8.61         7.17 
TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-5135 TCGA-27-1834 TCGA-27-1835 
       24.23         7.04        28.54         8.88        40.54        21.30 
TCGA-27-1836 TCGA-27-2521 TCGA-28-1756 TCGA-41-2572 TCGA-41-4097 TCGA-41-5651 
       30.05        16.77         2.83        13.35         0.20        15.12 
TCGA-4W-AA9R TCGA-76-4925 TCGA-76-4929 TCGA-76-4934 TCGA-RR-A6KC TCGA-02-0010 
        4.08         4.80         3.65         2.53        20.55        35.41 
TCGA-02-0011 TCGA-02-0026 TCGA-02-0052 TCGA-02-0069 TCGA-02-0084 TCGA-02-0104 
       20.71        24.59        12.59        28.70        12.62        65.00 
TCGA-02-0333 TCGA-02-2483 TCGA-06-0128 TCGA-06-0148 TCGA-06-0175 TCGA-06-0188 
        4.37        15.32        22.72        10.09         4.04        44.58 
TCGA-06-0211 TCGA-06-0237 TCGA-06-0414 TCGA-06-0644 TCGA-06-0649 TCGA-06-0686 
       11.84        13.64        35.11        12.62         2.10        14.20 
TCGA-06-0744 TCGA-06-1087 TCGA-06-2569 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 
       46.88         4.04         0.43         7.79       115.86        29.23 
TCGA-08-0386 TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 TCGA-12-0818 TCGA-14-0817 
       18.02        19.59        58.68         7.27        91.76         5.39 
TCGA-14-0867 TCGA-14-0871 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1387 
        2.04        28.93        50.53        53.19        16.37         5.95 
TCGA-26-5133 TCGA-28-5215 
       14.86        11.01 

$`DEL PEAK 14(5Q34) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 
        3.75         6.15         4.57         5.23         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-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
        2.56        14.60        15.35        21.73        15.65        25.68 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       26.33        15.95         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-14-1823 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 
        5.88         7.17        17.49         7.96         3.42        17.59 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 
        6.41        14.27         3.39        25.38         3.65        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-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16         4.08         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       16.80        14.96        17.79        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        7.13         9.37         9.40        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       16.60         9.86        24.23        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       18.08        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         0.13         0.66         6.74         4.77 
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-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85         8.94         9.53         0.99         4.44        11.84 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
       14.33         8.22         7.50         4.54         3.09         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        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        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
       36.20         5.92         6.28         7.63        11.77         4.73 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       18.35        23.18        10.59        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 
       77.65        20.12        53.10        42.74        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73         3.22        15.09         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-02-0070 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-02-0106 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         7.33        15.91        25.71 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
       11.74         2.33        20.09        17.79         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       19.66         3.29        13.12         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 
        5.56         0.39         7.66         8.42         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
        9.57         3.16         5.75         5.75         9.80        23.57 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        5.39       120.56         7.36        22.68        37.84         4.18 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 
        1.74         8.42        25.71        12.16         9.80        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 
        0.72        12.56         4.27        42.15        11.08        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
       10.75         4.80        15.98        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       14.53         3.98         4.14         2.24        11.24         1.35 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       19.30         0.79        13.78        19.10        13.28         3.91 
TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       26.07        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       12.95         4.64        31.33         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
       22.68        12.76         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                        0.2                         0.1 
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                     115.86                      127.59 
  DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE 
                     14.795                      11.870 
[1] "0.2 - 115.9 (14.8)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.4"
D38V2, continuous
D38V3, binary
                             cls
clus                            0   1
  DEL PEAK 14(5Q34) MUTATED    32  37
  DEL PEAK 14(5Q34) WILD-TYPE 193 311
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(5Q34) MUTATED     32   37
  DEL PEAK 14(5Q34) WILD-TYPE  193  311
        clus
vv       DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE
  FEMALE                        32                         193
  MALE                          37                         311
[1] 2 2
[1] FALSE
D38V4, binary
                             cls
clus                            0   1
  DEL PEAK 14(5Q34) MUTATED     7  58
  DEL PEAK 14(5Q34) WILD-TYPE  67 417
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(5Q34) MUTATED      7   58
  DEL PEAK 14(5Q34) WILD-TYPE   67  417
     clus
vv    DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE
  NO                          7                          67
  YES                        58                         417
[1] 2 2
[1] FALSE
D38V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 14(5Q34) MUTATED                               6                   1
  DEL PEAK 14(5Q34) WILD-TYPE                            24                  17
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 14(5Q34) MUTATED                                62
  DEL PEAK 14(5Q34) WILD-TYPE                             463
D38V6, multiclass
                                 clus
vv                                DEL PEAK 14(5Q34) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           6
  TREATED PRIMARY GBM                                     1
  UNTREATED PRIMARY (DE NOVO) GBM                        62
                                 clus
vv                                DEL PEAK 14(5Q34) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            24
  TREATED PRIMARY GBM                                      17
  UNTREATED PRIMARY (DE NOVO) GBM                         463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q34) MUTATED       3                        11    55
  DEL PEAK 14(5Q34) WILD-TYPE    10                        39   432
D38V7, multiclass
                           clus
vv                          DEL PEAK 14(5Q34) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                            55
                           clus
vv                          DEL PEAK 14(5Q34) WILD-TYPE
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          39
  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"
D38V8, binary
                             cls
clus                            0   1
  DEL PEAK 14(5Q34) MUTATED     3  56
  DEL PEAK 14(5Q34) WILD-TYPE   9 419
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(5Q34) MUTATED      3   56
  DEL PEAK 14(5Q34) WILD-TYPE    9  419
                        clus
vv                       DEL PEAK 14(5Q34) MUTATED DEL PEAK 14(5Q34) WILD-TYPE
  HISPANIC OR LATINO                             3                           9
  NOT HISPANIC OR LATINO                        56                         419
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 15(6Q22.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6Q22.1) MUTATED    19 135
  DEL PEAK 15(6Q22.1) WILD-TYPE  78 338
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                          154                           416 
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                          135                           338 
$`DEL PEAK 15(6Q22.1) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 
        3.98        15.32        11.74         3.55         8.81         8.55 
TCGA-06-5416 TCGA-06-5856 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-12-0615 TCGA-12-1602 
        6.71         3.75         1.87         2.56        15.35         6.77 
TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0865 TCGA-14-1396 
       44.02        14.53         3.22        15.12        16.50         1.12 
TCGA-14-1453 TCGA-14-1823 TCGA-14-4157 TCGA-16-1045 TCGA-16-1060 TCGA-16-1063 
        1.15        17.85         3.42        29.03         9.14        13.97 
TCGA-19-1392 TCGA-19-2619 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        3.65         9.67        24.23         7.04         6.64        18.90 
TCGA-19-5960 TCGA-26-1439 TCGA-26-1443 TCGA-27-1832 TCGA-27-1833 TCGA-27-2524 
       14.96        13.87         7.13         9.86        24.23         7.59 
TCGA-27-2526 TCGA-28-1750 TCGA-28-2506 TCGA-28-2509 TCGA-32-1976 TCGA-32-1980 
        2.86         8.35         6.74         4.77         0.49         1.18 
TCGA-32-2495 TCGA-32-2615 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 
       15.02        15.95        21.14         3.72        12.59        10.85 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 
        0.85        13.35         9.53         0.99         0.20        15.12 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-76-4925 TCGA-76-4928 TCGA-76-4929 
       25.58         3.45        20.91         4.80         3.09         3.65 
TCGA-76-4931 TCGA-76-6282 TCGA-76-6285 TCGA-OX-A56R TCGA-06-0209 TCGA-02-0003 
        9.17        17.06         8.35         5.92         7.63         4.73 
TCGA-02-0007 TCGA-02-0014 TCGA-02-0023 TCGA-02-0026 TCGA-02-0038 TCGA-02-0039 
       23.18        82.59        20.12        24.59        10.72        10.52 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0058 TCGA-02-0060 TCGA-02-0074 TCGA-02-0080 
        3.22        15.09         8.35         6.02        10.19        89.72 
TCGA-02-0086 TCGA-02-0099 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
        8.81         3.48        11.67        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0281 TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 
       16.54         3.98        15.95        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-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0154 TCGA-06-0162 TCGA-06-0166 
       12.95        24.23        10.29        13.94         3.42         5.85 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       69.90        73.84        27.22        15.02        24.16         0.72 
TCGA-06-0402 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 TCGA-06-2557 
        0.26        12.62         5.75         2.10         0.92         1.08 
TCGA-06-2561 TCGA-06-6390 TCGA-06-6694 TCGA-08-0246 TCGA-08-0358 TCGA-08-0375 
       17.65         5.39         7.36         4.18        22.29        12.23 
TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 TCGA-08-0525 
       14.93         0.72         4.27        42.15        58.68        15.98 
TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0691 TCGA-12-0692 
       14.73        10.45         7.59        94.78        12.13         3.65 
TCGA-12-0772 TCGA-12-0780 TCGA-12-0822 TCGA-12-1089 TCGA-12-1093 TCGA-12-1095 
       53.85        14.86        23.51         5.82        15.98        15.85 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0817 TCGA-14-1037 TCGA-15-0742 
        3.98         4.14         2.24         5.39        19.30        13.78 
TCGA-16-0846 TCGA-19-0962 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 
        3.91         0.66         5.26        14.93        11.28        14.53 
TCGA-28-5213 TCGA-28-5220 TCGA-28-6450 TCGA-76-6660 
       31.27        12.76         5.42         3.75 

$`DEL PEAK 15(6Q22.1) WILD-TYPE`
TCGA-06-6391 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 
        1.48         8.35         4.54         8.98         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL 
        4.77         4.96        26.79         3.12        14.60        17.72 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
       21.73        15.65        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 
       15.22        10.95        12.69        34.92        14.93         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
       11.97         0.95         6.21        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
        2.89        26.33        15.95         1.38         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-16-0848 
        5.88         7.17        17.49         7.96         3.78        17.59 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1460 TCGA-19-0960 
        4.57        10.29        14.01        21.24         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        7.00        17.19         8.02         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       22.49        14.07        16.80        17.79        28.54        10.03 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        9.73         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        5.06        16.60        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 
       11.51        24.76        18.08        16.77        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-32-1970 
        1.22         1.55         2.83         0.13         0.66        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2632 TCGA-32-2634 
       14.86        16.93        12.23        20.78         8.84        22.78 
TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2573 TCGA-41-3393 TCGA-41-3915 
       25.18        19.86        19.23         8.94         4.44        11.84 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       12.46         4.08         1.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        7.50         4.54         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        2.70        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0001 TCGA-02-0006 
       18.64        36.20         6.28        20.55        11.77        18.35 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       10.59        35.41        20.71        20.61        87.06        77.65 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0052 TCGA-02-0054 
        3.62        18.31         6.87        14.73        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        2.50        19.86         9.57        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 
       25.05         5.49        20.84        27.25        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 
       51.32        57.76        16.96        27.02        65.00        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       23.18        99.98        16.93        17.72        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0321 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 
       13.87        14.20         9.90         7.33        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       25.12        10.59        12.39        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
        3.35        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       25.35        14.30        26.70        11.90         0.20         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        12.33        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
        9.44        11.80        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       88.14        20.25         3.65        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0221 TCGA-06-0237 
        8.42         7.40        11.84         0.53        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       13.32        20.42        48.69        10.82         9.01        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 
        4.70         9.57         3.16        35.11         5.75         9.80 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        2.70        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 
        0.43        31.50         7.79       120.56        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       31.10        37.58         3.39        18.02        15.35        13.97 
TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       12.56        11.08        19.59        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0657 
        7.27        18.41         7.56        12.99        34.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       38.17        25.97        26.66        20.38        28.41        15.06 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63         9.73        14.93        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1090 TCGA-12-1091 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 
      127.59         7.59        33.21        12.23         9.11        14.53 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-0871 TCGA-14-1043 TCGA-15-1444 
       11.24         1.35         2.04        28.93         0.79        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 
       19.10        53.19        13.28        26.07        16.37        11.77 
TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
       21.90        10.75         9.07         5.95        12.95         4.64 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
        7.30        17.88        11.77        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 
        5.16        22.68         7.36        11.38         5.42         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                          0.2                           0.1 
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                        94.78                        127.59 
  DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE 
                       10.535                        12.640 
[1] "0.2 - 94.8 (10.5)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q22.1) MUTATED    67  88
  DEL PEAK 15(6Q22.1) WILD-TYPE 158 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q22.1) MUTATED     67   88
  DEL PEAK 15(6Q22.1) WILD-TYPE  158  260
        clus
vv       DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE
  FEMALE                          67                           158
  MALE                            88                           260
[1] 2 2
[1] FALSE
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q22.1) MUTATED    26 123
  DEL PEAK 15(6Q22.1) WILD-TYPE  48 352
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q22.1) MUTATED     26  123
  DEL PEAK 15(6Q22.1) WILD-TYPE   48  352
     clus
vv    DEL PEAK 15(6Q22.1) MUTATED DEL PEAK 15(6Q22.1) WILD-TYPE
  NO                           26                            48
  YES                         123                           352
[1] 2 2
[1] FALSE
D39V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 15(6Q22.1) MUTATED                               7
  DEL PEAK 15(6Q22.1) WILD-TYPE                            23
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 15(6Q22.1) MUTATED                     7
  DEL PEAK 15(6Q22.1) WILD-TYPE                  11
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 15(6Q22.1) MUTATED                               141
  DEL PEAK 15(6Q22.1) WILD-TYPE                             384
D39V6, multiclass
                                 clus
vv                                DEL PEAK 15(6Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             7
  TREATED PRIMARY GBM                                       7
  UNTREATED PRIMARY (DE NOVO) GBM                         141
                                 clus
vv                                DEL PEAK 15(6Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              23
  TREATED PRIMARY GBM                                        11
  UNTREATED PRIMARY (DE NOVO) GBM                           384
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6Q22.1) MUTATED       5                        15   128
  DEL PEAK 15(6Q22.1) WILD-TYPE     8                        35   359
D39V7, multiclass
                           clus
vv                          DEL PEAK 15(6Q22.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          15
  WHITE                                             128
                           clus
vv                          DEL PEAK 15(6Q22.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            35
  WHITE                                               359
[1] 3 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 15(6Q22.1) MUTATED     1 131
  DEL PEAK 15(6Q22.1) WILD-TYPE  11 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q22.1) MUTATED      1  131
  DEL PEAK 15(6Q22.1) WILD-TYPE   11  344
                        clus
vv                       DEL PEAK 15(6Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         131
                        clus
vv                       DEL PEAK 15(6Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 16(6Q26) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED    25 153
  DEL PEAK 16(6Q26) WILD-TYPE  72 320
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        178                         392 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        153                         320 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5415 
        3.98        15.32        11.74         3.55         8.81         8.55 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 
        6.71         3.75         4.57         1.55         1.87         2.56 
TCGA-12-0615 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 
       15.35         6.77        44.02        14.53         3.22        15.12 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1395 TCGA-14-1402 TCGA-14-1453 TCGA-14-1823 
        2.89        16.50         1.38        32.05         1.15        17.85 
TCGA-14-4157 TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 TCGA-19-1392 
        3.42        29.03         4.57         9.14        13.97         3.65 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        3.25         9.67        24.23         7.00         7.04         6.64 
TCGA-19-5952 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-1443 TCGA-27-1832 
       18.90        22.49        14.96        13.87         7.13         9.86 
TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 TCGA-27-2524 TCGA-28-1747 TCGA-28-1750 
       24.23        24.76        16.77         7.59         2.53         8.35 
TCGA-28-1753 TCGA-28-2506 TCGA-28-2509 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 
        1.22         6.74         4.77        15.85         1.18         4.67 
TCGA-32-2495 TCGA-32-2615 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 
       15.02        15.95        21.14         3.72        12.59        10.85 
TCGA-41-2572 TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9T TCGA-74-6573 
       13.35         0.99         0.20        15.12        25.58         3.45 
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 
TCGA-06-0209 TCGA-02-0003 TCGA-02-0007 TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 
        7.63         4.73        23.18        20.61        77.65        20.12 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 TCGA-02-0057 
       24.59        12.16        10.52         3.22        15.09        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0074 TCGA-02-0080 TCGA-02-0086 
        8.35         9.57         6.02        10.19        89.72         8.81 
TCGA-02-0089 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       16.96        11.67        92.65        15.65        48.95        16.54 
TCGA-02-0281 TCGA-02-0289 TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 
        3.98        14.20        12.23         7.73        10.62        15.91 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-2466 TCGA-02-2483 TCGA-06-0124 
       14.50        10.55        47.11        16.80        15.32        20.38 
TCGA-06-0125 TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0142 TCGA-06-0155 
       47.61        12.95        24.23        10.29         2.20        10.45 
TCGA-06-0162 TCGA-06-0166 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0214 
        3.42         5.85        69.90        73.84        27.22        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0750 
       24.16         0.72        12.62         5.75         2.10         0.92 
TCGA-06-0878 TCGA-06-0882 TCGA-06-1084 TCGA-06-1087 TCGA-06-2557 TCGA-06-2561 
        7.17        20.78        23.93         4.04         1.08        17.65 
TCGA-06-6390 TCGA-06-6694 TCGA-08-0246 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
        5.39         7.36         4.18         8.42        24.56        31.10 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 
       22.29        12.23        14.93         0.72         4.27        42.15 
TCGA-08-0517 TCGA-08-0525 TCGA-12-0616 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       58.68        15.98        14.73         7.59        94.78         0.10 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0780 
       12.13         3.65        28.41        15.06        53.85        14.86 
TCGA-12-0822 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1095 TCGA-12-1099 
       23.51         5.82        33.21        15.98        15.85         4.14 
TCGA-14-0817 TCGA-14-1037 TCGA-15-0742 TCGA-15-1446 TCGA-16-0846 TCGA-19-0962 
        5.39        19.30        13.78        19.10         3.91         0.66 
TCGA-19-1386 TCGA-26-6173 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 
        9.07         7.92         5.26        14.93        11.28        14.53 
TCGA-28-5213 TCGA-28-5220 TCGA-76-6660 TCGA-81-5911 
       31.27        12.76         3.75        17.72 

$`DEL PEAK 16(6Q26) WILD-TYPE`
TCGA-06-6391 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 
        1.48         8.35         4.54         8.98         2.73         6.15 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32        12.85         4.77         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1092 TCGA-12-1598 
       26.79         3.12        14.60        17.72        21.73        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68        14.73        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       12.69        34.92        14.93         2.04        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 
        6.21        23.05        13.78         3.25        26.33        15.95 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        1.12         3.75        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 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-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1460 
        3.78        17.59        10.29        14.01        21.24         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        8.61        14.27         3.39        25.38         7.17        12.66 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        0.13         4.87         1.08         7.53         0.16         4.08 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       17.19         8.02         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1799 
       16.80        17.79        28.54        10.03         9.73         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 
       40.54        21.30        30.05        14.04        11.51        18.08 
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-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1986 
       15.39        21.07         0.49         0.10        19.50        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2632 TCGA-32-2634 
       14.86        16.93        12.23        20.78         8.84        22.78 
TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 
       25.18        19.86        19.23         0.85         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6575 
        4.44        11.84        12.46         4.08         1.45        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-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6286 
        2.53        36.85        16.70         3.29         2.70        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0001 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 
        6.28        20.55        11.77        18.35        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 
       20.71        82.59        87.06        53.10        42.74        90.58 
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-02-0047 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0064 TCGA-02-0068 
       14.73        12.59         6.54         2.50        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 
       28.70        25.05         5.49        20.84        27.25        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       12.62        51.32        57.76         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       17.65        23.18        99.98        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0290 TCGA-02-0321 TCGA-02-0326 TCGA-02-0332 
       14.47        13.87        15.95         9.90         7.33        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0440 TCGA-02-0446 
        4.37        25.12        10.59        12.39        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.21         3.35        12.92        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 
        6.15         6.94         3.98        22.72        33.67        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0143 TCGA-06-0145 
       14.30        26.70        11.90         0.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.33        13.94         3.19        10.82         9.44        11.80 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91        10.65        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
        3.65        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 
        9.57         3.16        35.11         5.75         9.80        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1086 
       43.46        46.19        40.41        16.57        26.76         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79        11.84        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 
        4.37         0.43        31.50         7.79       120.56        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0357 
        9.80        29.23        65.33         1.28        17.95        37.58 
TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 
        3.39        18.02        15.35        13.97        12.56        11.08 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       19.59        19.33        10.75         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 
        7.56        12.99        34.92        10.45        38.17        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       26.66        20.38        43.23         7.63         9.73        14.93 
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-12-1094 TCGA-12-1096 
        8.94        20.58       127.59         7.59        12.23         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 
       14.53         3.98         2.24        11.24         1.35         2.04 
TCGA-14-0871 TCGA-14-1043 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
       28.93         0.79        50.53        53.19        13.28        26.07 
TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 
       16.37        11.77        21.90        10.75         5.95        12.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 
        4.64        31.33        14.86         5.49         1.58         2.33 
TCGA-28-2513 TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
        7.30        17.88        11.77        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68         5.42         7.36        11.38         5.42 
TCGA-81-5910 TCGA-87-5896 
        1.61        26.30 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        0.1                         0.1 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                      94.78                      127.59 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     11.705                      12.475 
[1] "0.1 - 94.8 (11.7)"  "0.1 - 127.6 (12.5)"
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    77 102
  DEL PEAK 16(6Q26) WILD-TYPE 148 246
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     77  102
  DEL PEAK 16(6Q26) WILD-TYPE  148  246
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        77                         148
  MALE                         102                         246
[1] 2 2
[1] FALSE
D40V4, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    25 145
  DEL PEAK 16(6Q26) WILD-TYPE  49 330
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     25  145
  DEL PEAK 16(6Q26) WILD-TYPE   49  330
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                         25                          49
  YES                       145                         330
[1] 2 2
[1] FALSE
D40V5, continuous
                             vv
clus                          GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DEL PEAK 16(6Q26) MUTATED                               8                   9
  DEL PEAK 16(6Q26) WILD-TYPE                            22                   9
                             vv
clus                          UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 16(6Q26) MUTATED                               162
  DEL PEAK 16(6Q26) WILD-TYPE                             363
D40V6, multiclass
                                 clus
vv                                DEL PEAK 16(6Q26) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           8
  TREATED PRIMARY GBM                                     9
  UNTREATED PRIMARY (DE NOVO) GBM                       162
                                 clus
vv                                DEL PEAK 16(6Q26) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                            22
  TREATED PRIMARY GBM                                       9
  UNTREATED PRIMARY (DE NOVO) GBM                         363
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q26) MUTATED       4                        16   152
  DEL PEAK 16(6Q26) WILD-TYPE     9                        34   335
D40V7, multiclass
                           clus
vv                          DEL PEAK 16(6Q26) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        16
  WHITE                                           152
                           clus
vv                          DEL PEAK 16(6Q26) WILD-TYPE
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          34
  WHITE                                             335
[1] 3 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 16(6Q26) MUTATED     2 152
  DEL PEAK 16(6Q26) WILD-TYPE  10 323
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      2  152
  DEL PEAK 16(6Q26) WILD-TYPE   10  323
                        clus
vv                       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                       152                         323
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 17(8P23.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(8P23.2) MUTATED    12  54
  DEL PEAK 17(8P23.2) WILD-TYPE  85 419
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                           66                           504 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                           54                           419 
$`DEL PEAK 17(8P23.2) MUTATED`
TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-A5U1 TCGA-12-1598 TCGA-12-3651 
       11.74         8.35         8.81         1.87        15.65        12.69 
TCGA-14-0736 TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 TCGA-14-1794 TCGA-14-1823 
       15.12         2.89        15.95        58.78         0.99        17.85 
TCGA-16-1056 TCGA-16-1063 TCGA-19-0960 TCGA-19-1786 TCGA-26-1439 TCGA-26-5136 
       14.01        13.97         8.61         7.17        13.87        18.97 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 
       16.77         7.59         8.35         0.13         0.66         4.77 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-4W-AA9T TCGA-76-4934 TCGA-02-0001 
       21.14         3.72        10.85        25.58         2.53        11.77 
TCGA-02-0009 TCGA-02-0025 TCGA-02-0051 TCGA-02-0059 TCGA-02-0060 TCGA-02-0086 
       10.59        42.74        15.09         9.57         6.02         8.81 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0115 TCGA-02-0281 TCGA-02-0324 TCGA-02-0430 
       11.67        23.18        15.65         3.98         7.73        10.55 
TCGA-02-2486 TCGA-06-0159 TCGA-06-0169 TCGA-06-0171 TCGA-06-0195 TCGA-06-0216 
       20.32         9.44         3.29        13.12         7.40        24.16 
TCGA-06-0410 TCGA-06-0743 TCGA-06-6693 TCGA-08-0246 TCGA-08-0392 TCGA-08-0510 
        4.70        26.40       120.56         4.18         0.72         4.27 
TCGA-08-0525 TCGA-12-0691 TCGA-12-0776 TCGA-12-0826 TCGA-12-0827 TCGA-12-1093 
       15.98        12.13         9.73        27.78        38.76        15.98 
TCGA-12-1098 TCGA-15-1447 TCGA-16-0846 TCGA-19-1385 TCGA-28-2514 TCGA-28-5204 
        3.98        53.19         3.91        10.75         5.26        14.93 

