[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-oTLGG-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/LGG-TP/10005995/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/10013777/transformed.cor.cli.txt"

nPatients in clinical file=403, in cluster file=512, common to both=400
[1]  50 400
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         35                         365 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         35                         365 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           34                           366 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           34                           366 
[1] "AMP PEAK  3(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           16                           384 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           16                           384 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            17                            383 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            17                            383 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         21                         379 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         21                         379 
[1] "AMP PEAK  6(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          101                           299 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          101                           299 
[1] "AMP PEAK  7(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          138                           262 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          138                           262 
[1] "AMP PEAK  8(7Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          144                           256 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          144                           256 
[1] "AMP PEAK  9(8Q24.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            77                            323 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            77                            323 
[1] "AMP PEAK 10(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           39                           361 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           39                           361 
[1] "AMP PEAK 11(10P15.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            52                            348 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            52                            348 
[1] "AMP PEAK 12(11Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            71                            329 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            71                            329 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             56                             344 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             56                             344 
[1] "AMP PEAK 14(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            29                            371 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            29                            371 
[1] "AMP PEAK 15(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          20                          380 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          20                          380 
[1] "AMP PEAK 16(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            14                            386 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            14                            386 
[1] "AMP PEAK 17(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            33                            367 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            33                            367 
[1] "AMP PEAK 18(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           103                            297 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           103                            297 
[1] "AMP PEAK 19(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            98                            302 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            98                            302 
[1] "AMP PEAK 20(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            32                            368 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            32                            368 
[1] "AMP PEAK 21(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            47                            353 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            47                            353 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           166                            234 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           166                            234 
[1] "DEL PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          157                           243 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          157                           243 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         20                         380 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         20                         380 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           59                           341 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           59                           341 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            33                            367 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            33                            367 
[1] "DEL PEAK  6(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                         34                         366 
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                         34                         366 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          109                           291 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          109                           291 
[1] "DEL PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                            37                            363 
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                            37                            363 
[1] "DEL PEAK  9(5Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                         51                         349 
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                         51                         349 
[1] "DEL PEAK 10(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           39                           361 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           39                           361 
[1] "DEL PEAK 11(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                            58                            342 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                            58                            342 
[1] "DEL PEAK 12(6Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                           61                           339 
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                           61                           339 
[1] "DEL PEAK 13(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                           16                           384 
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                           16                           384 
[1] "DEL PEAK 14(8Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                           21                           379 
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                           21                           379 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        110                         290 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        110                         290 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          132                           268 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          132                           268 
[1] "DEL PEAK 17(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           116                            284 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           116                            284 
[1] "DEL PEAK 18(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                            78                            322 
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                            78                            322 
[1] "DEL PEAK 19(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                            31                            369 
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                            31                            369 
[1] "DEL PEAK 20(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                          51                          349 
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                          51                          349 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           112                            288 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           112                            288 
[1] "DEL PEAK 22(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           114                            286 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           114                            286 
[1] "DEL PEAK 23(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          86                          314 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          86                          314 
[1] "DEL PEAK 24(14Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                            94                            306 
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                            94                            306 
[1] "DEL PEAK 25(15Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                            48                            352 
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                            48                            352 
[1] "DEL PEAK 26(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          64                          336 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          64                          336 
[1] "DEL PEAK 27(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            216                             184 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            216                             184 
[1] "DEL PEAK 28(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             59                             341 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             59                             341 