$`DEL PEAK 17(8P23.2) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 
        1.48         3.98        15.32         3.55         4.54         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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.96        26.79         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       15.35        21.73        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       44.02        26.93        15.22        10.95        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0865 TCGA-14-0866 TCGA-14-1395 
       23.05        13.78         3.25        16.50        26.33         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        1.12         3.75        32.05        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.78         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 
        9.14        21.24         6.41        14.27         3.39        25.38 
TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       17.79        28.54        10.03         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40         8.88        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        18.08        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-2506 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        1.55         2.83         6.74        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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 
        8.84        22.78        25.18        12.59        19.86        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
       11.84         0.20        15.12        12.46         4.08         1.45 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 
        5.92         6.28        20.55         7.63         4.73        18.35 
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       23.18        35.41        20.71        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       77.65        20.12        53.10        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
        2.83        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73         3.22        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
       19.86         8.35        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-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       12.62        51.32        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 
       65.00        17.65        92.65        99.98        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90        10.62         7.33        15.91 
TCGA-02-0332 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-02-0432 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-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.32        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       10.65         5.85        19.66         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        4.67         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84         0.53        15.02         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       72.36         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 
       31.50         7.79         5.39         7.36        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       18.41         7.56        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       10.62        23.51         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
        7.59        33.21        12.23        15.85         9.11        14.53 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 
        4.14         2.24        11.24         1.35         5.39         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       28.93        19.30         0.79        13.78        50.53        19.10 
TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       13.28        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
        9.07         5.95        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5207 
        5.49         1.58         7.92         2.33         7.30        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       120.56                        127.59 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       10.800                        12.475 
[1] "0.1 - 120.6 (10.8)" "0.1 - 127.6 (12.5)"
[1] "hr=" "1.1"
D41V2, continuous
D41V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED    30  36
  DEL PEAK 17(8P23.2) WILD-TYPE 195 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED     30   36
  DEL PEAK 17(8P23.2) WILD-TYPE  195  312
        clus
vv       DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  FEMALE                          30                           195
  MALE                            36                           312
[1] 2 2
[1] FALSE
D41V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED     7  56
  DEL PEAK 17(8P23.2) WILD-TYPE  67 419
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED      7   56
  DEL PEAK 17(8P23.2) WILD-TYPE   67  419
     clus
vv    DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  NO                            7                            67
  YES                          56                           419
[1] 2 2
[1] FALSE
D41V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 17(8P23.2) MUTATED                               3
  DEL PEAK 17(8P23.2) WILD-TYPE                            27
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 17(8P23.2) MUTATED                     1
  DEL PEAK 17(8P23.2) WILD-TYPE                  17
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 17(8P23.2) MUTATED                                62
  DEL PEAK 17(8P23.2) WILD-TYPE                             463
D41V6, multiclass
                                 clus
vv                                DEL PEAK 17(8P23.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             3
  TREATED PRIMARY GBM                                       1
  UNTREATED PRIMARY (DE NOVO) GBM                          62
                                 clus
vv                                DEL PEAK 17(8P23.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              27
  TREATED PRIMARY GBM                                        17
  UNTREATED PRIMARY (DE NOVO) GBM                           463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8P23.2) MUTATED       5                         4    53
  DEL PEAK 17(8P23.2) WILD-TYPE     8                        46   434
D41V7, multiclass
                           clus
vv                          DEL PEAK 17(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              53
                           clus
vv                          DEL PEAK 17(8P23.2) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               434
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED     0  57
  DEL PEAK 17(8P23.2) WILD-TYPE  12 418
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED      0   57
  DEL PEAK 17(8P23.2) WILD-TYPE   12  418
                        clus
vv                       DEL PEAK 17(8P23.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       DEL PEAK 17(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           418
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED    69 347
  DEL PEAK 18(9P21.3) WILD-TYPE  28 126
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          416                           154 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          347                           126 
$`DEL PEAK 18(9P21.3) MUTATED`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         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-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32        12.85         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-12-0615 
       26.79         1.87         3.12         2.56        17.72        15.35 
TCGA-12-1092 TCGA-12-1599 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       21.73        25.68         6.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
       15.12        11.97         0.95         6.21        23.05        13.78 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        2.89        16.50        26.33         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 
       32.05         7.10         1.15         0.92         6.67        12.43 
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-14-4157 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       17.49         7.96         3.42        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0960 TCGA-19-0963 
       14.01         9.14        21.24        13.97         8.61        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
        3.39        25.38         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        9.67         4.87         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1439 
        1.78        22.49        14.07        16.80        28.54        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.73         7.13         9.37        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 
        9.86        24.23        40.54        30.05        14.04        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59         2.86        15.78         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        0.66         6.74        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 
       15.85        19.50         4.67        12.69        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
       15.02        15.95        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85        19.23        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        0.99         4.44         0.20        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 
        2.53        36.85        16.70         3.29        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA 
        4.83         5.03        23.90        36.20         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
       20.55         7.63        23.18        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0027 
       20.61        87.06        77.65        20.12        53.10        12.16 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
        3.62        10.72        18.31        14.73         3.22        15.09 
TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 TCGA-02-0071 
        6.54        19.86         8.35        19.73        26.43         5.49 
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-02-0104 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-02-0281 
       48.95        16.54        16.93        17.72        10.75         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-02-0333 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        7.33        15.91         4.37        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       47.11         9.27        16.21        16.80        12.92        15.32 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
        3.98        22.72        25.35        14.30        26.70        11.90 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 
       10.29         2.20        11.74         2.33        10.09        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 
       46.59        13.94        10.45        10.82         3.42        56.91 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 
        5.85         3.29        13.12         4.47         4.04         4.18 
TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 
       20.25        73.84        27.22        44.58        10.42        38.96 
TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        0.39         8.42         7.40        11.84        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        19.82        13.64        48.69        10.82         9.01 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80         2.10        23.57        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        7.86         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       40.41        20.78        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2561 TCGA-06-2562 
       11.84        15.32        13.61         1.08        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0246 TCGA-08-0345 
        7.79       120.56         7.36        22.68         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        8.42        25.71        12.16         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56         4.27        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       58.68        19.33        10.75        15.98        18.41         7.56 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       10.45         7.59        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       12.13         3.65        28.41         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 
        8.94        20.58       127.59         5.82        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 
       12.23        15.85        14.53         3.98         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 
       11.24         1.35         5.39        28.93        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       11.77         0.66        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 
        4.64        31.33         5.49         1.58         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 
       11.01        13.64        12.76         5.42        11.38         3.75 
TCGA-81-5910 TCGA-87-5896 
        1.61        26.30 

$`DEL PEAK 18(9P21.3) WILD-TYPE`
TCGA-06-5411 TCGA-06-5416 TCGA-06-5858 TCGA-06-6698 TCGA-06-A7TK TCGA-12-1598 
        8.35         6.71         6.15         4.77        14.60        15.65 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-14-0812 TCGA-14-1034 TCGA-14-1450 
       14.73        59.77        44.02         3.25        15.95        58.78 
TCGA-14-1451 TCGA-14-1454 TCGA-14-1456 TCGA-14-1794 TCGA-14-3477 TCGA-16-0848 
       23.11        30.18        40.96         0.99         3.78        17.59 
TCGA-16-1460 TCGA-19-1787 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-5960 
        6.41        12.66         1.08         7.53         0.16        14.96 
TCGA-19-A60I TCGA-26-1438 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1835 
       17.79        10.03         9.40         8.88        18.97        21.30 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2527 TCGA-28-1746 TCGA-28-1752 
       11.51        24.76        18.08        14.40         0.20         8.48 
TCGA-28-2509 TCGA-32-1980 TCGA-32-1987 TCGA-32-2491 TCGA-32-2632 TCGA-32-2634 
        4.77         1.18        14.86        12.23         8.84        22.78 
TCGA-41-2571 TCGA-41-3915 TCGA-41-5651 TCGA-76-6193 TCGA-76-6286 TCGA-76-6662 
        0.85        11.84        15.12         2.70        20.98        34.45 
TCGA-76-6663 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0011 TCGA-02-0025 
       18.64        11.77         4.73        18.35        20.71        42.74 
TCGA-02-0026 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 
       24.59        90.58         2.83        14.14        10.52         6.87 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 TCGA-02-0070 
       12.59         2.50         9.57         6.02        28.70        25.05 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0084 TCGA-02-0087 TCGA-02-0102 
       10.19        20.84        27.25        12.62        57.76        27.02 
TCGA-02-0113 TCGA-02-0271 TCGA-02-0324 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 
       92.65        14.47         7.73        25.71        25.12        10.59 
TCGA-02-0440 TCGA-02-0456 TCGA-02-2485 TCGA-06-0129 TCGA-06-0130 TCGA-06-0138 
       11.34         3.35        15.45        33.67        12.95        24.23 
TCGA-06-0140 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0157 
        0.20        20.09        17.79         8.61        12.33         3.19 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 TCGA-06-0174 TCGA-06-0176 
        9.44        11.80        10.65        19.66         3.22        91.00 
TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 
       88.14         3.65        69.90        15.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0206 TCGA-06-0213 TCGA-06-0238 TCGA-06-0240 TCGA-06-0402 
        5.56         7.66         0.53        13.32        20.42         0.26 
TCGA-06-0414 TCGA-06-0686 TCGA-06-0749 TCGA-06-0881 TCGA-06-0939 TCGA-06-1805 
       35.11        14.20         2.70        16.57        26.76        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2570 TCGA-06-6390 TCGA-08-0245 TCGA-08-0344 
       12.49         4.93        31.50         5.39        37.84       115.86 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
        9.80        29.23        65.33        14.93        18.02        15.35 
TCGA-08-0512 TCGA-08-0521 TCGA-08-0524 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       42.15         4.80         7.27        14.73        12.99        34.92 
TCGA-12-0662 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 
       38.17        20.38        15.06        53.85        43.23         9.73 
TCGA-12-0820 TCGA-12-1090 TCGA-12-1096 TCGA-14-0867 TCGA-16-0849 TCGA-16-0850 
       18.48         7.59         9.11         2.04        26.07        16.37 
TCGA-19-0957 TCGA-26-5133 TCGA-26-6173 TCGA-28-5207 TCGA-28-5214 TCGA-28-5218 
       21.90        14.86         7.92        11.28        23.44         5.16 
TCGA-28-5219 TCGA-32-2616 TCGA-76-6283 TCGA-81-5911 
       22.68         7.36         5.42        17.72 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         0.10                          0.16 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       127.59                        115.86 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       11.770                        14.435 
[1] "0.1 - 127.6 (11.8)" "0.2 - 115.9 (14.4)"
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   168 251
  DEL PEAK 18(9P21.3) WILD-TYPE  57  97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    168  251
  DEL PEAK 18(9P21.3) WILD-TYPE   57   97
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                         168                            57
  MALE                           251                            97
[1] 2 2
[1] FALSE
D42V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    59 342
  DEL PEAK 18(9P21.3) WILD-TYPE  15 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     59  342
  DEL PEAK 18(9P21.3) WILD-TYPE   15  133
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                           59                            15
  YES                         342                           133
[1] 2 2
[1] FALSE
D42V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 18(9P21.3) MUTATED                              22
  DEL PEAK 18(9P21.3) WILD-TYPE                             8
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 18(9P21.3) MUTATED                    15
  DEL PEAK 18(9P21.3) WILD-TYPE                   3
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 18(9P21.3) MUTATED                               382
  DEL PEAK 18(9P21.3) WILD-TYPE                             143
D42V6, multiclass
                                 clus
vv                                DEL PEAK 18(9P21.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            22
  TREATED PRIMARY GBM                                      15
  UNTREATED PRIMARY (DE NOVO) GBM                         382
                                 clus
vv                                DEL PEAK 18(9P21.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               8
  TREATED PRIMARY GBM                                         3
  UNTREATED PRIMARY (DE NOVO) GBM                           143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9P21.3) MUTATED       9                        40   355
  DEL PEAK 18(9P21.3) WILD-TYPE     4                        10   132
D42V7, multiclass
                           clus
vv                          DEL PEAK 18(9P21.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                          40
  WHITE                                             355
                           clus
vv                          DEL PEAK 18(9P21.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               132
[1] 3 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 18(9P21.3) MUTATED     8 344
  DEL PEAK 18(9P21.3) WILD-TYPE   4 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      8  344
  DEL PEAK 18(9P21.3) WILD-TYPE    4  131
                        clus
vv                       DEL PEAK 18(9P21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         344
                        clus
vv                       DEL PEAK 18(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           131
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 19(9Q34.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(9Q34.2) MUTATED     8  69
  DEL PEAK 19(9Q34.2) WILD-TYPE  89 404
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                           77                           493 
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                           69                           404 
$`DEL PEAK 19(9Q34.2) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5412 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-12-1602 
        3.98        15.32         4.54         1.87         2.56         6.77 
TCGA-12-3648 TCGA-12-3652 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-1395 
       26.93        34.92        14.53        15.12        11.97         1.38 
TCGA-14-1396 TCGA-14-1456 TCGA-16-1045 TCGA-16-1047 TCGA-19-0963 TCGA-19-2631 
        1.12        40.96        29.03         4.57        14.27         7.00 
TCGA-19-5958 TCGA-26-1439 TCGA-26-5136 TCGA-27-2521 TCGA-27-2528 TCGA-28-1757 
       14.07        13.87        18.97        16.77        15.78         0.13 
TCGA-28-2506 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-4W-AA9S 
        6.74        21.14        19.86        10.85        13.35         1.45 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0006 TCGA-02-0015 TCGA-02-0016 TCGA-02-0034 
       20.55         7.63        18.35        20.61        87.06        14.14 
TCGA-02-0070 TCGA-02-0107 TCGA-02-0258 TCGA-02-0269 TCGA-02-0330 TCGA-02-2466 
       25.05        17.65        16.54        10.75        15.91        16.80 
TCGA-02-2470 TCGA-06-0128 TCGA-06-0132 TCGA-06-0141 TCGA-06-0162 TCGA-06-0173 
       12.92        22.72        25.35        10.29         3.42         4.47 
TCGA-06-0177 TCGA-06-0208 TCGA-06-0210 TCGA-06-0237 TCGA-06-0409 TCGA-06-0412 
        4.18         8.42         7.40        13.64        72.36         9.57 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0879 TCGA-06-1086 TCGA-06-2557 TCGA-06-2561 
       26.40         7.86        40.41         6.84         1.08        17.65 
TCGA-06-2565 TCGA-06-6694 TCGA-08-0246 TCGA-08-0353 TCGA-08-0355 TCGA-08-0510 
       16.64         7.36         4.18         8.42        24.56         4.27 
TCGA-12-0707 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-1091 TCGA-12-1093 
       28.41        10.62        27.78        38.76        33.21        15.98 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-28-5220 
       13.78        50.53        53.19         3.91        12.76 

$`DEL PEAK 19(9Q34.2) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 
        1.48        11.74         3.55         8.35         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-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 
        4.96        26.79         3.12        14.60        17.72        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
       21.73        15.65        25.68        14.73        59.77        44.02 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       15.22        10.95        12.69        14.93         3.22         2.04 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       16.50        26.33        15.95         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       23.11         7.10         1.15        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 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-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       17.59        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        6.41         8.61         3.39        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16         4.08        24.23         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       22.49        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-A7UX 
        9.73         7.13         9.37         9.40         8.88        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        18.08        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        14.40         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-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        0.66         4.77        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-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 
       22.78        25.18         3.72        12.59        19.23         0.85 
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-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.08        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        6.28        11.77         4.73        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.71        82.59        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16        90.58         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-02-0055 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-02-0071 TCGA-02-0074 
        6.02        19.73        26.43        28.70         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        23.18        92.65        99.98        15.65        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-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 
       47.61         6.94         3.98        33.67        12.95        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 
       26.70        24.23        11.90         0.20         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
        9.44        11.80        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.29        13.12         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        0.39         7.66        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        9.01         0.26         4.70         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       46.88         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
        7.17        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       26.79        11.84        15.32        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93        12.56        30.64         5.95         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 
        0.43        31.50         7.79         5.39       120.56        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 
        9.80        29.23        65.33         1.28        17.95        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97         0.72        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 
       26.66        12.13         3.65        20.38        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        18.48        23.51         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
        5.82         7.59        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.98         4.14         2.24        11.24         1.35         5.39 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-1446 TCGA-15-1449 
        2.04        28.93        19.30         0.79        19.10        13.28 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
       26.07        16.37        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
        9.07         5.95        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 
       23.44        11.01        13.64         5.16        22.68         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        7.36        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                        87.06                        127.59 
  DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE 
                        14.07                         12.10 
[1] "0.1 - 87.1 (14.1)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1"  
D43V2, continuous
D43V3, binary
                               cls
clus                              0   1
  DEL PEAK 19(9Q34.2) MUTATED    30  49
  DEL PEAK 19(9Q34.2) WILD-TYPE 195 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9Q34.2) MUTATED     30   49
  DEL PEAK 19(9Q34.2) WILD-TYPE  195  299
        clus
vv       DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE
  FEMALE                          30                           195
  MALE                            49                           299
[1] 2 2
[1] FALSE
D43V4, binary
                               cls
clus                              0   1
  DEL PEAK 19(9Q34.2) MUTATED     8  65
  DEL PEAK 19(9Q34.2) WILD-TYPE  66 410
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9Q34.2) MUTATED      8   65
  DEL PEAK 19(9Q34.2) WILD-TYPE   66  410
     clus
vv    DEL PEAK 19(9Q34.2) MUTATED DEL PEAK 19(9Q34.2) WILD-TYPE
  NO                            8                            66
  YES                          65                           410
[1] 2 2
[1] FALSE
D43V5, continuous
                               vv
clus                            GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 19(9Q34.2) MUTATED                               8
  DEL PEAK 19(9Q34.2) WILD-TYPE                            22
                               vv
clus                            TREATED PRIMARY GBM
  DEL PEAK 19(9Q34.2) MUTATED                     3
  DEL PEAK 19(9Q34.2) WILD-TYPE                  15
                               vv
clus                            UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 19(9Q34.2) MUTATED                                68
  DEL PEAK 19(9Q34.2) WILD-TYPE                             457
D43V6, multiclass
                                 clus
vv                                DEL PEAK 19(9Q34.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             8
  TREATED PRIMARY GBM                                       3
  UNTREATED PRIMARY (DE NOVO) GBM                          68
                                 clus
vv                                DEL PEAK 19(9Q34.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              22
  TREATED PRIMARY GBM                                        15
  UNTREATED PRIMARY (DE NOVO) GBM                           457
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9Q34.2) MUTATED       1                        11    66
  DEL PEAK 19(9Q34.2) WILD-TYPE    12                        39   421
D43V7, multiclass
                           clus
vv                          DEL PEAK 19(9Q34.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              66
                           clus
vv                          DEL PEAK 19(9Q34.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            39
  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"
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(9Q34.2) MUTATED     0  71
  DEL PEAK 19(9Q34.2) WILD-TYPE  12 404
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(9Q34.2) MUTATED      0   71
  DEL PEAK 19(9Q34.2) WILD-TYPE   12  404
                        clus
vv                       DEL PEAK 19(9Q34.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK 19(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           404
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 20(10P15.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(10P15.3) MUTATED    71 393
  DEL PEAK 20(10P15.3) WILD-TYPE  26  80
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           464                            106 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           393                             80 
$`DEL PEAK 20(10P15.3) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 
        8.32        12.85         4.77         1.55         4.77        26.79 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 
        1.87         2.56        14.60        15.35        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       13.78         3.25         2.89        16.50        26.33        15.95 
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-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        7.96        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 
        9.14        21.24        13.97        14.27         3.39         3.65 
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        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        9.73         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       30.05        14.04        24.76        18.08        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-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        4.77        15.39         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-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       15.02        15.95        22.78        25.18         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        9.53         0.99         4.44        11.84         0.20        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       23.90        34.45        18.64         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 
        7.63         4.73        18.35        10.59        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       20.12        53.10        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       10.72        10.52        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-02-0068 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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       12.62        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       11.67        17.65        92.65        15.65        48.95        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-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73        10.62        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       25.12        14.50        10.55        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        16.80        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.15        20.38         6.94        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       26.70        24.23        11.90         0.20        10.29        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
        2.33        17.79         8.61        19.46        46.59        12.33 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82         9.44         3.42        56.91 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
        4.04         4.18        20.25        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       48.69        10.82         0.26        72.36         4.70        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
       15.32        13.61         1.08        12.49        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 
       30.64         5.95        16.64         5.98         4.37         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
      120.56         7.36        22.68        37.84         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16         9.80         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       12.23        14.93        18.02        15.35        13.97        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 
        4.27        42.15        11.08        10.75         4.80        18.41 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1091 
       23.51        27.78        38.76         8.94        20.58        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        2.24        11.24         1.35         5.39         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       19.30         0.79        13.78        19.10        13.28         3.91 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 
       12.95         4.64        14.86         5.49         1.58         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`DEL PEAK 20(10P15.3) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5416 TCGA-06-5858 TCGA-06-6701 TCGA-06-A6S0 
        1.48        15.32         6.71         6.15         4.96         3.12 
TCGA-06-A7TL TCGA-12-1092 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-3477 
       17.72        21.73         1.12        40.96         6.67         3.78 
TCGA-14-4157 TCGA-16-1460 TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 
        3.42         6.41         8.61        25.38        12.66         0.13 
TCGA-19-2619 TCGA-19-5958 TCGA-26-1443 TCGA-27-1838 TCGA-27-2521 TCGA-27-2526 
        9.67        14.07         7.13        11.51        16.77         2.86 
TCGA-28-1755 TCGA-28-1756 TCGA-32-1973 TCGA-32-1991 TCGA-32-2632 TCGA-32-4208 
        1.55         2.83        21.07        16.93         8.84        21.14 
TCGA-41-5651 TCGA-76-6664 TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       15.12        36.20        11.77        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 
       82.59        20.61        42.74        24.59        90.58        14.73 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 
        8.35         6.02        28.70        89.72        22.72        57.76 
TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 
       65.00        23.18        99.98        16.54        17.72        14.47 
TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0125 
        7.33        10.59        12.39        47.11        12.92        47.61 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 
        3.98        22.72        33.67         2.20        20.09        10.09 
TCGA-06-0154 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 
       13.94        11.80        10.65        91.00        88.14         3.65 
TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0412 TCGA-06-0413 TCGA-06-1086 
        0.53        20.42         9.01         9.57         3.16         6.84 
TCGA-06-1805 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-08-0344 
       33.90         4.93         0.43        31.50         7.79       115.86 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       29.23        65.33         0.72        19.59        58.68        19.33 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 TCGA-12-1088 TCGA-12-1089 
        7.27        15.98         7.56        43.23       127.59         5.82 
TCGA-12-1090 TCGA-12-1099 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 
        7.59         4.14        50.53        53.19        26.07        16.37 
TCGA-26-1442 TCGA-26-6173 TCGA-28-5218 TCGA-32-2616 
       31.33         7.92         5.16         7.36 

  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                        12.115                         14.600 
[1] "0.1 - 120.6 (12.1)" "0.1 - 127.6 (14.6)"
[1] "hr=" "1.7"
D44V2, continuous
D44V3, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED   176 290
  DEL PEAK 20(10P15.3) WILD-TYPE  49  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED    176  290
  DEL PEAK 20(10P15.3) WILD-TYPE   49   58
        clus
vv       DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  FEMALE                          176                             49
  MALE                            290                             58
[1] 2 2
[1] FALSE
D44V4, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    62 383
  DEL PEAK 20(10P15.3) WILD-TYPE  12  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     62  383
  DEL PEAK 20(10P15.3) WILD-TYPE   12   92
     clus
vv    DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  NO                            62                             12
  YES                          383                             92
[1] 2 2
[1] FALSE
D44V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 20(10P15.3) MUTATED                              22
  DEL PEAK 20(10P15.3) WILD-TYPE                             8
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 20(10P15.3) MUTATED                    11
  DEL PEAK 20(10P15.3) WILD-TYPE                   7
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 20(10P15.3) MUTATED                               433
  DEL PEAK 20(10P15.3) WILD-TYPE                              92
D44V6, multiclass
                                 clus
vv                                DEL PEAK 20(10P15.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             22
  TREATED PRIMARY GBM                                       11
  UNTREATED PRIMARY (DE NOVO) GBM                          433
                                 clus
vv                                DEL PEAK 20(10P15.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                8
  TREATED PRIMARY GBM                                          7
  UNTREATED PRIMARY (DE NOVO) GBM                             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P15.3) MUTATED       8                        40   398
  DEL PEAK 20(10P15.3) WILD-TYPE     5                        10    89
D44V7, multiclass
                           clus
vv                          DEL PEAK 20(10P15.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           40
  WHITE                                              398
                           clus
vv                          DEL PEAK 20(10P15.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     8 381
  DEL PEAK 20(10P15.3) WILD-TYPE   4  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      8  381
  DEL PEAK 20(10P15.3) WILD-TYPE    4   94
                        clus
vv                       DEL PEAK 20(10P15.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          381
                        clus
vv                       DEL PEAK 20(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             94
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 21(10P13) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 21(10P13) MUTATED    70 395
  DEL PEAK 21(10P13) WILD-TYPE  27  78
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                         465                          105 
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                         395                           78 
$`DEL PEAK 21(10P13) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
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-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        2.56        14.60        15.35        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
       15.12        11.97         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       30.18         0.92        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       17.59        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 
       21.24        13.97        14.27         3.39         3.65         7.17 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        3.25         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96        17.79        28.54        10.03        13.87         9.73 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 
       16.60         9.86        24.23        40.54        21.30        14.04 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       24.76        18.08        16.77        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-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        8.48         1.22         0.13         0.66         6.74         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44        11.84         0.20        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 
       18.64         5.92         6.28        20.55         7.63         4.73 
TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       18.35        10.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       53.10        42.74        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       10.72        10.52        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-02-0068 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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       12.62        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       11.67        17.65        92.65        15.65        48.95        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-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73        10.62        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       25.12        14.50        10.55        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        16.80        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 
        6.15        20.38         6.94        22.72        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       11.74         2.33        17.79         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0184 
        4.47         3.22         4.04         4.18        20.25        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 
       13.64        13.32        48.69        10.82         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 
        4.04        26.79        11.84        15.32        13.61         1.08 
TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       12.49        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 
        5.98         4.37         5.39       120.56         7.36        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        9.80         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97        12.56         4.27        42.15        11.08 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       10.75         4.80        18.41        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       53.85         7.63         9.73        14.93        14.86        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       20.58        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       14.53         3.98         2.24        11.24         1.35         5.39 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 
        2.04        28.93        19.30         0.79        13.78        19.10 
TCGA-15-1449 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       13.28        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        5.95        12.95         4.64        14.86         5.49         1.58 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

$`DEL PEAK 21(10P13) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5416 TCGA-06-5858 TCGA-06-6701 TCGA-06-A5U0 
        1.48        15.32         6.71         6.15         4.96        26.79 
TCGA-06-A6S0 TCGA-06-A7TL TCGA-12-1092 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 
        3.12        17.72        21.73         1.12        40.96         6.67 
TCGA-14-3477 TCGA-14-4157 TCGA-16-1460 TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 
        3.78         3.42         6.41         8.61        25.38        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-5958 TCGA-26-1443 TCGA-27-1836 TCGA-27-1838 
        0.13         9.67        14.07         7.13        30.05        11.51 
TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-32-1973 TCGA-32-1976 TCGA-32-1991 
        2.86         1.55         2.83        21.07         0.49        16.93 
TCGA-32-2632 TCGA-32-4208 TCGA-41-5651 TCGA-76-6664 TCGA-02-0001 TCGA-02-0007 
        8.84        21.14        15.12        36.20        11.77        23.18 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 
       35.41        20.71        82.59        24.59        90.58        14.73 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 
        8.35         6.02        28.70        89.72        22.72        57.76 
TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 
       65.00        23.18        99.98        16.54        17.72        14.47 
TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0125 
        7.33        10.59        12.39        47.11        12.92        47.61 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 
        3.98        33.67         2.20        20.09        10.09        11.80 
TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0213 TCGA-06-0240 
       10.65        91.00        88.14         3.65         0.53        20.42 
TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1805 TCGA-06-2559 TCGA-06-2569 
        9.01         3.16         6.84        33.90         4.93         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 
       31.50         7.79       115.86        29.23        65.33         0.72 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 
       19.59        58.68        19.33         7.27        15.98         7.56 
TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1099 
       43.23        91.76       127.59         5.82         7.59         4.14 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-26-1442 
       50.53        53.19         3.91        26.07        16.37        31.33 
TCGA-26-6173 TCGA-28-5218 TCGA-32-2616 
        7.92         5.16         7.36 

  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                        0.10                         0.13 
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                      120.56                       127.59 
  DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE 
                       12.16                        14.47 
[1] "0.1 - 120.6 (12.2)" "0.1 - 127.6 (14.5)"
[1] "hr=" "1.8"
D45V2, continuous
D45V3, binary
                              cls
clus                             0   1
  DEL PEAK 21(10P13) MUTATED   174 293
  DEL PEAK 21(10P13) WILD-TYPE  51  55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(10P13) MUTATED    174  293
  DEL PEAK 21(10P13) WILD-TYPE   51   55
        clus
vv       DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE
  FEMALE                        174                           51
  MALE                          293                           55
[1] 2 2
[1] FALSE
D45V4, binary
                              cls
clus                             0   1
  DEL PEAK 21(10P13) MUTATED    60 386
  DEL PEAK 21(10P13) WILD-TYPE  14  89
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(10P13) MUTATED     60  386
  DEL PEAK 21(10P13) WILD-TYPE   14   89
     clus
vv    DEL PEAK 21(10P13) MUTATED DEL PEAK 21(10P13) WILD-TYPE
  NO                          60                           14
  YES                        386                           89
[1] 2 2
[1] FALSE
D45V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 21(10P13) MUTATED                              21
  DEL PEAK 21(10P13) WILD-TYPE                             9
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 21(10P13) MUTATED                    11
  DEL PEAK 21(10P13) WILD-TYPE                   7
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 21(10P13) MUTATED                               435
  DEL PEAK 21(10P13) WILD-TYPE                              90
D45V6, multiclass
                                 clus
vv                                DEL PEAK 21(10P13) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           21
  TREATED PRIMARY GBM                                     11
  UNTREATED PRIMARY (DE NOVO) GBM                        435
                                 clus
vv                                DEL PEAK 21(10P13) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                              9
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                           90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10P13) MUTATED       8                        39   400
  DEL PEAK 21(10P13) WILD-TYPE     5                        11    87
D45V7, multiclass
                           clus
vv                          DEL PEAK 21(10P13) MUTATED
  ASIAN                                              8
  BLACK OR AFRICAN AMERICAN                         39
  WHITE                                            400
                           clus
vv                          DEL PEAK 21(10P13) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                              cls
clus                             0   1
  DEL PEAK 21(10P13) MUTATED     8 382
  DEL PEAK 21(10P13) WILD-TYPE   4  93
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(10P13) MUTATED      8  382
  DEL PEAK 21(10P13) WILD-TYPE    4   93
                        clus
vv                       DEL PEAK 21(10P13) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                        382
                        clus
vv                       DEL PEAK 21(10P13) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           93
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 22(10P11.23) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(10P11.23) MUTATED    71 399
  DEL PEAK 22(10P11.23) WILD-TYPE  26  74
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                            470                             100 
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                            399                              74 
$`DEL PEAK 22(10P11.23) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 
       12.85         4.77         1.55         4.77         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        2.56        14.60        15.35        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
       15.12        11.97         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         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-16-0848 
        7.63         5.88         7.17        17.49         7.96        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 
       13.97         8.61        14.27         3.39         3.65         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        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        9.73         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 
       30.05        14.04        24.76        18.08        16.77         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-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        4.77        15.39         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-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       15.02        15.95        22.78        25.18         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-OX-A56R TCGA-RR-A6KA 
        5.03        23.90        34.45        18.64         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 
       20.55         7.63         4.73        18.35        10.59        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       77.65        20.12        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       10.72        10.52        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-02-0068 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-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       12.62        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       11.67        17.65        92.65        15.65        48.95        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-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73        10.62        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       25.12        14.50        10.55        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        3.35        16.80        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 
        0.20        10.29        11.74         2.33        17.79         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44         3.42        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
        3.29        13.12         4.47         3.22         4.04         4.18 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 
        0.39         7.66         8.42         7.40        11.84        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
       24.16         0.72        19.82        13.64        13.32        48.69 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 
       10.82         0.26        72.36         4.70         9.57        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
       15.32        13.61         1.08        12.49        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 
       30.64         5.95        16.64         5.98         4.37         5.39 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
      120.56        22.68        37.84         4.18         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       25.71        12.16         9.80         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       14.93        18.02        15.35        13.97        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       42.15        11.08        19.33        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       18.41         7.56        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        14.86        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 
        3.98         2.24        11.24         1.35         5.39         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
       28.93        19.30         0.79        13.78        19.10        13.28 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 
       12.95         4.64        14.86         5.49         1.58         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

$`DEL PEAK 22(10P11.23) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5416 TCGA-06-5858 TCGA-06-6695 TCGA-06-6701 
        1.48        15.32         6.71         6.15         8.32         4.96 
TCGA-06-A5U0 TCGA-06-A7TL TCGA-12-1092 TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 
       26.79        17.72        21.73         1.12        40.96         6.67 
TCGA-14-1821 TCGA-14-3477 TCGA-14-4157 TCGA-16-1460 TCGA-19-1390 TCGA-19-1787 
       17.79         3.78         3.42         6.41        25.38        12.66 
TCGA-19-1791 TCGA-19-5956 TCGA-26-1443 TCGA-27-1838 TCGA-27-2523 TCGA-27-2526 
        0.13        22.49         7.13        11.51        16.08         2.86 
TCGA-28-1755 TCGA-28-1756 TCGA-32-1973 TCGA-32-1991 TCGA-32-2632 TCGA-32-4208 
        1.55         2.83        21.07        16.93         8.84        21.14 
TCGA-76-6664 TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       36.20        11.77        23.18        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 
       20.61        53.10        42.74        24.59        90.58        14.73 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 
        8.35         6.02        28.70        89.72        22.72        57.76 
TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 
       65.00        23.18        99.98        16.54        17.72        14.47 
TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0129 
        7.33        10.59        12.39        47.11        12.92        33.67 
TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 
        2.20        20.09        10.09        11.80        10.65        91.00 
TCGA-06-0178 TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 
       88.14         0.53        20.42         9.01         3.16         6.84 
TCGA-06-1805 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 
       33.90         4.93         0.43        31.50         7.79         7.36 
TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 
      115.86        29.23        65.33         0.72        19.59        58.68 
TCGA-08-0524 TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
        7.27        43.23        91.76       127.59         5.82         7.59 
TCGA-12-1099 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
        4.14        50.53        53.19         3.91        26.07        16.37 
TCGA-26-1442 TCGA-26-6173 TCGA-28-5218 TCGA-32-2616 
       31.33         7.92         5.16         7.36 

  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                           0.10                            0.13 
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                         120.56                          127.59 
  DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE 
                         12.035                          16.225 
[1] "0.1 - 120.6 (12.0)" "0.1 - 127.6 (16.2)"
[1] "hr=" "1.9"
D46V2, continuous
D46V3, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10P11.23) MUTATED   178 294
  DEL PEAK 22(10P11.23) WILD-TYPE  47  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10P11.23) MUTATED    178  294
  DEL PEAK 22(10P11.23) WILD-TYPE   47   54
        clus
vv       DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE
  FEMALE                           178                              47
  MALE                             294                              54
[1] 2 2
[1] FALSE
D46V4, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10P11.23) MUTATED    62 390
  DEL PEAK 22(10P11.23) WILD-TYPE  12  85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10P11.23) MUTATED     62  390
  DEL PEAK 22(10P11.23) WILD-TYPE   12   85
     clus
vv    DEL PEAK 22(10P11.23) MUTATED DEL PEAK 22(10P11.23) WILD-TYPE
  NO                             62                              12
  YES                           390                              85
[1] 2 2
[1] FALSE
D46V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 22(10P11.23) MUTATED                              22
  DEL PEAK 22(10P11.23) WILD-TYPE                             8
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 22(10P11.23) MUTATED                    10
  DEL PEAK 22(10P11.23) WILD-TYPE                   8
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 22(10P11.23) MUTATED                               440
  DEL PEAK 22(10P11.23) WILD-TYPE                              85
D46V6, multiclass
                                 clus
vv                                DEL PEAK 22(10P11.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              22
  TREATED PRIMARY GBM                                        10
  UNTREATED PRIMARY (DE NOVO) GBM                           440
                                 clus
vv                                DEL PEAK 22(10P11.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 8
  TREATED PRIMARY GBM                                           8
  UNTREATED PRIMARY (DE NOVO) GBM                              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P11.23) MUTATED       8                        42   401
  DEL PEAK 22(10P11.23) WILD-TYPE     5                         8    86
D46V7, multiclass
                           clus
vv                          DEL PEAK 22(10P11.23) MUTATED
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            42
  WHITE                                               401
                           clus
vv                          DEL PEAK 22(10P11.23) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                               8
  WHITE                                                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10P11.23) MUTATED     8 388
  DEL PEAK 22(10P11.23) WILD-TYPE   4  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10P11.23) MUTATED      8  388
  DEL PEAK 22(10P11.23) WILD-TYPE    4   87
                        clus
vv                       DEL PEAK 22(10P11.23) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           388
                        clus
vv                       DEL PEAK 22(10P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              87
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 23(10Q11.23) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 23(10Q11.23) MUTATED    74 409
  DEL PEAK 23(10Q11.23) WILD-TYPE  23  64
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                            483                              87 
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                            409                              64 
$`DEL PEAK 23(10Q11.23) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 
        8.32        12.85         4.77         1.55         4.77         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 
        3.12         2.56        14.60        15.35        21.73        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       23.05        13.78         3.25         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
       15.95         1.38         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 
        7.10         1.15        30.18         0.92        12.43         0.99 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        7.96        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 
       21.24        13.97         8.61        14.27         3.39         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        7.17         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03        13.87         9.73         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.77         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         0.13         0.66         6.74 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        4.77        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        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        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 
       36.20         5.92        20.55         7.63         4.73        18.35 
TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       23.18        10.59        20.71        87.06        77.65        20.12 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
       18.31         6.87         3.22        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        2.50        19.86         9.57        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 
        5.49        10.19        20.84        27.25        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 
       51.32         8.81        16.96         3.48        27.02        11.67 
TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 
       17.65        92.65        15.65        48.95        16.93        10.75 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62        15.91        25.71         4.37        25.12 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
       20.38        47.61         6.94         3.98        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
       10.29        11.74         2.33        17.79         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         3.42        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.12         4.47         3.22         4.04         4.18        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
       24.16         0.72        19.82        13.64        13.32        48.69 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 
       10.82         0.26        72.36         4.70         9.57        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       15.32        13.61         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        5.39       120.56        22.68        37.84         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16         9.80         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
       12.56         4.27        42.15        11.08        19.33        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        4.80        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        26.66         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       53.85         7.63         9.73        14.93        14.86        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       20.58        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 
       14.53         2.24        11.24         1.35         5.39         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       28.93        19.30         0.79        13.78        50.53        19.10 
TCGA-15-1449 TCGA-16-0850 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       13.28        16.37        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        5.95         4.64        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

$`DEL PEAK 23(10Q11.23) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5416 TCGA-06-5858 TCGA-06-6701 TCGA-06-A5U0 
        1.48        15.32         6.71         6.15         4.96        26.79 
TCGA-06-A7TL TCGA-14-1396 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 TCGA-14-3477 
       17.72         1.12        40.96         6.67        17.79         3.78 
TCGA-14-4157 TCGA-16-1060 TCGA-16-1460 TCGA-19-1390 TCGA-19-1787 TCGA-26-1443 
        3.42         9.14         6.41        25.38        12.66         7.13 
TCGA-27-2523 TCGA-28-1756 TCGA-32-1973 TCGA-32-4208 TCGA-RR-A6KA TCGA-02-0001 
       16.08         2.83        21.07        21.14         6.28        11.77 
TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       35.41        82.59        20.61        53.10        42.74        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-02-0087 TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 
       57.76        65.00        23.18        99.98        16.54        17.72 
TCGA-02-0271 TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 
       14.47         7.33        10.59        12.39        47.11        12.92 
TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 
       33.67         2.20        20.09        10.09        11.80        10.65 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 
       91.00        88.14        20.42         9.01         3.16         6.84 
TCGA-06-1805 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 TCGA-08-0344 
       33.90         0.43        31.50         7.79         7.36       115.86 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 TCGA-12-0691 
       29.23        65.33        19.59        58.68         7.27        12.13 
TCGA-12-0773 TCGA-12-0818 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1098 
       43.23        91.76       127.59         5.82         7.59         3.98 
TCGA-12-1099 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-19-0955 TCGA-19-1388 
        4.14        53.19         3.91        26.07        11.77        12.95 
TCGA-26-1442 TCGA-28-5218 TCGA-32-2616 
       31.33         5.16         7.36 

  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                           0.10                            0.43 
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                         120.56                          127.59 
  DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE 
                          12.10                           14.73 
[1] "0.1 - 120.6 (12.1)" "0.4 - 127.6 (14.7)"
[1] "hr=" "2"  
D47V2, continuous
D47V3, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q11.23) MUTATED   186 299
  DEL PEAK 23(10Q11.23) WILD-TYPE  39  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q11.23) MUTATED    186  299
  DEL PEAK 23(10Q11.23) WILD-TYPE   39   49
        clus
vv       DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE
  FEMALE                           186                              39
  MALE                             299                              49
[1] 2 2
[1] FALSE
D47V4, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q11.23) MUTATED    66 398
  DEL PEAK 23(10Q11.23) WILD-TYPE   8  77
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q11.23) MUTATED     66  398
  DEL PEAK 23(10Q11.23) WILD-TYPE    8   77
     clus
vv    DEL PEAK 23(10Q11.23) MUTATED DEL PEAK 23(10Q11.23) WILD-TYPE
  NO                             66                               8
  YES                           398                              77
[1] 2 2
[1] FALSE
D47V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 23(10Q11.23) MUTATED                              22
  DEL PEAK 23(10Q11.23) WILD-TYPE                             8
                                 vv
clus                              TREATED PRIMARY GBM
  DEL PEAK 23(10Q11.23) MUTATED                    12
  DEL PEAK 23(10Q11.23) WILD-TYPE                   6
                                 vv
clus                              UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 23(10Q11.23) MUTATED                               451
  DEL PEAK 23(10Q11.23) WILD-TYPE                              74
D47V6, multiclass
                                 clus
vv                                DEL PEAK 23(10Q11.23) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              22
  TREATED PRIMARY GBM                                        12
  UNTREATED PRIMARY (DE NOVO) GBM                           451
                                 clus
vv                                DEL PEAK 23(10Q11.23) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 8
  TREATED PRIMARY GBM                                           6
  UNTREATED PRIMARY (DE NOVO) GBM                              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10Q11.23) MUTATED       7                        41   416
  DEL PEAK 23(10Q11.23) WILD-TYPE     6                         9    71
D47V7, multiclass
                           clus
vv                          DEL PEAK 23(10Q11.23) MUTATED
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            41
  WHITE                                               416
                           clus
vv                          DEL PEAK 23(10Q11.23) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                  71
[1] 3 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 23(10Q11.23) MUTATED     9 399
  DEL PEAK 23(10Q11.23) WILD-TYPE   3  76
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q11.23) MUTATED      9  399
  DEL PEAK 23(10Q11.23) WILD-TYPE    3   76
                        clus
vv                       DEL PEAK 23(10Q11.23) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           399
                        clus
vv                       DEL PEAK 23(10Q11.23) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              76
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED    80 427
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  46
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            507                              63 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            427                              46 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 
        8.32        12.85         4.77         1.55         4.77        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 
        1.87         3.12         2.56        14.60        17.72        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       21.73        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
       16.50        26.33        15.95         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-16-0848 TCGA-16-1045 
        7.17        17.49         7.96         3.78        17.59        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
        8.61        14.27         3.39         3.65         7.17         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        9.73         7.13         9.37         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        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-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-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
       11.84         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
        8.35        20.98         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 
       36.20         5.92         6.28        20.55         7.63         4.73 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       18.35        23.18        10.59        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 
       20.61        87.06        77.65        20.12        24.59        12.16 
TCGA-02-0033 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-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        6.87         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
        9.57        19.73        26.43        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       20.84        27.25        22.72        12.62        51.32         8.81 
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-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        92.65        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-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73        10.62        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       25.12        10.59        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 
       24.23        11.90         0.20        10.29        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        4.47         3.22         4.04         4.18        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.64        13.32        48.69        10.82 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 
        0.26        72.36         4.70         9.57        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 
       12.56         5.95        16.64         5.98         4.37         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
      120.56         7.36        22.68        37.84         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16         9.80         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
       12.56         4.27        42.15        11.08        19.33        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        4.80        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85         7.63         9.73        14.93        14.86 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 
        8.94        20.58       127.59         5.82        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 
       12.23        15.85         9.11        14.53         4.14         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
       11.24         1.35         5.39         2.04        28.93        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0850 
        0.79        13.78        50.53        19.10        13.28        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       12.95         4.64        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

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

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.10                            0.43 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         127.59                          115.86 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          12.16                           14.07 
[1] "0.1 - 127.6 (12.2)" "0.4 - 115.9 (14.1)"
[1] "hr=" "1.9"
D48V2, continuous
D48V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   199 311
  DEL PEAK 24(10Q23.31) WILD-TYPE  26  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    199  311
  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                           199                              26
  MALE                             311                              37
[1] 2 2
[1] FALSE
D48V4, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    67 421
  DEL PEAK 24(10Q23.31) WILD-TYPE   7  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     67  421
  DEL PEAK 24(10Q23.31) WILD-TYPE    7   54
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                             67                               7
  YES                           421                              54
[1] 2 2
[1] FALSE
D48V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 24(10Q23.31) MUTATED                              25
  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
D48V6, multiclass
                                 clus
vv                                DEL PEAK 24(10Q23.31) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              25
  TREATED PRIMARY GBM                                        13
  UNTREATED PRIMARY (DE NOVO) GBM                           472
                                 clus
vv                                DEL PEAK 24(10Q23.31) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                 5
  TREATED PRIMARY GBM                                           5
  UNTREATED PRIMARY (DE NOVO) GBM                              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED      10                        45   434
  DEL PEAK 24(10Q23.31) WILD-TYPE     3                         5    53
D48V7, multiclass
                           clus
vv                          DEL PEAK 24(10Q23.31) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            45
  WHITE                                               434
                           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"
D48V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    10 422
  DEL PEAK 24(10Q23.31) WILD-TYPE   2  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     10  422
  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                           422
                        clus
vv                       DEL PEAK 24(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              53
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 25(10Q26.3) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q26.3) MUTATED    82 426
  DEL PEAK 25(10Q26.3) WILD-TYPE  15  47
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           508                             62 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                           426                             47 
$`DEL PEAK 25(10Q26.3) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        3.98        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 
        8.32        12.85         4.77         1.55         4.77        26.79 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 
        1.87         3.12         2.56        14.60        17.72        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       21.73        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
        0.95         6.21        23.05        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
       16.50        26.33        15.95         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-14-4157 TCGA-16-0848 
        7.17        17.49         7.96         3.78         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 
       13.97         8.61        14.27         3.39        25.38         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        7.17         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 
        9.40         8.88        18.97        19.33         5.06         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        18.08        16.77         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        8.48         1.22         0.13         0.66         6.74         4.77 
TCGA-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-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02        15.95        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 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 
       36.85        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        23.90        34.45        18.64 
TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 
       36.20         5.92         6.28        20.55         7.63         4.73 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       18.35        23.18        10.59        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
       18.31         6.87         3.22        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
        2.50        19.86         8.35         9.57        19.73        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 
       25.05         5.49        10.19        20.84        27.25        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       12.62        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       65.00        11.67        17.65        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        10.75         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 
       15.95        12.23         9.90         7.73        10.62        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.71         4.37        25.12        14.50        10.55        47.11 
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-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44         3.42        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
        3.29        13.12         4.47         3.22         4.04         4.18 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         0.26        72.36         4.70         9.57 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
       16.57        20.78        26.76        23.93         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 
        5.98         4.37         5.39       120.56        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 
       58.68        19.33        10.75         4.80        15.98        18.41 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        7.56        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        9.73        14.93        14.86        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82        33.21        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       14.53         3.98         2.24        11.24         1.35         5.39 
TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        2.04        19.30         0.79        13.78        50.53        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       13.28         3.91        16.37        11.77        21.90         0.66 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        9.07         5.95         4.64        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
       13.64        22.68        12.76         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

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

  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                          0.10                           0.43 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                        127.59                          99.98 
  DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE 
                         12.23                          12.79 
[1] "0.1 - 127.6 (12.2)" "0.4 - 100.0 (12.8)"
[1] "hr=" "1.6"
D49V2, continuous
D49V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED   199 312
  DEL PEAK 25(10Q26.3) WILD-TYPE  26  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED    199  312
  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                          199                             26
  MALE                            312                             36
[1] 2 2
[1] FALSE
D49V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED    69 422
  DEL PEAK 25(10Q26.3) WILD-TYPE   5  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     69  422
  DEL PEAK 25(10Q26.3) WILD-TYPE    5   53
     clus
vv    DEL PEAK 25(10Q26.3) MUTATED DEL PEAK 25(10Q26.3) WILD-TYPE
  NO                            69                              5
  YES                          422                             53
[1] 2 2
[1] FALSE
D49V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 25(10Q26.3) MUTATED                              25
  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
D49V6, multiclass
                                 clus
vv                                DEL PEAK 25(10Q26.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             25
  TREATED PRIMARY GBM                                       14
  UNTREATED PRIMARY (DE NOVO) GBM                          472
                                 clus
vv                                DEL PEAK 25(10Q26.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                5
  TREATED PRIMARY GBM                                          4
  UNTREATED PRIMARY (DE NOVO) GBM                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q26.3) MUTATED       9                        46   435
  DEL PEAK 25(10Q26.3) WILD-TYPE     4                         4    52
D49V7, multiclass
                           clus
vv                          DEL PEAK 25(10Q26.3) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                           46
  WHITE                                              435
                           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"
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q26.3) MUTATED    10 423
  DEL PEAK 25(10Q26.3) WILD-TYPE   2  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q26.3) MUTATED     10  423
  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                          423
                        clus
vv                       DEL PEAK 25(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             52
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 26(11P15.5) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11P15.5) MUTATED    22 110
  DEL PEAK 26(11P15.5) WILD-TYPE  75 363
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           132                            438 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           110                            363 
$`DEL PEAK 26(11P15.5) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5856 TCGA-06-A7TK TCGA-06-A7TL 
        3.98        15.32        11.74         3.75        14.60        17.72 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0865 
        6.77        44.02        14.53        11.97         6.21        16.50 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 
        1.15        30.18        12.43         0.99        17.79        17.85 
TCGA-14-3477 TCGA-16-0848 TCGA-16-1045 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 
        3.78        17.59        29.03        25.38         3.65         7.53 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 
       16.80        14.96        17.79        13.87         5.06        16.77 
TCGA-28-1756 TCGA-28-2502 TCGA-28-2509 TCGA-32-1973 TCGA-32-1976 TCGA-32-2615 
        2.83         0.66         4.77        21.07         0.49        15.95 
TCGA-32-2632 TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 
        8.84        21.14         3.72        10.85        11.84         7.50 
TCGA-76-4934 TCGA-76-6286 TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
        2.53        20.98        35.41        82.59        20.61        87.06 
TCGA-02-0024 TCGA-02-0033 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       53.10         2.83        14.73         3.22        15.09        12.59 
TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 
        2.50         8.35         9.57        28.70        10.19        20.84 
TCGA-02-0084 TCGA-02-0086 TCGA-02-0087 TCGA-02-0099 TCGA-02-0104 TCGA-02-0113 
       12.62         8.81        57.76         3.48        65.00        92.65 
TCGA-02-0114 TCGA-02-0281 TCGA-02-0332 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 
       99.98         3.98        25.71         3.35        16.80        15.32 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0146 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 
       22.72        33.67        20.09         9.44         5.85         3.22 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0192 TCGA-06-0197 TCGA-06-0213 TCGA-06-0216 
        4.18        69.90        38.96         5.56         0.53        24.16 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
       19.82        13.32        72.36         4.70        35.11         2.10 
TCGA-06-0686 TCGA-06-1086 TCGA-06-1800 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
       14.20         6.84        26.79        13.61        33.90        12.49 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 
        0.43        31.50         7.79         7.36        37.84         4.18 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0353 TCGA-08-0355 TCGA-08-0375 TCGA-08-0380 
       12.16        65.33         8.42        24.56        12.23        14.93 
TCGA-08-0510 TCGA-08-0517 TCGA-12-0616 TCGA-12-0619 TCGA-12-0691 TCGA-12-0772 
        4.27        58.68        14.73        34.92        12.13        53.85 
TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 TCGA-14-0813 TCGA-14-0817 
       24.79        23.51        38.76         4.14         1.35         5.39 
TCGA-14-0867 TCGA-14-0871 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
        2.04        28.93        50.53        53.19        13.28         3.91 
TCGA-16-0850 TCGA-19-1387 TCGA-26-1442 TCGA-26-5133 TCGA-28-5216 TCGA-76-6280 
       16.37         5.95        31.33        14.86        13.64        11.38 