[1] "DEL PEAK 29(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           55                           345 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           55                           345 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 400 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
         143           NA           NA          552          323         1966 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        1222            3           NA          303           NA           NA 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
         725          546          378          258          230          244 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
         225          201         3733         2493         2289         1458 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
        2218         1419         1526         1354         1112         2381 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
         915          313          387          840          822          573 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
         559         2219          383          335          573          511 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
         182          489          469          846          448          415 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
         332           NA          968          922          438          244 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
          NA          901          479          237          117          548 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
         443          531           NA          407          257          207 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        5546          576          532          461         6423         1585 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
         682         1491         2286         1401           NA           37 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        2660          214           NA           NA          605           NA 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
          NA         3470          242          235           NA           NA 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        4752         4206           NA           NA           NA           NA 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
          NA         2761           NA          800           NA           NA 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        2869           NA           NA           NA           NA         1834 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
          NA         1277           84           NA           NA          121 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
         629          651          582          516          471          431 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
         433          383          460          151          111          172 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
         371          263           82         2372          220          182 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
          NA           NA          217           NA         3787         1525 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        2052         1251         2433         1762         4084         2379 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
        2907         3978          436         1453          547         1045 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
         979          571          454          760          729          413 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
         467          544          686          627          611          394 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
         416          433          487          611          455          361 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
         472          744           18          160          113          294 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
         214          202          214          128          124          322 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
         328          698          159            4            3          203 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
         238          268            4            1          503          114 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
         530          199          738          194          216         2287 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        1800         1826         4690          122          153          908 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
         705         3283          139          526           NA          671 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
        1399         1706         1752           NA          434            5 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
         494           23         1359          184         1300            3 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
         964          455            3            3           90          533 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
         210          442         1201          585         1189            7 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        1540           15          718         1130           10            4 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
         112          162           89           52          343          956 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
          50          494          286           NA          654         1004 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
         372          190            3           14           76          120 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
         143            7          900          118          488          478 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
           7          319            4            2          447            3 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
          NA           82          396           55          491          162 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
         910          409          253          585         1222         1092 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
         131          262          272          596          542          321 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
         240          294          201           NA         1301          159 
TCGA-KT-A7W1 TCGA-P5-A5ET TCGA-P5-A5EU TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
         144           NA           NA            7          204           50 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
          72           70          125          179           39          175 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
          77          147          237          125          127           NA 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
          90           NA           NA           67           96           18 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
         192          119          144           58            7          153 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
        2702         2860          993         1806           NA         2101 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
         571          860          856          684          658          498 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
         344          475          610          300         2878         2546 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
          NA         3156         1897         2208         2146          697 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
        2149          331          283          275          231          187 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
         103          434           NA          597          383          128 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
         285          249           62          247          109          123 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
         554          396           NA         2649          530         2549 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
          NA          152         1504         1093          770          687 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
        1472          365          459         1544         1045          738 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
         589          532           NA          502          910          575 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
         287          139          365         1006          915          411 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
           3           NA          815          333 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=300,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 400 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1Q22) MUTATED    23  12
  AMP PEAK  1(1Q22) WILD-TYPE 301  59
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         35                         360 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         12                          59 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DB-A64L TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-6396 
        7.69        12.43        11.01        30.21       211.17        75.16 
TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7304 
        1.22        11.64        14.99        90.77        10.36        23.31 
TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A6S7 TCGA-E1-5302 
        3.98        19.13        15.12         4.96         7.23        50.14 
TCGA-E1-5304 TCGA-E1-5319 TCGA-FG-5962 TCGA-FG-8185 TCGA-HT-7475 TCGA-HT-7477 
       41.13        95.57        47.77        14.24        17.42        24.26 
TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-8108 TCGA-HT-A4DS TCGA-HW-A5KM TCGA-QH-A6CV 
       16.24        31.69         2.50         0.23         6.61         2.96 
TCGA-S9-A6WM TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CA 
        9.30        12.00        19.36        17.49        13.51 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       12.59        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       52.11        22.42        49.02        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        30.67        26.30 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 
       60.30        41.98         2.76         5.10        23.74        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 
       67.46        79.99        57.93       134.27        78.21       130.78 
TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       16.54         3.75         6.54         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