$`DEL PEAK 26(11P15.5) WILD-TYPE`
TCGA-06-6391 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        1.48         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-12-0615 TCGA-12-1092 
       26.79         1.87         3.12         2.56        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
       15.12         0.95        23.05        13.78         3.25         2.89 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       26.33        15.95         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       58.78        23.11         7.10         0.92        40.96         6.67 
TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
        1.97         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        3.42         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1786 
       13.97         6.41         8.61        14.27         3.39         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 
       22.49        14.07        28.54        10.03         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1831 
        9.37         9.40         8.88        18.97        19.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        18.08        16.08         7.59         2.86 
TCGA-27-2527 TCGA-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-28-2506 
        7.63         8.48         1.22         1.55         0.13         6.74 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
       22.78        25.18        12.59        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         8.22         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        17.06         8.35         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0011 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       20.71        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
       90.58        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0054 TCGA-02-0057 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
        6.87         6.54        19.86         6.02        19.73        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 
       25.05         5.49        27.25        89.72        22.72        51.32 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0115 
       16.96        27.02        11.67        17.65        23.18        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-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
       10.62         7.33        15.91         4.37        25.12        10.59 
TCGA-02-0339 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-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.21        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 
       20.38        47.61         6.94         3.98        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
        2.20        11.74         2.33        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
       10.82        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
        3.29        13.12         4.47         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       10.42         4.67         7.40         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 
        7.40        11.84        15.02         0.72        13.64        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       48.69        10.82         9.01         0.26         9.57         3.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 
       12.62         5.75         5.75         9.80        23.57        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-2557 TCGA-06-2559 
       23.93         4.04        11.84        15.32         1.08         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 
        4.37         5.39       120.56        22.68       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0354 
        8.42        25.71         9.80        29.23         1.28        17.95 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 
       31.10        37.58        22.29         3.39        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        7.56        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        43.23         7.63         9.73        14.93        14.86 
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-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 
       15.85         9.11        14.53         3.98         2.24        11.24 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-16-0849 TCGA-19-0955 
       19.30         0.79        13.78        19.10        26.07        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 
       21.90         0.66        10.75         9.07        12.95         4.64 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01         5.16        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        7.36         5.42         3.75         1.61        17.72        26.30 

  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                         99.98                         127.59 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                        14.035                         11.770 
[1] "0.4 - 100.0 (14.0)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    58  74
  DEL PEAK 26(11P15.5) WILD-TYPE 167 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     58   74
  DEL PEAK 26(11P15.5) WILD-TYPE  167  274
        clus
vv       DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  FEMALE                           58                            167
  MALE                             74                            274
[1] 2 2
[1] FALSE
D50V4, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    17 109
  DEL PEAK 26(11P15.5) WILD-TYPE  57 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     17  109
  DEL PEAK 26(11P15.5) WILD-TYPE   57  366
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  NO                            17                             57
  YES                          109                            366
[1] 2 2
[1] FALSE
D50V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 26(11P15.5) MUTATED                               7
  DEL PEAK 26(11P15.5) WILD-TYPE                            23
                                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                               119
  DEL PEAK 26(11P15.5) WILD-TYPE                             406
D50V6, multiclass
                                 clus
vv                                DEL PEAK 26(11P15.5) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              7
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          119
                                 clus
vv                                DEL PEAK 26(11P15.5) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               23
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            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"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11P15.5) MUTATED       3                        12   112
  DEL PEAK 26(11P15.5) WILD-TYPE    10                        38   375
D50V7, multiclass
                           clus
vv                          DEL PEAK 26(11P15.5) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              112
                           clus
vv                          DEL PEAK 26(11P15.5) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             38
  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"
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED     2 108
  DEL PEAK 26(11P15.5) WILD-TYPE  10 367
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      2  108
  DEL PEAK 26(11P15.5) WILD-TYPE   10  367
                        clus
vv                       DEL PEAK 26(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          108
                        clus
vv                       DEL PEAK 26(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            367
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 27(11P11.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11P11.2) MUTATED    16  88
  DEL PEAK 27(11P11.2) WILD-TYPE  81 385
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                           104                            466 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                            88                            385 
$`DEL PEAK 27(11P11.2) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5856 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1602 
        3.98        15.32         3.75        14.60        17.72         6.77 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0865 TCGA-14-1454 
       44.02        14.53        11.97         6.21        16.50        30.18 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 TCGA-14-3477 TCGA-16-1045 
       12.43         0.99        17.79        17.85         3.78        29.03 
TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5951 TCGA-19-5959 TCGA-19-5960 
       25.38         3.65         7.53         8.02        16.80        14.96 
TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-28-2509 TCGA-32-1976 TCGA-32-1986 
       13.87         5.06        16.77         4.77         0.49        12.69 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 
       15.95         8.84         3.72        10.85        11.84         7.50 
TCGA-76-4934 TCGA-76-6286 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0047 
        2.53        20.98        35.41        53.10         2.83        14.73 
TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 
        3.22        12.59         2.50         9.57        28.70        10.19 
TCGA-02-0075 TCGA-02-0084 TCGA-02-0086 TCGA-02-0087 TCGA-02-0113 TCGA-02-0114 
       20.84        12.62         8.81        57.76        92.65        99.98 
TCGA-02-0115 TCGA-02-0266 TCGA-02-0281 TCGA-02-0332 TCGA-02-0456 TCGA-02-2466 
       15.65        17.72         3.98        25.71         3.35        16.80 
TCGA-06-0128 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 
       22.72         9.44         5.85         3.22         4.18        69.90 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0197 TCGA-06-0216 TCGA-06-0238 TCGA-06-0409 
       44.58        38.96         5.56        24.16        13.32        72.36 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1086 
        4.70        35.11         2.10        14.20        46.19         6.84 
TCGA-06-1800 TCGA-06-1805 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 
       26.79        33.90        31.50         7.79         7.36        37.84 
TCGA-08-0353 TCGA-08-0510 TCGA-12-0616 TCGA-12-0619 TCGA-12-0670 TCGA-12-0772 
        8.42         4.27        14.73        34.92        25.97        53.85 
TCGA-12-0819 TCGA-12-0822 TCGA-12-0827 TCGA-12-1099 TCGA-14-0817 TCGA-14-0867 
       24.79        23.51        38.76         4.14         5.39         2.04 
TCGA-14-0871 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-19-1387 
       28.93        53.19        13.28         3.91        16.37         5.95 
TCGA-26-5133 TCGA-28-5216 
       14.86        13.64 

$`DEL PEAK 27(11P11.2) WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-12-0615 
        4.96        26.79         1.87         3.12         2.56        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
       21.73        15.65        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 
        2.04        15.12         0.95        23.05        13.78         3.25 
TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        2.89        26.33        15.95         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-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       40.96         6.67         1.97         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1047 TCGA-16-1055 
       17.49         7.96         3.42        17.59         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       14.27         3.39         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 
        7.00         7.04         6.64        17.19        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A60I TCGA-19-A6J5 
       12.10         1.78        22.49        14.07        17.79        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97        19.33        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-32-1970 
        1.55         2.83         0.13         0.66         6.74        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       21.07         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2634 
       14.86        16.93        12.23        20.78        15.02        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
       25.18        21.14        12.59        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         8.22         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        17.06         8.35         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16        90.58        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0054 
       10.72        10.52        18.31         6.87        15.09         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
       19.86         8.35         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-02-0099 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-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       48.95        16.54        16.93        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.66         3.29        13.12         4.47         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       15.42        10.42         4.67         7.40         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        8.42         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.64        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.80        23.57        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        2.70         0.92        43.46         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93         4.04        11.84        15.32 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.39       120.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        7.56        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        43.23         7.63         9.73        14.93        14.86 
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-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 
       15.85         9.11        14.53         3.98         2.24        11.24 
TCGA-14-0813 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        1.35        19.30         0.79        13.78        50.53        19.10 
TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       26.07        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       12.95         4.64        31.33         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       14.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
       22.68        12.76         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                         99.98                         127.59 
  DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE 
                        14.035                         11.870 
[1] "0.5 - 100.0 (14.0)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.2"
D51V2, continuous
D51V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    47  58
  DEL PEAK 27(11P11.2) WILD-TYPE 178 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     47   58
  DEL PEAK 27(11P11.2) WILD-TYPE  178  290
        clus
vv       DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  FEMALE                           47                            178
  MALE                             58                            290
[1] 2 2
[1] FALSE
D51V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED    13  87
  DEL PEAK 27(11P11.2) WILD-TYPE  61 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED     13   87
  DEL PEAK 27(11P11.2) WILD-TYPE   61  388
     clus
vv    DEL PEAK 27(11P11.2) MUTATED DEL PEAK 27(11P11.2) WILD-TYPE
  NO                            13                             61
  YES                           87                            388
[1] 2 2
[1] FALSE
D51V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 27(11P11.2) MUTATED                               5
  DEL PEAK 27(11P11.2) WILD-TYPE                            25
                                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
D51V6, multiclass
                                 clus
vv                                DEL PEAK 27(11P11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                           94
                                 clus
vv                                DEL PEAK 27(11P11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(11P11.2) MUTATED       2                        11    88
  DEL PEAK 27(11P11.2) WILD-TYPE    11                        39   399
D51V7, multiclass
                           clus
vv                          DEL PEAK 27(11P11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               88
                           clus
vv                          DEL PEAK 27(11P11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                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"
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P11.2) MUTATED     2  84
  DEL PEAK 27(11P11.2) WILD-TYPE  10 391
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P11.2) MUTATED      2   84
  DEL PEAK 27(11P11.2) WILD-TYPE   10  391
                        clus
vv                       DEL PEAK 27(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 27(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            391
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 28(11Q14.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(11Q14.1) MUTATED     8  88
  DEL PEAK 28(11Q14.1) WILD-TYPE  89 385
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            96                            474 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                            88                            385 
$`DEL PEAK 28(11Q14.1) MUTATED`
TCGA-06-1806 TCGA-06-5856 TCGA-06-A7TK TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 
       15.32         3.75        14.60        15.65         6.77        44.02 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0865 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 
       14.53         6.21        16.50        30.18        12.43         0.99 
TCGA-14-1823 TCGA-14-3477 TCGA-16-1045 TCGA-19-1390 TCGA-19-1392 TCGA-19-5959 
       17.85         3.78        29.03        25.38         3.65        16.80 
TCGA-26-1439 TCGA-27-1830 TCGA-27-2521 TCGA-28-2509 TCGA-32-1976 TCGA-32-1986 
       13.87         5.06        16.77         4.77         0.49        12.69 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 
       15.95         8.84         3.72        10.85        11.84         7.50 
TCGA-76-4934 TCGA-76-6286 TCGA-76-6661 TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 
        2.53        20.98        23.90        11.77        23.18        35.41 
TCGA-02-0024 TCGA-02-0033 TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0059 
       53.10         2.83         3.22        12.59         2.50         9.57 
TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0086 TCGA-02-0111 TCGA-02-0113 
       28.70        10.19        20.84         8.81        23.18        92.65 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0332 TCGA-02-0339 TCGA-02-0456 TCGA-02-2466 
       17.72         3.98        25.71        12.39         3.35        16.80 
TCGA-06-0130 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 
       12.95         9.44         5.85         3.22         4.18        69.90 
TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0216 
       44.58        10.42        38.96         7.40         5.56        24.16 
TCGA-06-0238 TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
       13.32        48.69        72.36         4.70        35.11         2.10 
TCGA-06-0686 TCGA-06-0876 TCGA-06-1800 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 
       14.20        46.19        26.79         5.39         7.36        37.84 
TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 TCGA-12-0772 TCGA-12-0819 
        4.27        10.75        14.73        34.92        53.85        24.79 
TCGA-12-0822 TCGA-12-1091 TCGA-12-1099 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
       23.51        33.21         4.14         5.39         2.04        28.93 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-19-1387 TCGA-28-5216 TCGA-81-5910 
       13.28         3.91        16.37         5.95        13.64         1.61 

$`DEL PEAK 28(11Q14.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       17.72        15.35        21.73        25.68        14.73        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
       13.78         3.25         2.89        26.33        15.95         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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 
        1.15         0.92        40.96         6.67         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-16-0848 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       17.59         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1786 
       13.97         6.41         8.61        14.27         3.39         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        22.49        14.07        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03         9.73         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97        19.33        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-32-1970 
        1.55         2.83         0.13         0.66         6.74        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       21.07         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2634 
       14.86        16.93        12.23        20.78        15.02        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
       25.18        21.14        12.59        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         8.22         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 
        2.70        17.06         8.35         4.83         5.03        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 
        4.73        18.35        10.59        20.71        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       87.06        77.65        20.12        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
       90.58        14.14         3.62        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        6.87        14.73        15.09         6.54        19.86         8.35 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 
        6.02        19.73        26.43        25.05         5.49        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 
        3.48        27.02        65.00        11.67        17.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.54        16.93        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
       10.62         7.33        15.91         4.37        25.12        10.59 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.66         3.29        13.12         4.47         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
       15.42         4.67         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84         0.53        15.02         0.72        19.82        13.64 
TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       20.42        10.82         9.01         0.26         9.57         3.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 
       12.62         5.75         5.75         9.80        23.57        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84         4.04        11.84        15.32        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        7.79       120.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       58.68        19.33         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        7.56        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 
       14.86        91.76        18.48        10.62        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1093 
        8.94        20.58       127.59         5.82         7.59        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 
       12.23        15.85         9.11        14.53         3.98         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
       11.24         1.35        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       19.10        53.19        26.07        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         9.07        12.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01         5.16        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5911 TCGA-87-5896 
        7.36        11.38         5.42         3.75        17.72        26.30 

  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE 
                        13.115                         12.145 
[1] "0.5 - 92.7 (13.1)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1"  
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    42  54
  DEL PEAK 28(11Q14.1) WILD-TYPE 183 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     42   54
  DEL PEAK 28(11Q14.1) WILD-TYPE  183  294
        clus
vv       DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  FEMALE                           42                            183
  MALE                             54                            294
[1] 2 2
[1] FALSE
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED    14  79
  DEL PEAK 28(11Q14.1) WILD-TYPE  60 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED     14   79
  DEL PEAK 28(11Q14.1) WILD-TYPE   60  396
     clus
vv    DEL PEAK 28(11Q14.1) MUTATED DEL PEAK 28(11Q14.1) WILD-TYPE
  NO                            14                             60
  YES                           79                            396
[1] 2 2
[1] FALSE
D52V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 28(11Q14.1) MUTATED                               3
  DEL PEAK 28(11Q14.1) WILD-TYPE                            27
                                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
D52V6, multiclass
                                 clus
vv                                DEL PEAK 28(11Q14.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        5
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 28(11Q14.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         13
  UNTREATED PRIMARY (DE NOVO) GBM                            437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11Q14.1) MUTATED       2                         7    83
  DEL PEAK 28(11Q14.1) WILD-TYPE    11                        43   404
D52V7, multiclass
                           clus
vv                          DEL PEAK 28(11Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               83
                           clus
vv                          DEL PEAK 28(11Q14.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                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"
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q14.1) MUTATED     1  78
  DEL PEAK 28(11Q14.1) WILD-TYPE  11 397
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q14.1) MUTATED      1   78
  DEL PEAK 28(11Q14.1) WILD-TYPE   11  397
                        clus
vv                       DEL PEAK 28(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 28(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            397
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 29(12P13.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(12P13.1) MUTATED    16  55
  DEL PEAK 29(12P13.1) WILD-TYPE  81 418
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            71                            499 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            55                            418 
$`DEL PEAK 29(12P13.1) MUTATED`
TCGA-06-5415 TCGA-06-5859 TCGA-06-6697 TCGA-06-6700 TCGA-12-1598 TCGA-12-1600 
        8.55         4.57        12.85         4.77        15.65        14.73 
TCGA-12-3646 TCGA-14-0783 TCGA-14-1451 TCGA-14-1794 TCGA-14-3477 TCGA-16-1055 
       44.02         6.21        23.11         0.99         3.78        10.29 
TCGA-19-0960 TCGA-19-1390 TCGA-19-2623 TCGA-19-4065 TCGA-26-5132 TCGA-26-5136 
        8.61        25.38         7.53         7.04         9.40        18.97 
TCGA-27-1836 TCGA-32-1978 TCGA-32-2494 TCGA-32-4208 TCGA-76-4935 TCGA-76-6193 
       30.05        15.85        20.78        21.14        36.85         2.70 
TCGA-76-6664 TCGA-02-0014 TCGA-02-0026 TCGA-02-0034 TCGA-02-0038 TCGA-02-0055 
       36.20        82.59        24.59        14.14        10.72         2.50 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0085 TCGA-02-0087 TCGA-02-0104 TCGA-02-0113 
        5.49        20.84        51.32        57.76        65.00        92.65 
TCGA-06-0129 TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0175 TCGA-06-0190 
       33.67        17.79         8.61         9.44         4.04        10.42 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0414 TCGA-06-0646 
        7.40         5.56        19.82        13.64        35.11         5.75 
TCGA-06-1801 TCGA-06-2570 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 TCGA-08-0348 
       11.84        31.50         5.39         7.36        37.84        12.16 
TCGA-08-0349 TCGA-08-0359 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
        9.80         3.39        18.02         4.27        11.08        19.33 
TCGA-12-0619 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-16-0849 TCGA-16-0850 
       34.92         5.39         2.04        28.93        26.07        16.37 
TCGA-19-1385 TCGA-19-1388 TCGA-28-2514 TCGA-28-5204 TCGA-76-6283 
       10.75        12.95         5.26        14.93         5.42 

$`DEL PEAK 29(12P13.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6701 
        6.15         5.23         8.32         4.77         1.55         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
       26.79         1.87         3.12         2.56        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
       15.35        21.73        25.68         6.77        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       13.78         3.25         2.89        16.50        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
        1.38         1.12         3.75        32.05        58.78         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1795 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-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
       17.49         7.96         3.42        17.59        29.03         4.57 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0963 
       14.01         9.14        21.24        13.97         6.41        14.27 
TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        3.39         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       17.79        28.54        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.37         8.88        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        40.54        21.30        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        6.74         4.77        15.39        21.07         0.49         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
        0.20        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-OX-A56R TCGA-RR-A6KA 
        5.03        23.90        34.45        18.64         5.92         6.28 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
       20.55         7.63        11.77         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       10.59        35.41        20.71        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        42.74        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
        3.62        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-02-0074 
        6.02        19.73        26.43        28.70        25.05        10.19 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0086 TCGA-02-0089 
       27.25        89.72        22.72        12.62         8.81        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
        3.48        27.02        11.67        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
       20.38        47.61         6.94         3.98        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 
       10.29         2.20        11.74         2.33        20.09        10.09 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
       10.82        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       19.66         3.29        13.12         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 
       27.22        44.58        15.42        38.96         4.67         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       24.16         0.72        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
       12.62         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 
       26.76        23.93         6.84         4.04        26.79        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        0.43         7.79       120.56        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        1.74         8.42        25.71        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       42.15        19.59        58.68        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-1037 TCGA-14-1043 
        4.14         2.24        11.24         1.35        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       11.77        21.90         0.66         9.07         5.95         4.64 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42         7.36        11.38         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                          0.99                           0.10 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                         92.65                         127.59 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                         12.85                          12.23 
[1] "1.0 - 92.7 (12.8)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED    32  40
  DEL PEAK 29(12P13.1) WILD-TYPE 193 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED     32   40
  DEL PEAK 29(12P13.1) WILD-TYPE  193  308
        clus
vv       DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  FEMALE                           32                            193
  MALE                             40                            308
[1] 2 2
[1] FALSE
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED     7  61
  DEL PEAK 29(12P13.1) WILD-TYPE  67 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      7   61
  DEL PEAK 29(12P13.1) WILD-TYPE   67  414
     clus
vv    DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  NO                             7                             67
  YES                           61                            414
[1] 2 2
[1] FALSE
D53V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 29(12P13.1) MUTATED                               2
  DEL PEAK 29(12P13.1) WILD-TYPE                            28
                                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
D53V6, multiclass
                                 clus
vv                                DEL PEAK 29(12P13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              2
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           69
                                 clus
vv                                DEL PEAK 29(12P13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               28
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            456
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(12P13.1) MUTATED       2                         2    65
  DEL PEAK 29(12P13.1) WILD-TYPE    11                        48   422
D53V7, multiclass
                           clus
vv                          DEL PEAK 29(12P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               65
                           clus
vv                          DEL PEAK 29(12P13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             48
  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"
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED     1  60
  DEL PEAK 29(12P13.1) WILD-TYPE  11 415
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      1   60
  DEL PEAK 29(12P13.1) WILD-TYPE   11  415
                        clus
vv                       DEL PEAK 29(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 29(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            415
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 30(12Q12) MUTATION ANALYSIS
D54V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 30(12Q12) MUTATED    14  63
  DEL PEAK 30(12Q12) WILD-TYPE  83 410
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          77                          493 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                          63                          410 
$`DEL PEAK 30(12Q12) MUTATED`
TCGA-06-5856 TCGA-06-A7TL TCGA-12-1600 TCGA-12-3646 TCGA-14-0740 TCGA-14-0783 
        3.75        17.72        14.73        44.02        11.97         6.21 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1458 TCGA-14-1794 TCGA-14-1821 TCGA-14-3477 
       23.11         1.15         6.67         0.99        17.79         3.78 
TCGA-16-1056 TCGA-19-1390 TCGA-19-2623 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 
       14.01        25.38         7.53         7.04        14.96        10.03 
TCGA-26-5132 TCGA-26-5136 TCGA-28-1746 TCGA-28-1756 TCGA-32-1978 TCGA-32-2494 
        9.40        18.97         0.20         2.83        15.85        20.78 
TCGA-32-4208 TCGA-32-4210 TCGA-41-2571 TCGA-41-5651 TCGA-76-4935 TCGA-76-6193 
       21.14         3.72         0.85        15.12        36.85         2.70 
TCGA-RR-A6KA TCGA-02-0034 TCGA-02-0046 TCGA-02-0055 TCGA-02-0071 TCGA-02-0075 
        6.28        14.14         6.87         2.50         5.49        20.84 
TCGA-02-0084 TCGA-02-0087 TCGA-02-0102 TCGA-02-0104 TCGA-02-0113 TCGA-06-0146 
       12.62        57.76        27.02        65.00        92.65        20.09 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0173 TCGA-06-0175 TCGA-06-0184 
       17.79         8.61         9.44         4.47         4.04        69.90 
TCGA-06-0190 TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 
       10.42         7.40         5.56        19.82        13.64         4.70 
TCGA-06-0414 TCGA-06-0875 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 
       35.11        43.46         7.79         5.39         7.36        37.84 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 
       12.16         9.80        65.33        18.02         4.27        11.08 
TCGA-12-0619 TCGA-12-0662 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
       34.92        38.17         1.35         5.39         2.04        28.93 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 TCGA-19-1388 TCGA-76-6660 
       26.07        16.37        21.90        12.95         3.75 

$`DEL PEAK 30(12Q12) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
        2.56        14.60        15.35        21.73        15.65        25.68 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
        0.95        23.05        13.78         3.25         2.89        16.50 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       26.33        15.95         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
       58.78         7.10        30.18         0.92        40.96        12.43 
TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
        9.14        21.24        13.97         6.41         8.61        14.27 
TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        3.39         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         1.08         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I 
       12.10         1.78        22.49        14.07        16.80        17.79 
TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5135 
       28.54        13.87         9.73         7.13         9.37         8.88 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        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-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        1.55         0.13         0.66         6.74         4.77        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-32-2495 TCGA-32-2615 
       12.69        14.86        16.93        12.23        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        22.78        25.18        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       19.23        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
       20.55         7.63        11.77         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       10.59        35.41        20.71        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       77.65        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
       90.58         2.83         3.62        10.72        10.52        18.31 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         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-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 
       25.05        10.19        27.25        89.72        22.72        51.32 
TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        8.81        16.96         3.48        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-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0176 
        5.85        19.66         3.29        13.12         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
        4.18        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 
       44.58        15.42        38.96         4.67         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26        72.36         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       46.88         7.86         2.70         2.70         0.92        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
       31.50       120.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        8.42        25.71        29.23         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        2.24        11.24        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-19-0955 TCGA-19-0962 
       19.10        53.19        13.28         3.91        11.77         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       10.75         9.07         5.95         4.64        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 
        5.42         7.36        11.38         5.42         1.61        17.72 
TCGA-87-5896 
       26.30 

  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                       92.65                       127.59 
  DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE 
                       12.16                        12.23 
[1] "0.2 - 92.7 (12.2)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D54V2, continuous
D54V3, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    32  45
  DEL PEAK 30(12Q12) WILD-TYPE 193 303
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     32   45
  DEL PEAK 30(12Q12) WILD-TYPE  193  303
        clus
vv       DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  FEMALE                         32                          193
  MALE                           45                          303
[1] 2 2
[1] FALSE
D54V4, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED    13  58
  DEL PEAK 30(12Q12) WILD-TYPE  61 417
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED     13   58
  DEL PEAK 30(12Q12) WILD-TYPE   61  417
     clus
vv    DEL PEAK 30(12Q12) MUTATED DEL PEAK 30(12Q12) WILD-TYPE
  NO                          13                           61
  YES                         58                          417
[1] 2 2
[1] FALSE
D54V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 30(12Q12) MUTATED                               4
  DEL PEAK 30(12Q12) WILD-TYPE                            26
                              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
D54V6, multiclass
                                 clus
vv                                DEL PEAK 30(12Q12) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            4
  TREATED PRIMARY GBM                                      2
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 30(12Q12) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             26
  TREATED PRIMARY GBM                                       16
  UNTREATED PRIMARY (DE NOVO) GBM                          454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q12) MUTATED       0                         6    68
  DEL PEAK 30(12Q12) WILD-TYPE    13                        44   419
D54V7, multiclass
                           clus
vv                          DEL PEAK 30(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             68
                           clus
vv                          DEL PEAK 30(12Q12) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           44
  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"
D54V8, binary
                              cls
clus                             0   1
  DEL PEAK 30(12Q12) MUTATED     2  61
  DEL PEAK 30(12Q12) WILD-TYPE  10 414
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(12Q12) MUTATED      2   61
  DEL PEAK 30(12Q12) WILD-TYPE   10  414
                        clus
vv                       DEL PEAK 30(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 30(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          414
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 31(12Q15) MUTATION ANALYSIS
D55V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(12Q15) MUTATED    14  65
  DEL PEAK 31(12Q15) WILD-TYPE  83 408
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          79                          491 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                          65                          408 
$`DEL PEAK 31(12Q15) MUTATED`
TCGA-06-6695 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 
        8.32        14.60        17.72        14.73         6.77        44.02 
TCGA-14-0740 TCGA-14-0783 TCGA-14-1451 TCGA-14-1453 TCGA-14-1794 TCGA-14-3477 
       11.97         6.21        23.11         1.15         0.99         3.78 
TCGA-19-1390 TCGA-19-2623 TCGA-19-2624 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 
       25.38         7.53         0.16         7.04        14.96        10.03 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-32-4210 TCGA-32-4211 TCGA-41-2571 
        9.40         8.88        18.97         3.72        12.59         0.85 
TCGA-74-6584 TCGA-76-6193 TCGA-02-0034 TCGA-02-0052 TCGA-02-0055 TCGA-02-0071 
        7.50         2.70        14.14        12.59         2.50         5.49 
TCGA-02-0075 TCGA-02-0084 TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 TCGA-02-0113 
       20.84        12.62        57.76         3.48        27.02        92.65 
TCGA-02-0266 TCGA-02-2466 TCGA-06-0140 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 
       17.72        16.80         0.20        20.09        17.79         8.61 
TCGA-06-0152 TCGA-06-0159 TCGA-06-0162 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
       12.33         9.44         3.42         4.47         3.22         4.18 
TCGA-06-0184 TCGA-06-0190 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0410 
       69.90        10.42         5.56        19.82        13.64         4.70 
TCGA-06-0414 TCGA-06-0649 TCGA-06-0875 TCGA-06-0939 TCGA-06-6389 TCGA-06-6694 
       35.11         2.10        43.46        26.76         7.79         7.36 
TCGA-08-0245 TCGA-08-0349 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0616 
       37.84         9.80        18.02         4.27        11.08        14.73 
TCGA-12-0619 TCGA-12-1088 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
       34.92       127.59         1.35         5.39         2.04        28.93 
TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 TCGA-19-1388 TCGA-28-5214 
       53.19        26.07        16.37        21.90        12.95        23.44 
TCGA-76-6660 
        3.75 

$`DEL PEAK 31(12Q15) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6697 TCGA-06-6698 
        3.75         6.15         4.57         5.23        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 
        2.56        15.35        21.73        15.65        25.68        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 
       14.93         3.22         2.04        15.12         0.95        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
       13.78         3.25         2.89        16.50        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
        1.38         1.12         3.75        32.05        58.78         7.10 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-2629 
        0.13         9.67         4.87         1.08         4.08        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I 
       12.10         1.78        22.49        14.07        16.80        17.79 
TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-A7UX 
       28.54        13.87         9.73         7.13         9.37        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
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-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 
       21.14        19.86        10.85        19.23        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        36.85        16.70         3.29 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       20.12        53.10        42.74        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
        2.83         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       14.73         3.22        15.09         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-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 
       10.19        27.25        89.72        22.72        51.32         8.81 
TCGA-02-0089 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
       16.96        65.00        11.67        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 
       15.65        48.95        16.54        16.93        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27        16.21         3.35        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 
       14.30        26.70        24.23        11.90        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
       11.74         2.33        10.09        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
       10.45         3.19        10.82        11.80        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 
        5.85        19.66         3.29        13.12         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       88.14        20.25         3.65        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       15.42        38.96         4.67         7.40         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26        72.36         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 
        7.86         2.70         2.70         0.92        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       40.41        16.57        20.78        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6390 
       16.64         5.98         4.37         0.43        31.50         5.39 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
      120.56        22.68         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       25.71        12.16        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0620 
        7.27        15.98        18.41         7.56        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
        8.94        20.58         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-14-0787 TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        2.24        11.24        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 
       19.10        13.28         3.91        11.77         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07         5.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
       11.28        17.88        14.53        11.77        31.27        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         1.61        17.72        26.30 

  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                        0.16                         0.10 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                      127.59                       120.56 
  DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE 
                       11.97                        12.23 
[1] "0.2 - 127.6 (12.0)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D55V2, continuous
D55V3, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    34  45
  DEL PEAK 31(12Q15) WILD-TYPE 191 303
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     34   45
  DEL PEAK 31(12Q15) WILD-TYPE  191  303
        clus
vv       DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  FEMALE                         34                          191
  MALE                           45                          303
[1] 2 2
[1] FALSE
D55V4, binary
                              cls
clus                             0   1
  DEL PEAK 31(12Q15) MUTATED    14  59
  DEL PEAK 31(12Q15) WILD-TYPE  60 416
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED     14   59
  DEL PEAK 31(12Q15) WILD-TYPE   60  416
     clus
vv    DEL PEAK 31(12Q15) MUTATED DEL PEAK 31(12Q15) WILD-TYPE
  NO                          14                           60
  YES                         59                          416
[1] 2 2
[1] FALSE
D55V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 31(12Q15) MUTATED                               5
  DEL PEAK 31(12Q15) WILD-TYPE                            25
                              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
D55V6, multiclass
                                 clus
vv                                DEL PEAK 31(12Q15) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                            5
  TREATED PRIMARY GBM                                      3
  UNTREATED PRIMARY (DE NOVO) GBM                         71
                                 clus
vv                                DEL PEAK 31(12Q15) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             25
  TREATED PRIMARY GBM                                       15
  UNTREATED PRIMARY (DE NOVO) GBM                          454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(12Q15) MUTATED       0                         5    69
  DEL PEAK 31(12Q15) WILD-TYPE    13                        45   418
D55V7, multiclass
                           clus
vv                          DEL PEAK 31(12Q15) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             69
                           clus
vv                          DEL PEAK 31(12Q15) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           45
  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 31(12Q15) MUTATED     3  63
  DEL PEAK 31(12Q15) WILD-TYPE   9 412
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(12Q15) MUTATED      3   63
  DEL PEAK 31(12Q15) WILD-TYPE    9  412
                        clus
vv                       DEL PEAK 31(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         63
                        clus
vv                       DEL PEAK 31(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          412
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(13Q14.2) MUTATED    37 203
  DEL PEAK 32(13Q14.2) WILD-TYPE  60 270
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           240                            330 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           203                            270 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-06-1806 TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 TCGA-06-5416 TCGA-06-5856 
       15.32        11.74         4.54         8.98         6.71         3.75 
TCGA-06-5859 TCGA-06-6701 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 
        4.57         4.96        14.60        15.35        21.73        15.65 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
        6.77        59.77        44.02        34.92        14.53        14.93 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
       15.12        11.97         6.21         3.25         2.89        16.50 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 
       15.95         1.12        23.11         1.15        30.18        40.96 
TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-16-1045 TCGA-16-1055 
        6.67        17.85         7.63         3.78        29.03        10.29 
TCGA-16-1060 TCGA-19-1392 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        9.14         3.65         1.08         7.53         4.08        24.23 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5955 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 
        7.04         6.64         1.78        17.79        10.03        13.87 
TCGA-26-5132 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 
        9.40        18.97        19.33         5.06         9.86        40.54 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 
       18.08        16.77         7.59         8.35         8.48         0.66 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1987 
        4.77        15.39        21.07         0.49         0.10        14.86 
TCGA-32-2491 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 
       12.23         8.84        22.78         3.72        19.86        10.85 
TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9R 
        0.85         8.94         0.99        11.84         0.20         4.08 
TCGA-4W-AA9S TCGA-74-6573 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 
        1.45         3.45         3.65         2.53        36.85         3.29 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-76-6662 TCGA-06-0209 
        2.70         8.35        20.98        23.90        34.45         7.63 
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0023 
       11.77        18.35        23.18        35.41        20.71        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0051 
       53.10        24.59         2.83        14.14        10.52        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
       12.59         6.54         2.50         9.57        19.73        26.43 
TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
       28.70        20.84        27.25         3.48        65.00        11.67 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0321 TCGA-02-0325 TCGA-02-0330 
       92.65        99.98        15.65         9.90        10.62        15.91 
TCGA-02-0339 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 TCGA-02-2483 
       12.39        10.55        11.34         9.27         3.35        15.32 
TCGA-06-0122 TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0140 TCGA-06-0143 
        6.15        22.72        12.95        24.23         0.20        11.74 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       17.79         8.61        12.33        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 
       56.91         5.85         4.18         3.65        69.90        44.58 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         7.40         5.56         0.39         7.66 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0402 
        0.53        15.02        24.16         0.72        19.82         0.26 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 TCGA-06-0745 
        4.70         3.16        35.11         9.80         2.10         7.86 
TCGA-06-0875 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
       43.46        16.57        26.76        23.93         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 
        4.93         5.98         4.37        31.50         7.79         7.36 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
       37.84         4.18        25.71        12.16         9.80        29.23 
TCGA-08-0354 TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 
       17.95        37.58         3.39        18.02        15.35         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0520 TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0769 
       10.75        10.45        38.17        25.97        12.13        15.06 
TCGA-12-0772 TCGA-12-0776 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       53.85         9.73        24.79        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
       20.58       127.59        33.21        15.98        12.23         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 
       14.53         4.14         2.24         5.39         2.04        19.30 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
       13.78        50.53        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-26-5133 TCGA-26-6173 
       16.37        10.75         5.95         4.64        14.86         7.92 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-32-2616 TCGA-76-6283 TCGA-81-5911 
       11.01        13.64        22.68         7.36         5.42        17.72 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5415 
        1.48         3.98         3.55         8.35         8.81         8.55 
TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        2.73         6.15         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77        26.79         1.87         3.12         2.56 
TCGA-06-A7TL TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       17.72        25.68        14.73        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 
       12.69         3.22         2.04         0.95        23.05        13.78 
TCGA-14-0866 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
       26.33         1.38         3.75        32.05        58.78         7.10 
TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 
        0.92        12.43         0.99         1.97        17.79         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1047 
        7.17        17.49         7.96         3.42        17.59         4.57 
TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
       14.01        21.24        13.97         6.41         8.61        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        3.39        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        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5135 
       14.96        28.54         9.73         7.13         9.37         8.88 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       16.60        24.23        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       24.76        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        2.53         9.21         7.63         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2506 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.13         6.74        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 
       12.69        16.93        20.78        15.02        15.95        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 
       21.14        12.59        19.23        13.35         9.53         4.44 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       15.12        12.46        25.58        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
        8.22         7.50         4.80         4.54         3.09         9.17 
TCGA-76-6191 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6663 TCGA-76-6664 
       16.70        17.06         4.83         5.03        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 TCGA-02-0009 TCGA-02-0014 
        5.92         6.28        20.55         4.73        10.59        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 
       20.61        87.06        77.65        42.74        12.16        90.58 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
        3.62        10.72        18.31         6.87        14.73         3.22 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.86         8.35         6.02        25.05         5.49        10.19 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0116 TCGA-02-0258 
       16.96        27.02        17.65        23.18        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-02-0324 TCGA-02-0326 TCGA-02-0332 
       14.20        15.95        12.23         7.73         7.33        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0432 TCGA-02-0451 
        4.37        25.12        10.59        14.50        47.11        16.21 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 
       16.80        12.92        15.45        20.32         2.70        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
       47.61         6.94         3.98        33.67        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0146 
       26.70        11.90        10.29         2.20         2.33        20.09 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       10.09        19.46        46.59        13.94        10.45         3.19 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       11.80        10.65        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 
        3.22         4.04        91.00        88.14        20.25        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0194 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
       27.22        15.42         4.67         8.42         7.40        11.84 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 
       72.36         9.57        12.62         5.75         5.75        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40        46.88         2.70         2.70         0.92 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 TCGA-06-1086 TCGA-06-2561 
       46.19         7.17        40.41        20.78         6.84        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2569 TCGA-06-6390 
       12.56        30.64         5.95        16.64         0.43         5.39 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0351 
      120.56        22.68       115.86         1.74         8.42        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0375 
        1.28         8.42        24.56        31.10        22.29        12.23 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       14.93        13.97        19.33         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 
       18.41         7.56        14.73        12.99        34.92         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       94.78         0.10        26.66         3.65        20.38        28.41 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 
       43.23         7.63        14.93        14.86        91.76        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-1089 TCGA-12-1090 TCGA-12-1095 TCGA-12-1098 
       10.62        23.51         5.82         7.59        15.85         3.98 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0871 TCGA-14-1043 TCGA-15-1446 TCGA-19-0955 
       11.24         1.35        28.93         0.79        19.10        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 TCGA-19-1388 TCGA-26-1442 TCGA-26-5134 
       21.90         0.66         9.07        12.95        31.33         5.49 
TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        1.58         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 
       17.88        14.53        11.77        31.27        23.44         5.16 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-87-5896 
       12.76         5.42        11.38         3.75         1.61        26.30 

  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                         11.84                          12.62 
[1] "0.1 - 127.6 (11.8)" "0.1 - 120.6 (12.6)"
[1] "hr=" "1"  
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED    91 149
  DEL PEAK 32(13Q14.2) WILD-TYPE 134 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     91  149
  DEL PEAK 32(13Q14.2) WILD-TYPE  134  199
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                           91                            134
  MALE                            149                            199
[1] 2 2
[1] FALSE
D56V4, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED    38 193
  DEL PEAK 32(13Q14.2) WILD-TYPE  36 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     38  193
  DEL PEAK 32(13Q14.2) WILD-TYPE   36  282
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  NO                            38                             36
  YES                          193                            282
[1] 2 2
[1] FALSE
D56V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 32(13Q14.2) MUTATED                              10
  DEL PEAK 32(13Q14.2) WILD-TYPE                            20
                                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
D56V6, multiclass
                                 clus
vv                                DEL PEAK 32(13Q14.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             10
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          224
                                 clus
vv                                DEL PEAK 32(13Q14.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               20
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED       5                        17   212
  DEL PEAK 32(13Q14.2) WILD-TYPE     8                        33   275
D56V7, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              212
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             33
  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"
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(13Q14.2) MUTATED     5 203
  DEL PEAK 32(13Q14.2) WILD-TYPE   7 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      5  203
  DEL PEAK 32(13Q14.2) WILD-TYPE    7  272
                        clus
vv                       DEL PEAK 32(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       DEL PEAK 32(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            272
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 33(13Q22.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(13Q22.1) MUTATED    34 194
  DEL PEAK 33(13Q22.1) WILD-TYPE  63 279
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           228                            342 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           194                            279 
$`DEL PEAK 33(13Q22.1) MUTATED`
TCGA-06-1806 TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 TCGA-06-5416 TCGA-06-5856 
       15.32        11.74         4.54         8.98         6.71         3.75 
TCGA-06-5859 TCGA-06-6701 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 
        4.57         4.96         2.56        14.60        15.35        21.73 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-5295 TCGA-14-0736 
       15.65         6.77        59.77        44.02        14.93        15.12 
TCGA-14-0740 TCGA-14-0783 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
       11.97         6.21        13.78         3.25         2.89        16.50 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 
       15.95         1.12        23.11         1.15        30.18        40.96 
TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-16-1045 TCGA-16-1055 
        6.67        17.85         7.63         3.78        29.03        10.29 
TCGA-16-1060 TCGA-16-1062 TCGA-19-1392 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 
        9.14        21.24         3.65         1.08         7.53         4.08 
TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5955 TCGA-19-A60I TCGA-26-1439 
       24.23         7.04         6.64         1.78        17.79        13.87 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 TCGA-27-2519 
       18.97        19.33         5.06         9.86        40.54        18.08 
TCGA-27-2521 TCGA-28-1746 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 TCGA-28-2509 
       16.77         0.20         8.35         8.48         0.66         4.77 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2634 TCGA-32-4210 
       15.39         0.49        14.86        12.23        22.78         3.72 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 
       19.86        10.85         8.94         0.99        11.84         0.20 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6193 
        4.08         1.45         3.65         2.53        36.85         2.70 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-06-0209 TCGA-02-0001 TCGA-02-0006 
        8.35        20.98        23.90         7.63        11.77        18.35 
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0023 TCGA-02-0026 TCGA-02-0028 
       23.18        35.41        20.71        20.12        24.59        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
        2.83        14.14        10.52        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0075 
        2.50         9.57        19.73        26.43        28.70        20.84 
TCGA-02-0079 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 
       27.25         3.48        65.00        11.67        92.65        15.65 
TCGA-02-0258 TCGA-02-0321 TCGA-02-0325 TCGA-02-0330 TCGA-02-0339 TCGA-02-0440 
       16.54         9.90        10.62        15.91        12.39        11.34 
TCGA-02-0446 TCGA-02-0456 TCGA-02-2483 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
        9.27         3.35        15.32         6.15        20.38        47.61 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0143 
       22.72        12.95        24.23        11.90         0.20        11.74 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0152 TCGA-06-0158 
       20.09        17.79        10.09         8.61        12.33        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0177 TCGA-06-0182 
        9.44         3.42        56.91         5.85         4.18         3.65 
TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       69.90        44.58        38.96         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0402 TCGA-06-0410 
        7.66         0.53        15.02         0.72         0.26         4.70 
TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 TCGA-06-0745 TCGA-06-0875 TCGA-06-0881 
       35.11         9.80         2.10         7.86        43.46        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2567 TCGA-06-6389 
       13.61        33.90         1.08        12.49         4.37         7.79 
TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0354 
        7.36        37.84         4.18        25.71         9.80        17.95 
TCGA-08-0357 TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
       37.58         3.39        18.02        15.35         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-12-0619 
        4.27        42.15        19.59        58.68        10.75        34.92 
TCGA-12-0620 TCGA-12-0662 TCGA-12-0670 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 
       10.45        38.17        25.97        12.13        15.06        53.85 
TCGA-12-0776 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
        9.73        24.79        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 
      127.59        33.21        15.98        12.23         9.11        14.53 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 TCGA-15-0742 
        4.14         2.24         5.39         2.04        19.30        13.78 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-1385 
       53.19        13.28         3.91        26.07        16.37        10.75 
TCGA-19-1387 TCGA-19-1389 TCGA-26-5133 TCGA-26-6173 TCGA-28-5207 TCGA-28-5215 
        5.95         4.64        14.86         7.92        11.28        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-32-2616 TCGA-76-6283 TCGA-81-5911 
       13.64        22.68        12.76         7.36         5.42        17.72 

$`DEL PEAK 33(13Q22.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5415 
        1.48         3.98         3.55         8.35         8.81         8.55 
TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        2.73         6.15         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TL 
        1.55         4.77        26.79         1.87         3.12        17.72 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       25.68        14.73        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 
       34.92        14.53         3.22         2.04         0.95        23.05 
TCGA-14-0866 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
       26.33         1.38         3.75        32.05        58.78         7.10 
TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 
        0.92        12.43         0.99         1.97        17.79         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1047 
        7.17        17.49         7.96         3.42        17.59         4.57 
TCGA-16-1056 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       14.01        13.97         6.41         8.61        14.27         3.39 
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-19-2624 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.87         0.16         7.00        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10        22.49        14.07        16.80        14.96 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       28.54        10.03         9.73         7.13         9.37         9.40 
TCGA-26-5135 TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        8.88        16.60        24.23        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       11.51        24.76        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
       15.78         2.53         9.21         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
        2.83         0.13         6.74        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-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.02        15.95         8.84        25.18        21.14        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 
       19.23         0.85        13.35         9.53         4.44        15.12 
TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       12.46        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
        8.22         7.50         4.80         4.54         3.09         9.17 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 
       16.70         3.29        17.06         4.83         5.03        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0003 
       18.64        36.20         5.92         6.28        20.55         4.73 
TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0024 
       10.59        82.59        20.61        87.06        77.65        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 
       42.74        12.16         3.62        10.72        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0070 
       14.73         3.22        19.86         8.35         6.02        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 
        8.81        57.76        16.96        27.02        17.65        23.18 
TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       99.98        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-02-0324 
        3.98        13.87        14.20        15.95        12.23         7.73 
TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 
        7.33        25.71         4.37        25.12        10.59        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 
       10.55        47.11        16.21        16.80        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 
       20.32         2.70         6.94         3.98        33.67        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0150 
       14.30        26.70        10.29         2.20         2.33        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 TCGA-06-0165 
       46.59        13.94        10.45         3.19        11.80        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       91.00        88.14        20.25        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0216 
       10.42         4.67         8.42         7.40        11.84        24.16 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        9.01        72.36         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        5.75        23.57        14.20        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 
        2.70         0.92        46.19         7.17        40.41        20.78 
TCGA-06-1086 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        6.84         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-6390 TCGA-06-6693 
       16.64         5.98         0.43        31.50         5.39       120.56 
TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 
       22.68       115.86         1.74         8.42        12.16        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 
       65.33         1.28         8.42        24.56        31.10        22.29 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0514 TCGA-08-0518 TCGA-08-0521 
       12.23        14.93        13.97        11.08        19.33         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        7.59        94.78         0.10        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       28.41        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-1089 TCGA-12-1090 TCGA-12-1095 
       18.48        10.62        23.51         5.82         7.59        15.85 
TCGA-12-1098 TCGA-14-0789 TCGA-14-0813 TCGA-14-0871 TCGA-14-1043 TCGA-15-1444 
        3.98        11.24         1.35        28.93         0.79        50.53 
TCGA-15-1446 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 TCGA-19-1388 
       19.10        11.77        21.90         0.66         9.07        12.95 
TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
       31.33         5.49         1.58         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       14.93        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5218 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-87-5896 
        5.16         5.42        11.38         3.75         1.61        26.30 

  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                           0.2                            0.1 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE 
                        12.180                         12.445 
[1] "0.2 - 127.6 (12.2)" "0.1 - 120.6 (12.4)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q22.1) MUTATED    89 139
  DEL PEAK 33(13Q22.1) WILD-TYPE 136 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED     89  139
  DEL PEAK 33(13Q22.1) WILD-TYPE  136  209
        clus
vv       DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE
  FEMALE                           89                            136
  MALE                            139                            209
[1] 2 2
[1] FALSE
D57V4, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q22.1) MUTATED    36 185
  DEL PEAK 33(13Q22.1) WILD-TYPE  38 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED     36  185
  DEL PEAK 33(13Q22.1) WILD-TYPE   38  290
     clus
vv    DEL PEAK 33(13Q22.1) MUTATED DEL PEAK 33(13Q22.1) WILD-TYPE
  NO                            36                             38
  YES                          185                            290
[1] 2 2
[1] FALSE
D57V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 33(13Q22.1) MUTATED                              10
  DEL PEAK 33(13Q22.1) WILD-TYPE                            20
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 33(13Q22.1) MUTATED                     5
  DEL PEAK 33(13Q22.1) WILD-TYPE                  13
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 33(13Q22.1) MUTATED                               213
  DEL PEAK 33(13Q22.1) WILD-TYPE                             312
D57V6, multiclass
                                 clus
vv                                DEL PEAK 33(13Q22.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                             10
  TREATED PRIMARY GBM                                        5
  UNTREATED PRIMARY (DE NOVO) GBM                          213
                                 clus
vv                                DEL PEAK 33(13Q22.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               20
  TREATED PRIMARY GBM                                         13
  UNTREATED PRIMARY (DE NOVO) GBM                            312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q22.1) MUTATED       5                        18   200
  DEL PEAK 33(13Q22.1) WILD-TYPE     8                        32   287
D57V7, multiclass
                           clus
vv                          DEL PEAK 33(13Q22.1) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              200
                           clus
vv                          DEL PEAK 33(13Q22.1) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             32
  WHITE                                                287
[1] 3 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 33(13Q22.1) MUTATED     3 191
  DEL PEAK 33(13Q22.1) WILD-TYPE   9 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q22.1) MUTATED      3  191
  DEL PEAK 33(13Q22.1) WILD-TYPE    9  284
                        clus
vv                       DEL PEAK 33(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          191
                        clus
vv                       DEL PEAK 33(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            284
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 34(14Q13.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q13.1) MUTATED    35 140
  DEL PEAK 34(14Q13.1) WILD-TYPE  62 333
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           175                            395 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                           140                            333 
$`DEL PEAK 34(14Q13.1) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 
        3.98        11.74         8.35         8.81         6.71         3.75 
TCGA-06-6388 TCGA-06-6697 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TL 
        5.23        12.85         1.55         1.87         2.56        17.72 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 
       21.73        15.65        25.68         6.77        12.69        14.53 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 TCGA-14-0862 TCGA-14-0865 TCGA-14-1455 
       14.93        15.12         6.21         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-16-0848 TCGA-16-1045 TCGA-19-1390 TCGA-19-1791 TCGA-19-2623 TCGA-19-2625 
       17.59        29.03        25.38         0.13         7.53         4.08 
TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 
       24.23         6.64        22.49        14.96        10.03        13.87 
TCGA-26-1440 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2527 
        9.73         9.86        40.54        21.30        18.08        14.40 
TCGA-28-1750 TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 TCGA-32-1976 TCGA-32-1980 
        8.35         2.83         6.74         4.77         0.49         1.18 
TCGA-32-2615 TCGA-32-2634 TCGA-32-4210 TCGA-32-5222 TCGA-41-2573 TCGA-41-2575 
       15.95        22.78         3.72        19.23         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9R TCGA-74-6575 
        0.99         4.44        11.84         0.20         4.08        20.91 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-6191 
        8.22         7.50         3.09         3.65         2.53        16.70 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6664 TCGA-OX-A56R TCGA-02-0001 
        2.70        17.06         8.35        36.20         5.92        11.77 
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 
       23.18        35.41        20.71        87.06        53.10        42.74 
TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       14.14        10.72        10.52        14.73         3.22        15.09 
TCGA-02-0055 TCGA-02-0074 TCGA-02-0086 TCGA-02-0099 TCGA-02-0107 TCGA-02-0113 
        2.50        10.19         8.81         3.48        17.65        92.65 
TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0440 
        3.98         7.73        10.62        15.91        25.71        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2486 
        9.27        16.21         3.35        16.80        15.32        20.32 
TCGA-06-0125 TCGA-06-0128 TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 
       47.61        22.72        12.95        24.23        10.29        11.74 
TCGA-06-0146 TCGA-06-0162 TCGA-06-0166 TCGA-06-0188 TCGA-06-0194 TCGA-06-0216 
       20.09         3.42         5.85        44.58         4.67        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 
        0.72        19.82        48.69         9.01        72.36         4.70 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 
       12.62         5.75         2.10         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-1084 TCGA-06-2561 TCGA-06-6389 
       43.46        46.19         7.17        23.93        17.65         7.79 
TCGA-06-6390 TCGA-08-0245 TCGA-08-0347 TCGA-08-0352 TCGA-08-0380 TCGA-08-0390 
        5.39        37.84        25.71         1.28        14.93        13.97 
TCGA-08-0392 TCGA-08-0512 TCGA-08-0520 TCGA-08-0524 TCGA-12-0616 TCGA-12-0654 
        0.72        42.15        10.75         7.27        14.73         7.59 
TCGA-12-0662 TCGA-12-0692 TCGA-12-0703 TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 
       38.17         3.65        20.38         7.63        10.62       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 TCGA-12-1096 TCGA-12-1099 TCGA-14-0813 
        5.82        33.21        15.98         9.11         4.14         1.35 
TCGA-14-0817 TCGA-15-0742 TCGA-15-1447 TCGA-19-1389 TCGA-26-5133 TCGA-26-5134 
        5.39        13.78        53.19         4.64        14.86         5.49 
TCGA-26-6173 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
        7.92         5.26        11.28        31.27        11.01        13.64 
TCGA-28-5220 
       12.76 

$`DEL PEAK 34(14Q13.1) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 
        1.48        15.32         3.55         4.54         8.98         8.55 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6695 TCGA-06-6698 TCGA-06-6700 
        2.73         6.15         4.57         8.32         4.77         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1600 
        4.96        26.79         3.12        14.60        15.35        14.73 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.77        44.02        26.93        15.22        10.95        34.92 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04        11.97         0.95        23.05        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        3.25        26.33        15.95         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-14-1456 TCGA-14-1458 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 
       40.96         6.67         0.99         1.97        17.79         5.88 
TCGA-14-2555 TCGA-14-4157 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        7.96         3.42         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       21.24        13.97         6.41         8.61        14.27         3.39 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 
        3.65         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        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       17.79        28.54         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 
       18.97        19.33         5.06        16.60        24.23        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        16.77        16.08         7.59 
TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
        2.86        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-32-1970 
        8.48         1.22         1.55         0.13         0.66        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2632 
       14.86        16.93        12.23        20.78        15.02         8.84 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       25.18        21.14        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       13.35        15.12        12.46         1.45        25.58         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 
        4.34        14.33         4.80         4.54         9.17        36.85 
TCGA-76-6192 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        3.29        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 
       18.64         6.28        20.55         7.63         4.73        18.35 
TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 
       10.59        82.59        20.61        77.65        20.12        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0043 TCGA-02-0046 
       12.16        90.58         2.83         3.62        18.31         6.87 
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-02-0075 
       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-02-0087 
       27.25        89.72        22.72        12.62        51.32        57.76 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0111 TCGA-02-0114 
       16.96        27.02        65.00        11.67        23.18        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-02-0326 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
        7.33         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-2470 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 
       10.55        47.11        12.92        15.45         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
       20.38         6.94         3.98        33.67        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 
       26.70        11.90         0.20         2.20         2.33        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       10.45         3.19        10.82         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       10.65        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       69.90        73.84        27.22        15.42        10.42        38.96 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53        15.02        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 
       10.82         0.26         9.57         3.16        35.11         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        9.80        23.57        14.20        26.40        46.88         2.70 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1086 TCGA-06-1087 
       40.41        16.57        20.78        26.76         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
       12.49         4.93        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6693 TCGA-06-6694 
        5.98         4.37         0.43        31.50       120.56         7.36 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       22.68         4.18       115.86         1.74         8.42        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 
       31.10        37.58        22.29         3.39        12.23        18.02 
TCGA-08-0389 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       15.35        12.56         4.27        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 
       19.33         4.80        15.98        18.41         7.56        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       34.92        10.45        94.78         0.10        25.97        26.66 
TCGA-12-0691 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 
       12.13        28.41        15.06        53.85        43.23         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 
       14.93        14.86        91.76        24.79        18.48        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1094 
       27.78        38.76         8.94        20.58         7.59        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0867 
       15.85        14.53         3.98         2.24        11.24         2.04 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
       28.93        19.30         0.79        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        3.91        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-26-1442 TCGA-26-5139 
       10.75         9.07         5.95        12.95        31.33         1.58 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        2.33         7.30        14.93        17.88        14.53        11.77 
TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 
       23.44         5.16        22.68         5.42         7.36        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE 
                         10.75                          12.59 
[1] "0.1 - 127.6 (10.8)" "0.1 - 120.6 (12.6)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED    78  98
  DEL PEAK 34(14Q13.1) WILD-TYPE 147 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED     78   98
  DEL PEAK 34(14Q13.1) WILD-TYPE  147  250
        clus
vv       DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE
  FEMALE                           78                            147
  MALE                             98                            250
[1] 2 2
[1] FALSE
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED    26 146
  DEL PEAK 34(14Q13.1) WILD-TYPE  48 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED     26  146
  DEL PEAK 34(14Q13.1) WILD-TYPE   48  329
     clus
vv    DEL PEAK 34(14Q13.1) MUTATED DEL PEAK 34(14Q13.1) WILD-TYPE
  NO                            26                             48
  YES                          146                            329
[1] 2 2
[1] FALSE
D58V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 34(14Q13.1) MUTATED                               6
  DEL PEAK 34(14Q13.1) WILD-TYPE                            24
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 34(14Q13.1) MUTATED                     6
  DEL PEAK 34(14Q13.1) WILD-TYPE                  12
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 34(14Q13.1) MUTATED                               164
  DEL PEAK 34(14Q13.1) WILD-TYPE                             361
D58V6, multiclass
                                 clus
vv                                DEL PEAK 34(14Q13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        6
  UNTREATED PRIMARY (DE NOVO) GBM                          164
                                 clus
vv                                DEL PEAK 34(14Q13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         12
  UNTREATED PRIMARY (DE NOVO) GBM                            361
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q13.1) MUTATED       2                        19   147
  DEL PEAK 34(14Q13.1) WILD-TYPE    11                        31   340
D58V7, multiclass
                           clus
vv                          DEL PEAK 34(14Q13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           19
  WHITE                                              147
                           clus
vv                          DEL PEAK 34(14Q13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             31
  WHITE                                                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"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q13.1) MUTATED     1 145
  DEL PEAK 34(14Q13.1) WILD-TYPE  11 330
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q13.1) MUTATED      1  145
  DEL PEAK 34(14Q13.1) WILD-TYPE   11  330
                        clus
vv                       DEL PEAK 34(14Q13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 34(14Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            330
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 35(14Q24.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(14Q24.2) MUTATED    31 139
  DEL PEAK 35(14Q24.2) WILD-TYPE  66 334
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           170                            400 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                           139                            334 
$`DEL PEAK 35(14Q24.2) MUTATED`
TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5411 TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 
        3.98        11.74         8.35         6.71         3.75         4.57 
TCGA-06-6697 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TL TCGA-12-0615 
       12.85         1.55         1.87         2.56        17.72        15.35 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 
       21.73        15.65        14.73         6.77        12.69        14.53 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
       14.93        15.12         6.21         2.89        16.50         1.12 
TCGA-14-1401 TCGA-14-1453 TCGA-14-1455 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
        3.75         1.15         0.92        17.79        17.85         7.63 
TCGA-14-1829 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-19-1390 
        7.17         3.78         3.42        17.59        29.03        25.38 
TCGA-19-1791 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 
        0.13         7.53         4.08        24.23         6.64        22.49 
TCGA-19-5960 TCGA-26-1439 TCGA-26-1440 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
       14.96        13.87         9.73         9.86        40.54        21.30 
TCGA-27-2519 TCGA-27-2527 TCGA-28-1750 TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 
       18.08        14.40         8.35         2.83         6.74         4.77 
TCGA-32-1976 TCGA-32-1980 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 
        0.49         1.18        20.78        15.95        22.78        21.14 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-4097 TCGA-76-4928 TCGA-76-4929 
        8.94         9.53         0.99         0.20         3.09         3.65 
TCGA-76-4934 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-OX-A56R TCGA-02-0007 
        2.53         2.70        17.06         8.35         5.92        23.18 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       35.41        20.71        87.06        53.10        42.74        24.59 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0055 
       14.14        10.52        14.73         3.22        15.09         2.50 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0074 TCGA-02-0086 TCGA-02-0099 
        8.35         6.02        28.70        10.19         8.81         3.48 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0113 TCGA-02-0258 TCGA-02-0266 TCGA-02-0281 
       65.00        17.65        92.65        16.54        17.72         3.98 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0432 TCGA-02-0446 
        7.73        10.62        15.91        25.71        47.11         9.27 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        3.35        16.80        15.32        22.72        33.67        12.95 
TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 TCGA-06-0146 TCGA-06-0155 TCGA-06-0162 
       24.23        10.29        11.74        20.09        10.45         3.42 
TCGA-06-0166 TCGA-06-0171 TCGA-06-0188 TCGA-06-0194 TCGA-06-0214 TCGA-06-0216 
        5.85        13.12        44.58         4.67        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
        0.72        19.82        48.69        72.36         4.70         9.57 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 TCGA-06-0750 TCGA-06-0875 
       12.62         5.75         2.10         7.86         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-2561 TCGA-06-6389 TCGA-06-6390 TCGA-08-0245 
       46.19         7.17        17.65         7.79         5.39        37.84 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 
       14.93        13.97         0.72        42.15        58.68        10.75 
TCGA-12-0616 TCGA-12-0654 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0776 
       14.73         7.59        38.17        12.13         3.65         9.73 
TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1096 
       10.62        38.76       127.59         5.82        33.21         9.11 
TCGA-14-0813 TCGA-14-0817 TCGA-15-1447 TCGA-19-0962 TCGA-19-1389 TCGA-26-5133 
        1.35         5.39        53.19         0.66         4.64        14.86 
TCGA-26-5134 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
        5.49         5.26        11.28        31.27        11.01        13.64 
TCGA-28-5220 TCGA-32-2616 
       12.76         7.36 

$`DEL PEAK 35(14Q24.2) WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
        1.48        15.32         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6698 
        8.55         2.73         6.15         5.23         8.32         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-12-1599 
        4.77         4.96        26.79         3.12        14.60        25.68 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.77        44.02        26.93        15.22        10.95        34.92 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04        11.97         0.95        23.05        13.78 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1402 TCGA-14-1450 
        3.25        26.33        15.95         1.38        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
       23.11         7.10        30.18        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-16-1047 
        0.99         1.97         5.88        17.49         7.96         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        8.61        14.27         3.39         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2631 
        3.25         9.67         4.87         1.08         0.16         7.00 
TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.04        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
        1.78        14.07        16.80        17.79        28.54        10.03 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
        7.13         9.37         9.40         8.88        18.97        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        5.06        16.60        24.23        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       24.76        16.77        16.08         7.59         2.86        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
        1.55         0.13         0.66        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-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       12.23        15.02         8.84        25.18         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3393 
       19.86        10.85        19.23         0.85        13.35         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84        15.12        12.46         4.08         1.45        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        4.80         4.54         9.17        36.85        16.70         3.29 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
       36.20         6.28        20.55         7.63        11.77         4.73 
TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0021 TCGA-02-0023 
       18.35        10.59        82.59        20.61        77.65        20.12 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       12.16        90.58         2.83         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 
        6.87        12.59         6.54        19.86         9.57        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       26.43        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 
       22.72        12.62        51.32        57.76        16.96        27.02 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 
       11.67        23.18        99.98        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-02-0326 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        9.90         7.33         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0451 TCGA-02-2470 TCGA-02-2485 
       14.50        10.55        11.34        16.21        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
        3.98        25.35        14.30        26.70        11.90         0.20 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.20         2.33        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.33        13.94         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 
       11.80        56.91        10.65        19.66         3.29         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        3.65        69.90        73.84        27.22        15.42        10.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
        7.40        11.84         0.53        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 
       10.82         9.01         0.26         3.16        35.11         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
        9.80        23.57        14.20        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        2.70        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
      120.56         7.36        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 
       22.29         3.39        12.23        18.02        15.35        12.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
        4.27        11.08        19.59        19.33         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        18.41         7.56        12.99        34.92        10.45 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 
       94.78         0.10        25.97        26.66        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85        43.23         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       91.76        24.79        18.48        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1090 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
       20.58         7.59        15.98        12.23        15.85        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0867 TCGA-14-0871 
        3.98         4.14         2.24        11.24         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
       19.30         0.79        13.78        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1385 
        3.91        26.07        16.37        11.77        21.90        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-26-1442 TCGA-26-5139 TCGA-26-6173 
        9.07         5.95        12.95        31.33         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        2.33         7.30        14.93        17.88        14.53        11.77 
TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
       23.44         5.16        22.68         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                        127.59                         120.56 
  DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE 
                        11.145                         12.445 
[1] "0.1 - 127.6 (11.1)" "0.1 - 120.6 (12.4)"
[1] "hr=" "1"  
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q24.2) MUTATED    74  97
  DEL PEAK 35(14Q24.2) WILD-TYPE 151 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED     74   97
  DEL PEAK 35(14Q24.2) WILD-TYPE  151  251
        clus
vv       DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE
  FEMALE                           74                            151
  MALE                             97                            251
[1] 2 2
[1] FALSE
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q24.2) MUTATED    29 139
  DEL PEAK 35(14Q24.2) WILD-TYPE  45 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED     29  139
  DEL PEAK 35(14Q24.2) WILD-TYPE   45  336
     clus
vv    DEL PEAK 35(14Q24.2) MUTATED DEL PEAK 35(14Q24.2) WILD-TYPE
  NO                            29                             45
  YES                          139                            336
[1] 2 2
[1] FALSE
D59V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 35(14Q24.2) MUTATED                               5
  DEL PEAK 35(14Q24.2) WILD-TYPE                            25
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 35(14Q24.2) MUTATED                     7
  DEL PEAK 35(14Q24.2) WILD-TYPE                  11
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 35(14Q24.2) MUTATED                               159
  DEL PEAK 35(14Q24.2) WILD-TYPE                             366
D59V6, multiclass
                                 clus
vv                                DEL PEAK 35(14Q24.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        7
  UNTREATED PRIMARY (DE NOVO) GBM                          159
                                 clus
vv                                DEL PEAK 35(14Q24.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         11
  UNTREATED PRIMARY (DE NOVO) GBM                            366
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q24.2) MUTATED       5                        16   145
  DEL PEAK 35(14Q24.2) WILD-TYPE     8                        34   342
D59V7, multiclass
                           clus
vv                          DEL PEAK 35(14Q24.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              145
                           clus
vv                          DEL PEAK 35(14Q24.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             34
  WHITE                                                342
[1] 3 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 35(14Q24.2) MUTATED     3 141
  DEL PEAK 35(14Q24.2) WILD-TYPE   9 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q24.2) MUTATED      3  141
  DEL PEAK 35(14Q24.2) WILD-TYPE    9  334
                        clus
vv                       DEL PEAK 35(14Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK 35(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 36(15Q14) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(15Q14) MUTATED    24 129
  DEL PEAK 36(15Q14) WILD-TYPE  73 344
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         153                          417 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         129                          344 
$`DEL PEAK 36(15Q14) MUTATED`
TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK 
        8.81         6.71         3.75         1.87         3.12        14.60 
TCGA-06-A7TL TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 
       17.72        15.65        14.73         6.77        44.02        26.93 
TCGA-12-3651 TCGA-14-0736 TCGA-14-0783 TCGA-14-1459 TCGA-14-1794 TCGA-16-0848 
       12.69        15.12         6.21        12.43         0.99        17.59 
TCGA-16-1045 TCGA-16-1063 TCGA-19-0963 TCGA-19-1390 TCGA-19-1392 TCGA-19-2629 
       29.03        13.97        14.27        25.38         3.65        24.23 
TCGA-19-4065 TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 
        7.04         1.78        22.49        14.96        10.03        13.87 
TCGA-27-1830 TCGA-27-1834 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 
        5.06        40.54        18.08         7.59         2.86         0.20 
TCGA-28-1750 TCGA-28-1756 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-2494 
        8.35         2.83        15.39        21.07         0.49        20.78 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 
       22.78         3.72        12.59        10.85         0.85         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S 
        9.53         0.99        11.84        15.12         4.08         1.45 
TCGA-74-6578 TCGA-76-4925 TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 TCGA-76-6193 
       14.33         4.80         3.65        36.85        16.70         2.70 
TCGA-76-6285 TCGA-76-6286 TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0011 
        8.35        20.98         7.63        11.77         4.73        20.71 
TCGA-02-0016 TCGA-02-0024 TCGA-02-0026 TCGA-02-0034 TCGA-02-0038 TCGA-02-0047 
       87.06        53.10        24.59        14.14        10.72        14.73 
TCGA-02-0048 TCGA-02-0054 TCGA-02-0074 TCGA-02-0079 TCGA-02-0084 TCGA-02-0087 
        3.22         6.54        10.19        27.25        12.62        57.76 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 TCGA-02-0269 TCGA-02-0281 
       23.18        92.65        15.65        16.54        10.75         3.98 
TCGA-02-0321 TCGA-02-0324 TCGA-02-2470 TCGA-02-2483 TCGA-06-0119 TCGA-06-0124 
        9.90         7.73        12.92        15.32         2.70        20.38 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0141 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 
       22.72        33.67        10.29         5.85         3.22         4.18 
TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0201 TCGA-06-0213 TCGA-06-0216 
       44.58        10.42        38.96         0.39         0.53        24.16 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0402 TCGA-06-0410 TCGA-06-0645 TCGA-06-0646 
       13.64        13.32         0.26         4.70         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0745 TCGA-06-0875 TCGA-06-1801 
        9.80         2.10        14.20         7.86        43.46        11.84 
TCGA-06-2558 TCGA-06-2562 TCGA-06-6694 TCGA-08-0246 TCGA-08-0344 TCGA-08-0348 
       12.49        12.56         7.36         4.18       115.86        12.16 
TCGA-08-0349 TCGA-08-0355 TCGA-08-0359 TCGA-08-0386 TCGA-08-0510 TCGA-08-0525 
        9.80        24.56         3.39        18.02         4.27        15.98 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0707 TCGA-12-0775 TCGA-12-0821 TCGA-12-1088 
       12.99        34.92        28.41         7.63        10.62       127.59 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-14-0817 TCGA-14-0867 TCGA-15-1447 
        9.11        14.53         4.14         5.39         2.04        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-1385 TCGA-19-1387 
       13.28         3.91        26.07        16.37        10.75         5.95 
TCGA-19-1388 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5215 TCGA-28-5219 
       12.95         2.33         7.30         5.26        11.01        22.68 
TCGA-32-2616 TCGA-76-6283 TCGA-76-6660 
        7.36         5.42         3.75 

$`DEL PEAK 36(15Q14) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        4.54         8.98         8.55         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 
        4.96        26.79         2.56        15.35        21.73        25.68 
TCGA-12-3644 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       59.77        15.22        10.95        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04        11.97         0.95        23.05        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         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-14-1795 
        1.15        30.18         0.92        40.96         6.67         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-16-1047 TCGA-16-1055 TCGA-16-1056 
        7.96         3.78         3.42         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 TCGA-19-1786 
        9.14        21.24         6.41         8.61         3.39         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        7.53         0.16         4.08         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 
        8.02        18.90         4.73        12.10        14.07        16.80 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       17.79        28.54         9.73         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97        19.33        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 
       21.30        30.05        14.04        11.51        24.76        16.77 
TCGA-27-2523 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       16.08        14.40        15.78         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         0.13         0.66         6.74 
TCGA-28-2509 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        4.77         0.10        15.85        19.50         1.18         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-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 TCGA-32-5222 TCGA-41-2572 
        8.84        25.18        21.14        19.86        19.23        13.35 
TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        4.44         0.20        12.46        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
        4.34         8.22         7.50         4.54         3.09         9.17 
TCGA-76-4934 TCGA-76-6192 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.53         3.29        17.06         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 TCGA-02-0015 
       18.35        23.18        10.59        35.41        82.59        20.61 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       77.65        20.12        42.74        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 
        3.62        10.52        18.31         6.87        15.09        12.59 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0080 
       26.43        28.70        25.05         5.49        20.84        89.72 
TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       22.72        51.32         8.81        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       65.00        11.67        17.65        99.98        48.95        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21         3.35        16.80        15.45        20.32 
TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 
        6.15        47.61         6.94         3.98        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 
       14.30        26.70        24.23        11.90         0.20         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         4.47         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 TCGA-06-0208 
       15.42         4.67         7.40         5.56         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 
        7.40        11.84        15.02         0.72        19.82        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       48.69        10.82         9.01        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.11        12.62        23.57        26.40        46.88         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        2.70         0.92        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 
       15.32        13.61        33.90         1.08         4.93        17.65 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 
       31.50         7.79         5.39       120.56        22.68        37.84 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        1.74         8.42        25.71        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
        8.42        17.95        31.10        37.58        22.29        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 
        7.27        18.41         7.56        14.73        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0776 
        3.65        20.38        15.06        53.85        43.23         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 
       14.93        14.86        91.76        24.79        18.48        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 
       27.78        38.76         8.94        20.58         5.82         7.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-14-0787 
       33.21        15.98        12.23        15.85         3.98         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 
       50.53        19.10        11.77        21.90         0.66         9.07 
TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        4.64        31.33        14.86         5.49         1.58         7.92 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       23.44        13.64         5.16        12.76         5.42        11.38 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                      127.59                       120.56 
  DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE 
                       11.01                        12.56 
[1] "0.2 - 127.6 (11.0)" "0.1 - 120.6 (12.6)"
[1] "hr=" "1.1"
D60V2, continuous
D60V3, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED    58  96
  DEL PEAK 36(15Q14) WILD-TYPE 167 252
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED     58   96
  DEL PEAK 36(15Q14) WILD-TYPE  167  252
        clus
vv       DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE
  FEMALE                         58                          167
  MALE                           96                          252
[1] 2 2
[1] FALSE
D60V4, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED    24 122
  DEL PEAK 36(15Q14) WILD-TYPE  50 353
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED     24  122
  DEL PEAK 36(15Q14) WILD-TYPE   50  353
     clus
vv    DEL PEAK 36(15Q14) MUTATED DEL PEAK 36(15Q14) WILD-TYPE
  NO                          24                           50
  YES                        122                          353
[1] 2 2
[1] FALSE
D60V5, continuous
                              vv
clus                           GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 36(15Q14) MUTATED                              10
  DEL PEAK 36(15Q14) WILD-TYPE                            20
                              vv
clus                           TREATED PRIMARY GBM
  DEL PEAK 36(15Q14) MUTATED                     4
  DEL PEAK 36(15Q14) WILD-TYPE                  14
                              vv
clus                           UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 36(15Q14) MUTATED                               140
  DEL PEAK 36(15Q14) WILD-TYPE                             385
D60V6, multiclass
                                 clus
vv                                DEL PEAK 36(15Q14) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                           10
  TREATED PRIMARY GBM                                      4
  UNTREATED PRIMARY (DE NOVO) GBM                        140
                                 clus
vv                                DEL PEAK 36(15Q14) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                             20
  TREATED PRIMARY GBM                                       14
  UNTREATED PRIMARY (DE NOVO) GBM                          385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q14) MUTATED       5                        11   131
  DEL PEAK 36(15Q14) WILD-TYPE     8                        39   356
D60V7, multiclass
                           clus
vv                          DEL PEAK 36(15Q14) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                         11
  WHITE                                            131
                           clus
vv                          DEL PEAK 36(15Q14) WILD-TYPE
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           39
  WHITE                                              356
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                              cls
clus                             0   1
  DEL PEAK 36(15Q14) MUTATED     5 132
  DEL PEAK 36(15Q14) WILD-TYPE   7 343
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(15Q14) MUTATED      5  132
  DEL PEAK 36(15Q14) WILD-TYPE    7  343
                        clus
vv                       DEL PEAK 36(15Q14) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        132
                        clus
vv                       DEL PEAK 36(15Q14) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          343
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 37(16P12.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16P12.2) MUTATED     9  82
  DEL PEAK 37(16P12.2) WILD-TYPE  88 391
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            91                            479 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                            82                            391 
$`DEL PEAK 37(16P12.2) MUTATED`
TCGA-06-5418 TCGA-06-6698 TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        2.73         4.77         4.77         1.87         3.12         2.56 
TCGA-12-1600 TCGA-12-3649 TCGA-12-3651 TCGA-12-3653 TCGA-12-5301 TCGA-14-0736 
       14.73        15.22        12.69        14.53         2.04        15.12 
TCGA-14-0812 TCGA-14-1823 TCGA-19-1392 TCGA-19-1786 TCGA-19-2620 TCGA-19-5953 
        3.25        17.85         3.65         7.17         4.87         4.73 
TCGA-19-5955 TCGA-19-5956 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-2521 
        1.78        22.49        40.54        21.30        30.05        16.77 
TCGA-27-2524 TCGA-28-1750 TCGA-28-1753 TCGA-32-1978 TCGA-32-1980 TCGA-32-2494 
        7.59         8.35         1.22        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 TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 
       16.70        17.06        42.74        12.59         2.50        10.19 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0266 TCGA-02-0281 TCGA-02-0337 TCGA-02-0456 
       48.95        16.54        17.72         3.98        25.12         3.35 
TCGA-02-2486 TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 
       20.32        25.35        56.91        19.66        13.12         4.18 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0394 TCGA-06-0410 TCGA-06-0414 
       15.02        24.16        19.82        10.82         4.70        35.11 
TCGA-06-0645 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0879 
        5.75         2.10        14.20        26.40        46.88        40.41 
TCGA-06-0882 TCGA-06-1087 TCGA-06-2557 TCGA-06-2569 TCGA-06-6389 TCGA-08-0347 
       20.78         4.04         1.08         0.43         7.79        25.71 
TCGA-08-0353 TCGA-08-0386 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
        8.42        18.02         0.72        12.56         4.27        11.08 
TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 TCGA-12-0776 TCGA-12-0822 TCGA-12-0826 
       15.98        34.92        10.45         9.73        23.51        27.78 
TCGA-12-0827 TCGA-12-1099 TCGA-14-0813 TCGA-14-0871 TCGA-19-1389 TCGA-28-5204 
       38.76         4.14         1.35        28.93         4.64        14.93 
TCGA-28-5216 
       13.64 

$`DEL PEAK 37(16P12.2) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
        4.54         8.81         8.98         8.55         6.71         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        6.15         4.57         5.23         8.32        12.85         1.55 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
        4.96        26.79        14.60        17.72        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68         6.77        59.77        44.02        26.93 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 
       10.95        34.92        14.93         3.22        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        6.21        23.05        13.78         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       17.59        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
       21.24        13.97         6.41         8.61        14.27         3.39 
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        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        6.64        17.19         8.02        18.90        12.10        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        9.73         7.13         9.37         9.40         8.88        18.97 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1837 
       19.33         5.06        16.60         9.86        24.23        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       11.51        24.76        18.08        16.08         2.86        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-28-1755 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-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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        4.44         0.20        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 
        4.54         3.65         9.17         2.53        36.85         3.29 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       34.45        18.64        36.20         5.92         6.28        20.55 
TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
        7.63        11.77         4.73        18.35        23.18        10.59 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
       35.41        20.71        82.59        20.61        87.06        77.65 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       20.12        53.10        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       14.73         3.22        15.09         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 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-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       15.65        16.93        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91        25.71         4.37        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 
       10.55        47.11        11.34         9.27        16.21        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.32        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        3.19        10.82         9.44        11.80         3.42        10.65 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        5.85         3.29         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.53         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        9.01         0.26        72.36         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        5.75         9.80        23.57         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0939 
        0.92        43.46        46.19         7.17        16.57        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6390 
        5.95        16.64         5.98         4.37        31.50         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
      120.56         7.36        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74         8.42        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0512 
        3.39        12.23        14.93        15.35        13.97        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 TCGA-12-0656 
       18.41         7.56        14.73        12.99         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 
        2.24        11.24         5.39         2.04        19.30         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 
       26.07        16.37        11.77        21.90         0.66        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        9.07         5.95        12.95        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 
        1.58         7.92         2.33         7.30         5.26        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 
        5.16        22.68        12.76         5.42         7.36        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                         56.91                         127.59 
  DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE 
                         12.59                          12.23 
[1] "0.4 - 56.9 (12.6)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
                                cls
clus                               0   1
  DEL PEAK 37(16P12.2) MUTATED    32  60
  DEL PEAK 37(16P12.2) WILD-TYPE 193 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED     32   60
  DEL PEAK 37(16P12.2) WILD-TYPE  193  288
        clus
vv       DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE
  FEMALE                           32                            193
  MALE                             60                            288
[1] 2 2
[1] FALSE
D61V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(16P12.2) MUTATED    16  71
  DEL PEAK 37(16P12.2) WILD-TYPE  58 404
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED     16   71
  DEL PEAK 37(16P12.2) WILD-TYPE   58  404
     clus
vv    DEL PEAK 37(16P12.2) MUTATED DEL PEAK 37(16P12.2) WILD-TYPE
  NO                            16                             58
  YES                           71                            404
[1] 2 2
[1] FALSE
D61V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 37(16P12.2) MUTATED                               3
  DEL PEAK 37(16P12.2) WILD-TYPE                            27
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 37(16P12.2) MUTATED                     1
  DEL PEAK 37(16P12.2) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 37(16P12.2) MUTATED                                88
  DEL PEAK 37(16P12.2) WILD-TYPE                             437
D61V6, multiclass
                                 clus
vv                                DEL PEAK 37(16P12.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           88
                                 clus
vv                                DEL PEAK 37(16P12.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16P12.2) MUTATED       2                         9    77
  DEL PEAK 37(16P12.2) WILD-TYPE    11                        41   410
D61V7, multiclass
                           clus
vv                          DEL PEAK 37(16P12.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               77
                           clus
vv                          DEL PEAK 37(16P12.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             41
  WHITE                                                410
[1] 3 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 37(16P12.2) MUTATED     2  78
  DEL PEAK 37(16P12.2) WILD-TYPE  10 397
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16P12.2) MUTATED      2   78
  DEL PEAK 37(16P12.2) WILD-TYPE   10  397
                        clus
vv                       DEL PEAK 37(16P12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 37(16P12.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            397
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 38(16Q23.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.1) MUTATED     8  92
  DEL PEAK 38(16Q23.1) WILD-TYPE  89 381
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           100                            470 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            92                            381 
$`DEL PEAK 38(16Q23.1) MUTATED`
TCGA-06-5418 TCGA-06-5859 TCGA-06-6698 TCGA-06-6700 TCGA-06-A6S0 TCGA-06-A6S1 
        2.73         4.57         4.77         4.77         3.12         2.56 
TCGA-12-1600 TCGA-12-3649 TCGA-12-3653 TCGA-12-5295 TCGA-12-5301 TCGA-14-0736 
       14.73        15.22        14.53        14.93         2.04        15.12 
TCGA-14-0812 TCGA-14-0862 TCGA-14-1453 TCGA-14-1823 TCGA-14-2554 TCGA-16-1045 
        3.25         2.89         1.15        17.85        17.49        29.03 
TCGA-19-1392 TCGA-19-5947 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-27-1832 
        3.65         6.64         4.73         1.78        22.49         9.86 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1755 TCGA-32-1973 TCGA-32-1978 
       16.77         7.59         8.35         1.55        21.07        15.85 
TCGA-32-1980 TCGA-32-1987 TCGA-32-2494 TCGA-32-4210 TCGA-41-3915 TCGA-41-5651 
        1.18        14.86        20.78         3.72        11.84        15.12 
TCGA-74-6578 TCGA-76-4928 TCGA-OX-A56R TCGA-02-0009 TCGA-02-0026 TCGA-02-0038 
       14.33         3.09         5.92        10.59        24.59        10.72 
TCGA-02-0039 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 TCGA-02-0114 TCGA-02-0258 
       10.52        12.59         2.50        10.19        99.98        16.54 
TCGA-02-0281 TCGA-02-0321 TCGA-02-0337 TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 
        3.98         9.90        25.12         3.35        12.92        20.32 
TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0174 TCGA-06-0177 
       25.35        56.91        19.66        13.12         3.22         4.18 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0414 TCGA-06-0645 
       15.02        24.16         0.72        19.82        35.11         5.75 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0749 TCGA-06-0879 TCGA-06-0882 
       14.20        26.40        46.88         2.70        40.41        20.78 
TCGA-06-1087 TCGA-06-2557 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-6389 
        4.04         1.08         5.98         4.37         0.43         7.79 
TCGA-06-6693 TCGA-08-0353 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0520 
      120.56         8.42         0.72        12.56        42.15        10.75 
TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 TCGA-12-0692 TCGA-12-0826 
       15.98        12.99        34.92         7.59         3.65        27.78 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1099 TCGA-14-0787 TCGA-14-0813 TCGA-14-0871 
      127.59        33.21         4.14         2.24         1.35        28.93 
TCGA-19-1389 TCGA-28-5204 TCGA-28-5216 TCGA-76-6660 
        4.64        14.93        13.64         3.75 

$`DEL PEAK 38(16Q23.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
        4.54         8.81         8.98         8.55         6.71         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6701 
        6.15         5.23         8.32        12.85         1.55         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
       26.79         1.87        14.60        17.72        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68         6.77        59.77        44.02        26.93 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 
       10.95        12.69        34.92         3.22        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 
        6.21        23.05        13.78        16.50        26.33        15.95 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 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-16-0848 TCGA-16-1047 TCGA-16-1055 
        7.96         3.78         3.42        17.59         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 
       14.01         9.14        21.24        13.97         6.41         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       14.27         3.39        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         7.04        17.19         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
       18.90        12.10        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        9.40         8.88        18.97        19.33         5.06        16.60 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        18.08        16.08         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        2.83         0.13         0.66         6.74         4.77        15.39 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.49         0.10        19.50         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       13.35         8.94         9.53         0.99         4.44         0.20 
TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       12.46         4.08         1.45        25.58         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 
        4.34         8.22         7.50         4.80         4.54         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       34.45        18.64        36.20         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 
       18.31         6.87        14.73         3.22        15.09         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       28.70        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       92.65        15.65        48.95        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 
       14.47        13.87        14.20        15.95        12.23         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 
       10.62         7.33        15.91        25.71         4.37        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 
       16.21        16.80        15.32        15.45         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       12.95        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       10.65         5.85         3.29         4.47         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.53        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 
       12.62         5.75         9.80         2.10        23.57         7.86 
TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 
        2.70         0.92        43.46        46.19         7.17        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61        33.90        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2570 TCGA-06-6390 TCGA-06-6694 
       30.64         5.95        16.64        31.50         5.39         7.36 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 
       12.23        14.93        18.02        15.35        13.97         4.27 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        58.68        19.33         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 
       18.41         7.56        14.73        10.45        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66        12.13        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1093 
       38.76         8.94        20.58         5.82         7.59        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-14-0789 
       12.23        15.85         9.11        14.53         3.98        11.24 
TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        5.39         2.04        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19        13.28         3.91        26.07        16.37 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
       11.77        21.90         0.66        10.75         9.07         5.95 
TCGA-19-1388 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       12.95        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        2.33         7.30         5.26        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        23.44        11.01         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 
       12.76         5.42         7.36        11.38         5.42         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                        127.59                         115.86 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                        10.735                         12.360 
[1] "0.4 - 127.6 (10.7)" "0.1 - 115.9 (12.4)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    40  60
  DEL PEAK 38(16Q23.1) WILD-TYPE 185 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     40   60
  DEL PEAK 38(16Q23.1) WILD-TYPE  185  288
        clus
vv       DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  FEMALE                           40                            185
  MALE                             60                            288
[1] 2 2
[1] FALSE
D62V4, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    18  75
  DEL PEAK 38(16Q23.1) WILD-TYPE  56 400
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     18   75
  DEL PEAK 38(16Q23.1) WILD-TYPE   56  400
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  NO                            18                             56
  YES                           75                            400
[1] 2 2
[1] FALSE
D62V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 38(16Q23.1) MUTATED                               4
  DEL PEAK 38(16Q23.1) WILD-TYPE                            26
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 38(16Q23.1) MUTATED                     2
  DEL PEAK 38(16Q23.1) WILD-TYPE                  16
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 38(16Q23.1) MUTATED                                94
  DEL PEAK 38(16Q23.1) WILD-TYPE                             431
D62V6, multiclass
                                 clus
vv                                DEL PEAK 38(16Q23.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              4
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           94
                                 clus
vv                                DEL PEAK 38(16Q23.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               26
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16Q23.1) MUTATED       2                        11    85
  DEL PEAK 38(16Q23.1) WILD-TYPE    11                        39   402
D62V7, multiclass
                           clus
vv                          DEL PEAK 38(16Q23.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                               85
                           clus
vv                          DEL PEAK 38(16Q23.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             39
  WHITE                                                402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED     1  87
  DEL PEAK 38(16Q23.1) WILD-TYPE  11 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED      1   87
  DEL PEAK 38(16Q23.1) WILD-TYPE   11  388
                        clus
vv                       DEL PEAK 38(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK 38(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            388
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 39(17P13.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P13.1) MUTATED    17  81
  DEL PEAK 39(17P13.1) WILD-TYPE  80 392
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            98                            472 
  DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE 
                            81                            392 
$`DEL PEAK 39(17P13.1) MUTATED`
TCGA-06-5408 TCGA-06-A5U0 TCGA-12-1598 TCGA-12-3646 TCGA-12-3653 TCGA-14-0783 
       11.74        26.79        15.65        44.02        14.53         6.21 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1453 TCGA-14-1794 TCGA-14-3477 TCGA-19-0960 
       15.95         1.12         1.15         0.99         3.78         8.61 
TCGA-19-1791 TCGA-19-2623 TCGA-19-2629 TCGA-19-4065 TCGA-27-1835 TCGA-28-1756 
        0.13         7.53        24.23         7.04        21.30         2.83 
TCGA-28-2509 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-4210 TCGA-41-2573 
        4.77         0.49        14.86        12.23         3.72         8.94 
TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-76-4925 
        0.99        11.84        15.12         4.08         1.45         4.80 
TCGA-76-4934 TCGA-76-6285 TCGA-76-6662 TCGA-02-0001 TCGA-02-0024 TCGA-02-0033 
        2.53         8.35        34.45        11.77        53.10         2.83 
TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0079 TCGA-02-0086 TCGA-02-0104 
        2.50         9.57        28.70        27.25         8.81        65.00 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 TCGA-02-0269 TCGA-02-0281 
       11.67        92.65        15.65        16.54        10.75         3.98 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0339 TCGA-02-0456 TCGA-06-0130 TCGA-06-0147 
        9.90        10.62        12.39         3.35        12.95        17.79 
TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
        8.61        12.33         9.44         4.18        69.90        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 
       44.58        15.42        10.42        38.96         5.56         7.66 
TCGA-06-0213 TCGA-06-0241 TCGA-06-0397 TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 
        0.53        48.69         9.01         4.70        12.62         5.75 
TCGA-06-0744 TCGA-06-0875 TCGA-06-1086 TCGA-06-1087 TCGA-06-2557 TCGA-06-2558 
       46.88        43.46         6.84         4.04         1.08        12.49 
TCGA-06-2561 TCGA-06-2569 TCGA-06-6694 TCGA-08-0245 TCGA-08-0353 TCGA-08-0386 
       17.65         0.43         7.36        37.84         8.42        18.02 
TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 TCGA-14-0871 
       13.97        34.92        53.85        27.78         3.98        28.93 
TCGA-15-1449 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-28-5215 TCGA-32-2616 
       13.28         3.91        31.33        14.86        11.01         7.36 
TCGA-76-6283 TCGA-76-6660 
        5.42         3.75 

$`DEL PEAK 39(17P13.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        15.32         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 
       14.60        17.72        15.35        21.73        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
        0.95        23.05        13.78         3.25         2.89        16.50 
TCGA-14-0866 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
       26.33         1.38         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 
       17.49         7.96         3.42        17.59        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       14.27         3.39        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 
        3.25         9.67         4.87         1.08         0.16         4.08 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       17.79        28.54        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        24.23        40.54        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        16.77        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-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
        0.66         6.74        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        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 
        9.53         4.44         0.20        12.46        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        17.06        20.98         4.83         5.03        23.90 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       24.59        12.16        90.58        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 
       26.43        25.05         5.49        10.19        20.84        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       27.02        17.65        23.18        99.98        48.95        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       20.09        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.04        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        4.67         7.40         0.39         8.42         7.40        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       20.42        10.82         0.26        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
       35.11         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       26.40         7.86         2.70         2.70         0.92        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2559 
       26.79        11.84        15.32        13.61        33.90         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 
       31.50         7.79         5.39       120.56        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       29.23        65.33         1.28        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
       18.41         7.56        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 
        3.65        20.38        28.41        15.06        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
        9.11        14.53         4.14         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        5.39         2.04        19.30         0.79        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 
       19.10        53.19        26.07        16.37        11.77        21.90 
TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        0.66        10.75         9.07         5.95        12.95         4.64 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        13.64         5.16        22.68        12.76         5.42 
TCGA-76-6280 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         1.61        17.72        26.30 

  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 
                        10.685                         12.605 
[1] "0.1 - 92.7 (10.7)"  "0.1 - 127.6 (12.6)"
[1] "hr=" "1.1"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.1) MUTATED    46  52
  DEL PEAK 39(17P13.1) WILD-TYPE 179 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED     46   52
  DEL PEAK 39(17P13.1) WILD-TYPE  179  296
        clus
vv       DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE
  FEMALE                           46                            179
  MALE                             52                            296
[1] 2 2
[1] FALSE
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.1) MUTATED    13  80
  DEL PEAK 39(17P13.1) WILD-TYPE  61 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED     13   80
  DEL PEAK 39(17P13.1) WILD-TYPE   61  395
     clus
vv    DEL PEAK 39(17P13.1) MUTATED DEL PEAK 39(17P13.1) WILD-TYPE
  NO                            13                             61
  YES                           80                            395
[1] 2 2
[1] FALSE
D63V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 39(17P13.1) MUTATED                               6
  DEL PEAK 39(17P13.1) WILD-TYPE                            24
                                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                                89
  DEL PEAK 39(17P13.1) WILD-TYPE                             436
D63V6, multiclass
                                 clus
vv                                DEL PEAK 39(17P13.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              6
  TREATED PRIMARY GBM                                        3
  UNTREATED PRIMARY (DE NOVO) GBM                           89
                                 clus
vv                                DEL PEAK 39(17P13.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               24
  TREATED PRIMARY GBM                                         15
  UNTREATED PRIMARY (DE NOVO) GBM                            436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17P13.1) MUTATED       2                        10    84
  DEL PEAK 39(17P13.1) WILD-TYPE    11                        40   403
D63V7, multiclass
                           clus
vv                          DEL PEAK 39(17P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               84
                           clus
vv                          DEL PEAK 39(17P13.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                403
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.1) MUTATED     2  85
  DEL PEAK 39(17P13.1) WILD-TYPE  10 390
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.1) MUTATED      2   85
  DEL PEAK 39(17P13.1) WILD-TYPE   10  390
                        clus
vv                       DEL PEAK 39(17P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 39(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            390
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 40(17Q11.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17Q11.2) MUTATED    11  61
  DEL PEAK 40(17Q11.2) WILD-TYPE  86 412
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            72                            498 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            61                            412 
$`DEL PEAK 40(17Q11.2) MUTATED`
TCGA-06-5408 TCGA-06-6697 TCGA-12-3653 TCGA-14-0862 TCGA-14-1034 TCGA-14-1396 
       11.74        12.85        14.53         2.89        15.95         1.12 
TCGA-14-1453 TCGA-19-2623 TCGA-19-4065 TCGA-19-5947 TCGA-19-5953 TCGA-19-A60I 
        1.15         7.53         7.04         6.64         4.73        17.79 
TCGA-27-2527 TCGA-28-2502 TCGA-28-2509 TCGA-32-1986 TCGA-32-2491 TCGA-41-3392 
       14.40         0.66         4.77        12.69        12.23         0.99 
TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9S TCGA-74-6573 TCGA-76-4934 TCGA-76-6285 
        0.20        15.12         1.45         3.45         2.53         8.35 
TCGA-02-0001 TCGA-02-0033 TCGA-02-0039 TCGA-02-0055 TCGA-02-0059 TCGA-02-0079 
       11.77         2.83        10.52         2.50         9.57        27.25 
TCGA-02-0086 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0258 TCGA-02-0269 
        8.81        11.67        92.65        15.65        16.54        10.75 
TCGA-02-0456 TCGA-06-0130 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 
        3.35        12.95        17.79         8.61        12.33         9.44 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0175 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
       56.91         5.85         4.04         4.18        69.90        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0197 TCGA-06-0206 TCGA-06-0644 
       15.42        10.42        38.96         5.56         7.66        12.62 
TCGA-06-0744 TCGA-06-0882 TCGA-06-2569 TCGA-08-0353 TCGA-08-0386 TCGA-08-0390 
       46.88        20.78         0.43         8.42        18.02        13.97 
TCGA-08-0512 TCGA-12-0619 TCGA-12-0703 TCGA-12-0772 TCGA-12-0775 TCGA-12-0826 
       42.15        34.92        20.38        53.85         7.63        27.78 
TCGA-12-1098 TCGA-14-0871 TCGA-15-1447 TCGA-26-5133 TCGA-76-6283 TCGA-76-6660 
        3.98        28.93        53.19        14.86         5.42         3.75 

$`DEL PEAK 40(17Q11.2) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        15.32         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 
        6.15         4.57         5.23         8.32         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 
       14.60        17.72        15.35        21.73        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
       15.12        11.97         0.95         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0865 TCGA-14-0866 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
        3.25        16.50        26.33         1.38         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
        9.14        21.24        13.97         6.41         8.61        14.27 
TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        3.39        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 
        0.13         9.67         4.87         1.08         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 
       24.23         7.00        17.19         8.02        18.90        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78        22.49        14.07        16.80        14.96        28.54 
TCGA-26-1438 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-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        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-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-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
        1.18         4.67        14.86        16.93        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9R 
        8.94         9.53         4.44        11.84        12.46         4.08 
TCGA-4W-AA9T TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 
       16.70         3.29         2.70        17.06        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R 
        5.03        23.90        34.45        18.64        36.20         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 
        6.28        20.55         7.63         4.73        18.35        23.18 
TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       10.59        35.41        20.71        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       77.65        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 
       90.58        14.14         3.62        10.72        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         6.54        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-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        10.19        20.84        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 
       17.65        23.18        99.98        48.95        16.93        17.72 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
       47.11        11.34         9.27        16.21        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 
       47.61         6.94         3.98        22.72        33.67        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 
        2.20        11.74         2.33        20.09        10.09        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       46.59        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
        3.42        10.65        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        3.22        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0188 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 
       44.58         4.67         7.40         0.39         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       26.40         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17        40.41        16.57        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0244 TCGA-08-0245 
        7.79         5.39       120.56         7.36        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 
       15.35         0.72        12.56         4.27        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
       18.41         7.56        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0776 TCGA-12-0778 
        3.65        28.41        15.06        43.23         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 
        4.14         2.24        11.24         1.35         5.39         2.04 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
       19.30         0.79        13.78        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
        3.91        26.07        16.37        11.77        21.90         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 
       10.75         9.07         5.95        12.95         4.64        31.33 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         7.36        11.38         1.61        17.72        26.30 

  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 
                        11.210                         12.475 
[1] "0.2 - 92.7 (11.2)"  "0.1 - 127.6 (12.5)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    27  45
  DEL PEAK 40(17Q11.2) WILD-TYPE 198 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     27   45
  DEL PEAK 40(17Q11.2) WILD-TYPE  198  303
        clus
vv       DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  FEMALE                           27                            198
  MALE                             45                            303
[1] 2 2
[1] FALSE
D64V4, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    11  57
  DEL PEAK 40(17Q11.2) WILD-TYPE  63 418
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     11   57
  DEL PEAK 40(17Q11.2) WILD-TYPE   63  418
     clus
vv    DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  NO                            11                             63
  YES                           57                            418
[1] 2 2
[1] FALSE
D64V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 40(17Q11.2) MUTATED                               5
  DEL PEAK 40(17Q11.2) WILD-TYPE                            25
                                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
D64V6, multiclass
                                 clus
vv                                DEL PEAK 40(17Q11.2) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           65
                                 clus
vv                                DEL PEAK 40(17Q11.2) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            460
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17Q11.2) MUTATED       2                         7    61
  DEL PEAK 40(17Q11.2) WILD-TYPE    11                        43   426
D64V7, multiclass
                           clus
vv                          DEL PEAK 40(17Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               61
                           clus
vv                          DEL PEAK 40(17Q11.2) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                             43
  WHITE                                                426
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED     1  61
  DEL PEAK 40(17Q11.2) WILD-TYPE  11 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED      1   61
  DEL PEAK 40(17Q11.2) WILD-TYPE   11  414
                        clus
vv                       DEL PEAK 40(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 40(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            414
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 41(18Q22.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q22.3) MUTATED    18  64
  DEL PEAK 41(18Q22.3) WILD-TYPE  79 409
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            82                            488 
  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                            64                            409 
$`DEL PEAK 41(18Q22.3) MUTATED`
TCGA-06-1806 TCGA-06-5413 TCGA-06-5859 TCGA-06-6388 TCGA-06-A5U0 TCGA-06-A5U1 
       15.32         8.81         4.57         5.23        26.79         1.87 
TCGA-12-5301 TCGA-14-0812 TCGA-14-0865 TCGA-19-1390 TCGA-19-2619 TCGA-19-4065 
        2.04         3.25        16.50        25.38         9.67         7.04 
TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-5136 TCGA-27-1834 TCGA-27-1838 
       14.96        10.03        13.87        18.97        40.54        11.51 
TCGA-28-1750 TCGA-32-1973 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2634 
        8.35        21.07         0.49        14.86        12.23        22.78 
TCGA-32-4210 TCGA-41-3392 TCGA-4W-AA9S TCGA-74-6575 TCGA-76-4929 TCGA-76-4934 
        3.72         0.99         1.45        20.91         3.65         2.53 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6662 TCGA-02-0006 TCGA-02-0011 TCGA-02-0024 
        8.35        20.98        34.45        18.35        20.71        53.10 
TCGA-02-0025 TCGA-02-0034 TCGA-02-0039 TCGA-02-0075 TCGA-02-0079 TCGA-02-0106 
       42.74        14.14        10.52        20.84        27.25        11.67 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0324 TCGA-06-0129 TCGA-06-0151 TCGA-06-0173 
       23.18        92.65         7.73        33.67        46.59         4.47 
TCGA-06-0206 TCGA-06-0237 TCGA-06-0648 TCGA-06-0649 TCGA-06-0749 TCGA-06-1086 
        7.66        13.64         9.80         2.10         2.70         6.84 
TCGA-06-1800 TCGA-06-2559 TCGA-06-6694 TCGA-08-0245 TCGA-08-0357 TCGA-08-0359 
       26.79         4.93         7.36        37.84        37.58         3.39 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0525 TCGA-12-0691 TCGA-12-0775 
        4.27        11.08        19.33        15.98        12.13         7.63 
TCGA-12-0776 TCGA-12-0826 TCGA-12-1096 TCGA-12-1098 TCGA-14-0817 TCGA-16-0846 
        9.73        27.78         9.11         3.98         5.39         3.91 
TCGA-16-0849 TCGA-19-0962 TCGA-19-1388 TCGA-26-5133 TCGA-26-6173 TCGA-28-2514 
       26.07         0.66        12.95        14.86         7.92         5.26 
TCGA-28-5207 TCGA-28-5213 TCGA-28-5216 TCGA-81-5911 
       11.28        31.27        13.64        17.72 

$`DEL PEAK 41(18Q22.3) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        11.74         3.55         8.35         4.54 
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-06-6695 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-06-A7TK TCGA-06-A7TL TCGA-12-0615 TCGA-12-1092 
        3.12         2.56        14.60        17.72        15.35        21.73 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
       23.05        13.78         2.89        26.33        15.95         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 
        7.17        17.49         7.96         3.78         3.42        17.59 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 
       13.97         6.41         8.61        14.27         3.39         3.65 
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-19-2629 TCGA-19-2631 TCGA-19-5947 
        7.53         0.16         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1440 
       22.49        14.07        16.80        17.79        28.54         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1830 
        7.13         9.37         9.40         8.88        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        24.23        21.30        30.05        14.04 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       14.40        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        6.74         4.77        15.39         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
        1.18         4.67        12.69        16.93        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
       15.95         8.84        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R 
        4.44        11.84         0.20        15.12        12.46         4.08 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       25.58         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.80         4.54         3.09         9.17        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        3.29         2.70        17.06         4.83         5.03        23.90 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       18.64        36.20         5.92         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
       11.77         4.73        23.18        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 
       20.61        87.06        77.65        20.12        24.59        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 
       90.58         2.83         3.62        10.72        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 
       28.70        25.05         5.49        10.19        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       27.02        65.00        17.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 
       13.87        14.20        15.95        12.23         9.90        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29        13.12         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        5.56         0.39         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93         4.04        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 
       13.61        33.90         1.08        12.49        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0246 
       31.50         7.79         5.39       120.56        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       31.10        22.29        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       13.97         0.72        12.56        42.15        19.59        58.68 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
       10.75         4.80         7.27        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       15.06        53.85        43.23        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 
       12.23        15.85        14.53         4.14         2.24        11.24 
TCGA-14-0813 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 
        1.35         2.04        28.93        19.30         0.79        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0850 TCGA-19-0955 
       50.53        19.10        53.19        13.28        16.37        11.77 
TCGA-19-0957 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 
       21.90        10.75         9.07         5.95         4.64        31.33 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
        5.49         1.58         2.33         7.30        14.93        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77        23.44        11.01         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       12.76         5.42         7.36        11.38         5.42         3.75 
TCGA-81-5910 TCGA-87-5896 
        1.61        26.30 

  DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE 
                          0.49                           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 
                         11.59                          12.41 
[1] "0.5 - 92.7 (11.6)"  "0.1 - 127.6 (12.4)"
[1] "hr=" "1"  
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.3) MUTATED    31  51
  DEL PEAK 41(18Q22.3) WILD-TYPE 194 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED     31   51
  DEL PEAK 41(18Q22.3) WILD-TYPE  194  297
        clus
vv       DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE
  FEMALE                           31                            194
  MALE                             51                            297
[1] 2 2
[1] FALSE
D65V4, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.3) MUTATED    14  64
  DEL PEAK 41(18Q22.3) WILD-TYPE  60 411
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED     14   64
  DEL PEAK 41(18Q22.3) WILD-TYPE   60  411
     clus
vv    DEL PEAK 41(18Q22.3) MUTATED DEL PEAK 41(18Q22.3) WILD-TYPE
  NO                            14                             60
  YES                           64                            411
[1] 2 2
[1] FALSE
D65V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 41(18Q22.3) MUTATED                               5
  DEL PEAK 41(18Q22.3) WILD-TYPE                            25
                                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
D65V6, multiclass
                                 clus
vv                                DEL PEAK 41(18Q22.3) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              5
  TREATED PRIMARY GBM                                        2
  UNTREATED PRIMARY (DE NOVO) GBM                           75
                                 clus
vv                                DEL PEAK 41(18Q22.3) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               25
  TREATED PRIMARY GBM                                         16
  UNTREATED PRIMARY (DE NOVO) GBM                            450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q22.3) MUTATED       3                         9    67
  DEL PEAK 41(18Q22.3) WILD-TYPE    10                        41   420
D65V7, multiclass
                           clus
vv                          DEL PEAK 41(18Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               67
                           clus
vv                          DEL PEAK 41(18Q22.3) WILD-TYPE
  ASIAN                                                 10
  BLACK OR AFRICAN AMERICAN                             41
  WHITE                                                420
[1] 3 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 41(18Q22.3) MUTATED     3  69
  DEL PEAK 41(18Q22.3) WILD-TYPE   9 406
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.3) MUTATED      3   69
  DEL PEAK 41(18Q22.3) WILD-TYPE    9  406
                        clus
vv                       DEL PEAK 41(18Q22.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 41(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            406
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 42(19Q13.41) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 42(19Q13.41) MUTATED    15  84
  DEL PEAK 42(19Q13.41) WILD-TYPE  82 389
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             99                             471 
  DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE 
                             84                             389 
$`DEL PEAK 42(19Q13.41) MUTATED`
TCGA-06-5411 TCGA-06-5415 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-12-1598 TCGA-12-3651 
        8.35         8.55        26.79         2.56        15.65        12.69 
TCGA-14-0740 TCGA-14-0783 TCGA-14-0862 TCGA-14-0865 TCGA-14-1451 TCGA-14-1458 
       11.97         6.21         2.89        16.50        23.11         6.67 
TCGA-14-4157 TCGA-16-1460 TCGA-19-0960 TCGA-19-1390 TCGA-19-2629 TCGA-26-5136 
        3.42         6.41         8.61        25.38        24.23        18.97 
TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 TCGA-28-1746 TCGA-32-1970 TCGA-32-1973 
       40.54        18.08        16.77         0.20        15.39        21.07 
TCGA-32-1976 TCGA-32-1978 TCGA-32-1987 TCGA-32-2491 TCGA-32-4208 TCGA-32-4210 
        0.49        15.85        14.86        12.23        21.14         3.72 
TCGA-41-2575 TCGA-41-5651 TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 TCGA-76-6193 
        9.53        15.12         4.80         3.65         9.17         2.70 
TCGA-76-6285 TCGA-76-6662 TCGA-76-6664 TCGA-02-0026 TCGA-02-0028 TCGA-02-0034 
        8.35        34.45        36.20        24.59        90.58        14.14 
TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0079 TCGA-02-0104 
        2.50         8.35         9.57         6.02        27.25        65.00 
TCGA-02-0106 TCGA-02-0114 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 
       11.67        99.98        16.54        16.93        10.75         3.98 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0432 TCGA-02-0456 TCGA-02-2466 TCGA-06-0132 
        9.90        10.62        47.11         3.35        16.80        25.35 
TCGA-06-0149 TCGA-06-0152 TCGA-06-0237 TCGA-06-0394 TCGA-06-0745 TCGA-06-0875 
        8.61        12.33        13.64        10.82         7.86        43.46 
TCGA-06-0878 TCGA-06-1084 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2569 
        7.17        23.93        17.65        12.56        30.64         0.43 
TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0346 TCGA-08-0348 
      120.56        22.68        37.84       115.86         8.42        12.16 
TCGA-08-0349 TCGA-08-0351 TCGA-08-0358 TCGA-08-0386 TCGA-08-0392 TCGA-08-0517 
        9.80        65.33        22.29        18.02         0.72        58.68 
TCGA-12-0619 TCGA-12-0656 TCGA-12-0772 TCGA-12-0827 TCGA-12-1088 TCGA-12-1094 
       34.92        94.78        53.85        38.76       127.59        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-15-1444 TCGA-16-0850 TCGA-19-1388 
       15.85        14.53         4.14        50.53        16.37        12.95 
TCGA-28-2514 TCGA-28-5211 TCGA-87-5896 
        5.26        11.77        26.30 

$`DEL PEAK 42(19Q13.41) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        15.32        11.74         3.55         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-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL 
        4.77         4.96         1.87         3.12        14.60        17.72 
TCGA-12-0615 TCGA-12-1092 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       15.35        21.73        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       44.02        26.93        15.22        10.95        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 
       14.93         3.22         2.04        15.12         0.95        23.05 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 
       13.78         3.25        26.33        15.95         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
        3.75        32.05        58.78         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96        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-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.78        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0963 TCGA-19-0964 TCGA-19-1392 
        9.14        21.24        13.97        14.27         3.39         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 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        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40         8.88        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2523 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-28-2506 TCGA-28-2509 TCGA-32-1977 
        2.83         0.13         0.66         6.74         4.77         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 
       19.50         1.18         4.67        12.69        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 
       15.02        15.95         8.84        22.78        25.18        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R 
        0.99         4.44        11.84         0.20        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 
        8.22         7.50         4.54         3.09         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29        17.06        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6663 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 
       23.90        18.64         5.92         6.28        20.55         7.63 
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 
       53.10        42.74        12.16         2.83         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       12.59         6.54        19.86        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        20.84        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       27.02        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 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-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.21        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        12.95        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       17.79        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 
       23.57        14.20        26.40        46.88         2.70         2.70 
TCGA-06-0750 TCGA-06-0876 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        0.92        46.19        40.41        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2564 TCGA-06-2565 
       33.90         1.08        12.49         4.93         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 
        5.98         4.37        31.50         7.79         5.39         7.36 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0347 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 
        4.18         1.74        25.71        29.23         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 
       17.95        24.56        31.10        37.58         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       14.93        15.35        13.97        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 
        3.65        20.38        28.41        15.06        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 
       10.62        23.51        27.78         8.94        20.58         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1096 TCGA-12-1098 TCGA-14-0787 
        7.59        33.21        15.98         9.11         3.98         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
       11.24         1.35         5.39         2.04        28.93        19.30 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
        0.79        13.78        19.10        53.19        13.28         3.91 
TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       26.07        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        5.95         4.64        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        7.92         2.33         7.30        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       14.53        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
       22.68        12.76         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        3.75         1.61        17.72 

  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 
                          14.53                           11.84 
[1] "0.2 - 127.6 (14.5)" "0.1 - 92.7 (11.8)" 
[1] "hr=" "1.4"
D66V2, continuous
D66V3, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED    40  60
  DEL PEAK 42(19Q13.41) WILD-TYPE 185 288
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED     40   60
  DEL PEAK 42(19Q13.41) WILD-TYPE  185  288
        clus
vv       DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE
  FEMALE                            40                             185
  MALE                              60                             288
[1] 2 2
[1] FALSE
D66V4, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED     8  87
  DEL PEAK 42(19Q13.41) WILD-TYPE  66 388
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED      8   87
  DEL PEAK 42(19Q13.41) WILD-TYPE   66  388
     clus
vv    DEL PEAK 42(19Q13.41) MUTATED DEL PEAK 42(19Q13.41) WILD-TYPE
  NO                              8                              66
  YES                            87                             388
[1] 2 2
[1] FALSE
D66V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 42(19Q13.41) MUTATED                               3
  DEL PEAK 42(19Q13.41) WILD-TYPE                            27
                                 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                                93
  DEL PEAK 42(19Q13.41) WILD-TYPE                             432
D66V6, multiclass
                                 clus
vv                                DEL PEAK 42(19Q13.41) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                               3
  TREATED PRIMARY GBM                                         4
  UNTREATED PRIMARY (DE NOVO) GBM                            93
                                 clus
vv                                DEL PEAK 42(19Q13.41) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                27
  TREATED PRIMARY GBM                                          14
  UNTREATED PRIMARY (DE NOVO) GBM                             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"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(19Q13.41) MUTATED       2                        11    84
  DEL PEAK 42(19Q13.41) WILD-TYPE    11                        39   403
D66V7, multiclass
                           clus
vv                          DEL PEAK 42(19Q13.41) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                                84
                           clus
vv                          DEL PEAK 42(19Q13.41) WILD-TYPE
  ASIAN                                                  11
  BLACK OR AFRICAN AMERICAN                              39
  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"
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.41) MUTATED     2  83
  DEL PEAK 42(19Q13.41) WILD-TYPE  10 392
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.41) MUTATED      2   83
  DEL PEAK 42(19Q13.41) WILD-TYPE   10  392
                        clus
vv                       DEL PEAK 42(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            83
                        clus
vv                       DEL PEAK 42(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             392
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 43(21Q21.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(21Q21.1) MUTATED     9  47
  DEL PEAK 43(21Q21.1) WILD-TYPE  88 426
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                            56                            514 
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                            47                            426 
$`DEL PEAK 43(21Q21.1) MUTATED`
TCGA-06-5856 TCGA-06-6695 TCGA-06-A7TL TCGA-12-1600 TCGA-12-3653 TCGA-12-5295 
        3.75         8.32        17.72        14.73        14.53        14.93 
TCGA-14-0740 TCGA-14-1823 TCGA-14-3477 TCGA-16-0848 TCGA-16-1055 TCGA-19-0960 
       11.97        17.85         3.78        17.59        10.29         8.61 
TCGA-19-1789 TCGA-19-2629 TCGA-19-5958 TCGA-19-A6J5 TCGA-27-2521 TCGA-32-1978 
        3.25        24.23        14.07        28.54        16.77        15.85 
TCGA-41-3392 TCGA-76-4925 TCGA-76-4934 TCGA-06-0209 TCGA-02-0011 TCGA-02-0015 
        0.99         4.80         2.53         7.63        20.71        20.61 
TCGA-02-0051 TCGA-02-0080 TCGA-02-0106 TCGA-02-0114 TCGA-02-0266 TCGA-02-0281 
       15.09        89.72        11.67        99.98        17.72         3.98 
TCGA-02-0339 TCGA-02-0451 TCGA-06-0126 TCGA-06-0150 TCGA-06-0221 TCGA-06-0402 
       12.39        16.21         6.94        19.46        19.82         0.26 
TCGA-06-0414 TCGA-06-0648 TCGA-06-0875 TCGA-06-1801 TCGA-06-6389 TCGA-06-6693 
       35.11         9.80        43.46        11.84         7.79       120.56 
TCGA-06-6694 TCGA-08-0353 TCGA-08-0516 TCGA-12-0820 TCGA-12-0826 TCGA-12-0827 
        7.36         8.42        19.59        18.48        27.78        38.76 
TCGA-12-1099 TCGA-14-0817 TCGA-15-0742 TCGA-16-0846 TCGA-16-0850 TCGA-28-2514 
        4.14         5.39        13.78         3.91        16.37         5.26 
TCGA-28-5219 TCGA-76-6280 
       22.68        11.38 

$`DEL PEAK 43(21Q21.1) WILD-TYPE`
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        1.48         3.98        15.32        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        6.15         4.57         5.23        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96        26.79         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       14.60        15.35        21.73        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       34.92         3.22         2.04        15.12         0.95         6.21 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       23.05        13.78         3.25         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-16-1045 
        5.88         7.17        17.49         7.96         3.42        29.03 
TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        4.57        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       14.27         3.39        25.38         3.65         7.17        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
       14.96        17.79        10.03        13.87         9.73         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 
        9.37         9.40         8.88        18.97        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 
        0.13         0.66         6.74         4.77        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.08         1.45        25.58         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         7.50         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        9.17        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-02-0001 
       18.64        36.20         5.92         6.28        20.55        11.77 
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
        4.73        18.35        23.18        10.59        35.41        82.59 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       87.06        77.65        20.12        53.10        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 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-02-0059 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-02-0070 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-02-0084 TCGA-02-0085 TCGA-02-0086 
       20.84        27.25        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 
       57.76        16.96         3.48        27.02        65.00        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        92.65        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 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-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 
        7.86         2.70         2.70         0.92        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
        4.04        26.79        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6390 
       16.64         5.98         4.37         0.43        31.50         5.39 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        42.15        11.08        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0821 
        9.73        14.93        14.86        91.76        24.79        10.62 
TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       23.51         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0867 TCGA-14-0871 
        3.98         2.24        11.24         1.35         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
       19.30         0.79        50.53        19.10        53.19        13.28 
TCGA-16-0849 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 
       26.07        11.77        21.90         0.66        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        5.95        12.95         4.64        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        1.58         7.92         2.33         7.30        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6283 
       13.64         5.16        12.76         5.42         7.36         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                          0.26                           0.10 
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                        120.56                         127.59 
  DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE 
                        14.300                         12.195 
[1] "0.3 - 120.6 (14.3)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q21.1) MUTATED    23  33
  DEL PEAK 43(21Q21.1) WILD-TYPE 202 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q21.1) MUTATED     23   33
  DEL PEAK 43(21Q21.1) WILD-TYPE  202  315
        clus
vv       DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE
  FEMALE                           23                            202
  MALE                             33                            315
[1] 2 2
[1] FALSE
D67V4, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q21.1) MUTATED     7  46
  DEL PEAK 43(21Q21.1) WILD-TYPE  67 429
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q21.1) MUTATED      7   46
  DEL PEAK 43(21Q21.1) WILD-TYPE   67  429
     clus
vv    DEL PEAK 43(21Q21.1) MUTATED DEL PEAK 43(21Q21.1) WILD-TYPE
  NO                             7                             67
  YES                           46                            429
[1] 2 2
[1] FALSE
D67V5, continuous
                                vv
clus                             GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 43(21Q21.1) MUTATED                               3
  DEL PEAK 43(21Q21.1) WILD-TYPE                            27
                                vv
clus                             TREATED PRIMARY GBM
  DEL PEAK 43(21Q21.1) MUTATED                     1
  DEL PEAK 43(21Q21.1) WILD-TYPE                  17
                                vv
clus                             UNTREATED PRIMARY (DE NOVO) GBM
  DEL PEAK 43(21Q21.1) MUTATED                                52
  DEL PEAK 43(21Q21.1) WILD-TYPE                             473
D67V6, multiclass
                                 clus
vv                                DEL PEAK 43(21Q21.1) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              3
  TREATED PRIMARY GBM                                        1
  UNTREATED PRIMARY (DE NOVO) GBM                           52
                                 clus
vv                                DEL PEAK 43(21Q21.1) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                               27
  TREATED PRIMARY GBM                                         17
  UNTREATED PRIMARY (DE NOVO) GBM                            473
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(21Q21.1) MUTATED       1                         4    50
  DEL PEAK 43(21Q21.1) WILD-TYPE    12                        46   437
D67V7, multiclass
                           clus
vv                          DEL PEAK 43(21Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               50
                           clus
vv                          DEL PEAK 43(21Q21.1) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                             46
  WHITE                                                437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q21.1) MUTATED     2  49
  DEL PEAK 43(21Q21.1) WILD-TYPE  10 426
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q21.1) MUTATED      2   49
  DEL PEAK 43(21Q21.1) WILD-TYPE   10  426
                        clus
vv                       DEL PEAK 43(21Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       DEL PEAK 43(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            426
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 44(22Q13.32) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(22Q13.32) MUTATED    32 180
  DEL PEAK 44(22Q13.32) WILD-TYPE  65 293
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            212                             358 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            180                             293 
$`DEL PEAK 44(22Q13.32) MUTATED`
TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5418 
        3.98        15.32        11.74         8.35         8.81         2.73 
TCGA-06-5856 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-12-1598 
        3.75        12.85         4.77         1.87         2.56        15.65 
TCGA-12-1600 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 
       14.73        44.02        12.69        14.53        14.93        15.12 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0862 TCGA-14-0865 TCGA-14-1034 TCGA-14-1402 
        6.21        23.05         2.89        16.50        15.95        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-16-1056 TCGA-16-1062 TCGA-19-0964 TCGA-19-1392 TCGA-19-1791 TCGA-19-2620 
       14.01        21.24         3.39         3.65         0.13         4.87 
TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5956 
        7.53         4.08        24.23         7.00         6.64        22.49 
TCGA-19-5958 TCGA-19-5960 TCGA-19-A60I TCGA-26-5132 TCGA-26-5136 TCGA-27-1830 
       14.07        14.96        17.79         9.40        18.97         5.06 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 TCGA-27-2519 TCGA-27-2521 
        9.86        40.54        21.30        11.51        18.08        16.77 
TCGA-27-2523 TCGA-27-2527 TCGA-28-1746 TCGA-28-1752 TCGA-28-1756 TCGA-28-2506 
       16.08        14.40         0.20         8.48         2.83         6.74 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 TCGA-32-1980 
        4.77        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        12.46 
TCGA-4W-AA9S TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 
        1.45        20.91         8.22         4.80         4.54         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-6285 TCGA-76-6657 TCGA-OX-A56R TCGA-02-0007 
        9.17         2.53         8.35         5.03         5.92        23.18 
TCGA-02-0010 TCGA-02-0015 TCGA-02-0016 TCGA-02-0026 TCGA-02-0027 TCGA-02-0039 
       35.41        20.61        87.06        24.59        12.16        10.52 
TCGA-02-0043 TCGA-02-0054 TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 TCGA-02-0075 
       18.31         6.54        19.86         9.57         6.02        20.84 
TCGA-02-0079 TCGA-02-0086 TCGA-02-0099 TCGA-02-0113 TCGA-02-0260 TCGA-02-0266 
       27.25         8.81         3.48        92.65        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0333 
       10.75        14.47         9.90        10.62         7.33         4.37 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2486 TCGA-06-0129 TCGA-06-0140 
        3.35        16.80        15.32        20.32        33.67         0.20 
TCGA-06-0141 TCGA-06-0145 TCGA-06-0147 TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 
       10.29         2.33        17.79        12.33        10.82         9.44 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0175 TCGA-06-0182 
        3.42        56.91         5.85        19.66         4.04         3.65 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 
       73.84        27.22        44.58        15.42         4.67         7.40 
TCGA-06-0197 TCGA-06-0211 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        5.56        11.84        24.16         0.72        19.82        13.64 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0744 TCGA-06-0745 
       48.69         9.01         0.26         4.70        46.88         7.86 
TCGA-06-0747 TCGA-06-0875 TCGA-06-0878 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        2.70        43.46         7.17        20.78        26.76        23.93 
TCGA-06-1804 TCGA-06-2558 TCGA-06-2562 TCGA-06-2565 TCGA-06-2567 TCGA-06-6389 
       13.61        12.49        12.56        16.64         4.37         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0349 
        5.39       120.56        22.68        37.84         4.18         9.80 
TCGA-08-0350 TCGA-08-0354 TCGA-08-0357 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 
       29.23        17.95        37.58        18.02        15.35         0.72 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0520 TCGA-08-0525 TCGA-12-0619 
       42.15        11.08        19.59        10.75        15.98        34.92 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0707 TCGA-12-0820 
       10.45        94.78        38.17        25.97        28.41        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-1088 TCGA-12-1091 TCGA-12-1096 
       10.62        27.78        38.76       127.59        33.21         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
       14.53         3.98         2.24         2.04        28.93        19.30 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-19-0962 TCGA-19-1385 TCGA-19-1389 
       13.78        50.53        53.19         0.66        10.75         4.64 
TCGA-26-1442 TCGA-26-6173 TCGA-28-5207 TCGA-28-5208 TCGA-28-5213 TCGA-28-5214 
       31.33         7.92        11.28        17.88        31.27        23.44 
TCGA-76-6280 TCGA-87-5896 
       11.38        26.30 

$`DEL PEAK 44(22Q13.32) WILD-TYPE`
TCGA-06-6391 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        1.48         3.55         4.54         8.98         8.55         6.71 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6699 TCGA-06-6700 
        6.15         4.57         5.23         8.32         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-0615 
        4.96        26.79         3.12        14.60        17.72        15.35 
TCGA-12-1092 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       21.73        25.68         6.77        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       10.95        34.92         3.22         2.04        11.97         0.95 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       13.78         3.25        26.33         1.38         1.12         3.75 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1795 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-14-2555 TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        7.96         3.42        17.59        29.03         4.57        10.29 
TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 TCGA-19-1390 
        9.14        13.97         6.41         8.61        14.27        25.38 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 TCGA-19-2624 
        7.17        12.66         3.25         9.67         1.08         0.16 
TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.04        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        1.78        16.80        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5135 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1833 
        7.13         9.37         8.88        19.33        16.60        24.23 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       30.05        14.04        24.76         7.59         2.86        15.78 
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-28-1757 TCGA-28-2502 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
        0.13         0.66         0.10        19.50         4.67        14.86 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       16.93        20.78        15.02        25.18         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-3392 TCGA-41-3393 
       19.86        10.85        19.23         0.85         0.99         4.44 
TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 
       15.12         4.08        25.58         3.45         4.34        14.33 
TCGA-74-6584 TCGA-76-4928 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        7.50         3.09        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       17.06        20.98         4.83        23.90        34.45        18.64 
TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
       36.20         6.28        20.55         7.63        11.77         4.73 
TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 TCGA-02-0021 TCGA-02-0023 
       18.35        10.59        20.71        82.59        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       53.10        42.74        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       10.72         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0055 TCGA-02-0058 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        2.50         8.35        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        89.72        22.72        12.62        51.32 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       57.76        16.96        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0281 
       23.18        99.98        15.65        48.95        16.54         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 TCGA-02-0330 
       13.87        14.20        15.95        12.23         7.73        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-02-2470 TCGA-02-2485 
       47.11        11.34         9.27        16.21        12.92        15.45 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0148 TCGA-06-0149 
       11.90         2.20        11.74        20.09        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 
       19.46        46.59        13.94        10.45         3.19        11.80 
TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       10.65         3.29        13.12         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0190 TCGA-06-0192 
        4.18        88.14        20.25        69.90        10.42        38.96 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        0.39         7.66         8.42         7.40         0.53        15.02 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0394 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       13.32        20.42        10.82        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       23.57        14.20        26.40         2.70         0.92        46.19 
TCGA-06-0879 TCGA-06-0881 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       40.41        16.57         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 
       15.32        33.90         1.08         4.93        17.65        30.64 
TCGA-06-2564 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-6694 TCGA-08-0344 
        5.95         5.98         0.43        31.50         7.36       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 
        1.74         8.42        25.71        12.16        65.33         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
        8.42        24.56        31.10        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0517 TCGA-08-0518 
       14.93        13.97        12.56         4.27        58.68        19.33 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        4.80         7.27        18.41         7.56        14.73        12.99 
TCGA-12-0654 TCGA-12-0657 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        7.59         0.10        26.66        12.13         3.65        20.38 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 
       14.86        91.76        24.79        23.51         8.94        20.58 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1099 
        5.82         7.59        15.98        12.23        15.85         4.14 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-1043 TCGA-15-1446 TCGA-15-1449 
       11.24         1.35         5.39         0.79        19.10        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 TCGA-19-0957 TCGA-19-1386 
        3.91        26.07        16.37        11.77        21.90         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 
        5.95        12.95        14.86         5.49         1.58         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5209 TCGA-28-5211 TCGA-28-5215 
        7.30         5.26        14.93        14.53        11.77        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 
       13.64         5.16        22.68        12.76         5.42         7.36 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42         3.75         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                          115.86 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                         12.690                          12.035 
[1] "0.1 - 127.6 (12.7)" "0.1 - 115.9 (12.0)"
[1] "hr=" "1.1"
D68V2, continuous
D68V3, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED    84 128
  DEL PEAK 44(22Q13.32) WILD-TYPE 141 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED     84  128
  DEL PEAK 44(22Q13.32) WILD-TYPE  141  220
        clus
vv       DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  FEMALE                            84                             141
  MALE                             128                             220
[1] 2 2
[1] FALSE
D68V4, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED    29 176
  DEL PEAK 44(22Q13.32) WILD-TYPE  45 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED     29  176
  DEL PEAK 44(22Q13.32) WILD-TYPE   45  299
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  NO                             29                              45
  YES                           176                             299
[1] 2 2
[1] FALSE
D68V5, continuous
                                 vv
clus                              GLIOBLASTOMA MULTIFORME (GBM)
  DEL PEAK 44(22Q13.32) MUTATED                              10
  DEL PEAK 44(22Q13.32) WILD-TYPE                            20
                                 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
D68V6, multiclass
                                 clus
vv                                DEL PEAK 44(22Q13.32) MUTATED
  GLIOBLASTOMA MULTIFORME (GBM)                              10
  TREATED PRIMARY GBM                                         6
  UNTREATED PRIMARY (DE NOVO) GBM                           196
                                 clus
vv                                DEL PEAK 44(22Q13.32) WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                                20
  TREATED PRIMARY GBM                                          12
  UNTREATED PRIMARY (DE NOVO) GBM                             329
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(22Q13.32) MUTATED       6                        13   184
  DEL PEAK 44(22Q13.32) WILD-TYPE     7                        37   303
D68V7, multiclass
                           clus
vv                          DEL PEAK 44(22Q13.32) MUTATED
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               184
                           clus
vv                          DEL PEAK 44(22Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              37
  WHITE                                                 303
[1] 3 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 44(22Q13.32) MUTATED     4 180
  DEL PEAK 44(22Q13.32) WILD-TYPE   8 295
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      4  180
  DEL PEAK 44(22Q13.32) WILD-TYPE    8  295
                        clus
vv                       DEL PEAK 44(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           180
                        clus
vv                       DEL PEAK 44(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             295
[1] 2 2
[1] FALSE