        3.88        16.04        15.72        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 
       17.82        10.55         7.89         9.67        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       48.39        15.09        50.76        34.36        24.26        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       33.07        30.08         0.10         7.89        26.79        10.95 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       0.23                        0.03 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     211.17                      182.33 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      14.99                       14.96 
[1] "0.2 - 211.2 (15.0)" "0.0 - 182.3 (15.0)"
[1] "hr=" "2"  
D1V2, continuous
D1V3, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    16  19
  AMP PEAK  1(1Q22) WILD-TYPE 160 205
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     16   19
  AMP PEAK  1(1Q22) WILD-TYPE  160  205
        clus
vv       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  FEMALE                        16                         160
  MALE                          19                         205
[1] 2 2
[1] FALSE
D1V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  1(1Q22) MUTATED            15                6                14
  AMP PEAK  1(1Q22) WILD-TYPE         128               98               139
D1V5, multiclass
                   clus
vv                  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  ASTROCYTOMA                              15                         128
  OLIGOASTROCYTOMA                          6                          98
  OLIGODENDROGLIOMA                        14                         139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    10  25
  AMP PEAK  1(1Q22) WILD-TYPE  79 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     10   25
  AMP PEAK  1(1Q22) WILD-TYPE   79  286
     clus
vv    AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  NO                         10                          79
  YES                        25                         286
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q22) MUTATED                                  0     1
  AMP PEAK  1(1Q22) WILD-TYPE                                1     1
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED                           1    32
  AMP PEAK  1(1Q22) WILD-TYPE                        13   344
D1V7, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   32
                                  clus
vv                                 AMP PEAK  1(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED     0  33
  AMP PEAK  1(1Q22) WILD-TYPE  15 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      0   33
  AMP PEAK  1(1Q22) WILD-TYPE   15  326
                        clus
vv                       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             0                          15
  NOT HISPANIC OR LATINO                        33                         326
[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    21  12
  AMP PEAK  2(1Q32.1) WILD-TYPE 303  59
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           33                           362 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           12                            59 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-6665 TCGA-DB-5277 TCGA-DB-A64L TCGA-DH-A669 
        7.69        21.01        12.43        46.65        11.01        30.21 
TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7290 
      211.17         1.22        11.64        14.99        90.77        10.36 
TCGA-DU-7292 TCGA-DU-7304 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-FG-5962 
        7.96        23.31         3.98        19.13         4.96        47.77 
TCGA-FG-6688 TCGA-FG-A4MW TCGA-HT-7475 TCGA-HT-7603 TCGA-HT-7688 TCGA-HT-8011 
       18.77         5.26        17.42        23.18        31.69        16.24 
TCGA-HT-8104 TCGA-HT-A4DS TCGA-QH-A6CV TCGA-S9-A6WM TCGA-S9-A7R2 TCGA-TM-A7C3 
       12.23         0.23         2.96         9.30        10.39        49.45 
TCGA-TM-A84B TCGA-TM-A84I TCGA-VM-A8CA 
       12.00        19.36        13.51 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O 
       27.02        18.84        18.38        72.95        12.59        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       13.64        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
        8.02        29.62        15.75         7.79         3.85        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        87.45         7.04 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
        6.54         8.84       117.40        30.67        26.30        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10        23.74        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 
       78.21        95.57       130.78        14.33        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       32.19        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       24.46         0.59         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        7.04         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40        63.55        21.50        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04        15.72        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        4.18         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R3 
        8.12         3.58         4.04        18.21        13.02        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        83.80        31.59         5.00        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       22.59        48.39        15.09        50.76        34.36        24.26 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        12.00        33.07        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.23                          0.03 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       13.510                        15.025 
[1] "0.2 - 211.2 (13.5)" "0.0 - 182.3 (15.0)"
[1] "hr=" "2.5"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    15  19
  AMP PEAK  2(1Q32.1) WILD-TYPE 161 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     15   19
  AMP PEAK  2(1Q32.1) WILD-TYPE  161  205
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          15                           161
  MALE                            19                           205
[1] 2 2
[1] FALSE
D2V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  2(1Q32.1) MUTATED            17                6                11
  AMP PEAK  2(1Q32.1) WILD-TYPE         126               98               142
D2V5, multiclass
                   clus
vv                  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  ASTROCYTOMA                                17                           126
  OLIGOASTROCYTOMA                            6                            98
  OLIGODENDROGLIOMA                          11                           142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    10  24
  AMP PEAK  2(1Q32.1) WILD-TYPE  79 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     10   24
  AMP PEAK  2(1Q32.1) WILD-TYPE   79  287
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           10                            79
  YES                          24                           287
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q32.1) MUTATED                                  0     1
  AMP PEAK  2(1Q32.1) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED                           2    30
  AMP PEAK  2(1Q32.1) WILD-TYPE                        12   346
D2V7, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     30
                                  clus
vv                                 AMP PEAK  2(1Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      346
[1] 4 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     0  32
  AMP PEAK  2(1Q32.1) WILD-TYPE  15 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      0   32
  AMP PEAK  2(1Q32.1) WILD-TYPE   15  327
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           327
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2P24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.3) MUTATED    11   5
  AMP PEAK  3(2P24.3) WILD-TYPE 313  66
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           16                           379 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                            5                            66 
$`AMP PEAK  3(2P24.3) MUTATED`
TCGA-DB-5274 TCGA-DB-5277 TCGA-DH-A669 TCGA-DU-6407 TCGA-DU-8165 TCGA-E1-5304 
       75.25        46.65        30.21        94.52        19.13        41.13 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HW-A5KM TCGA-S9-A6U0 TCGA-S9-A6WM 
       15.72         0.23         0.13         6.61        16.37         9.30 
TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA TCGA-VM-A8CD 
        9.37        18.90        13.51         7.89 

$`AMP PEAK  3(2P24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        4.70         0.23        29.59         3.88        16.04        10.49 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 
       19.59        17.82        10.55         7.89         9.67        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       22.49        21.63        11.31        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        4.21         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R 
       19.36        17.49        40.83        16.50        29.92         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CE 
        4.57        12.00        33.07        30.08         0.10        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                        94.52                        211.17 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       16.045                        14.960 
[1] "0.1 - 94.5 (16.0)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.9"
D3V2, continuous
D3V3, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     7   9
  AMP PEAK  3(2P24.3) WILD-TYPE 169 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      7    9
  AMP PEAK  3(2P24.3) WILD-TYPE  169  215
        clus
vv       AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  FEMALE                           7                           169
  MALE                             9                           215
[1] 2 2
[1] FALSE
D3V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  3(2P24.3) MUTATED             9                1                 6
  AMP PEAK  3(2P24.3) WILD-TYPE         134              103               147
D3V5, multiclass
                   clus
vv                  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ASTROCYTOMA                                 9                           134
  OLIGOASTROCYTOMA                            1                           103
  OLIGODENDROGLIOMA                           6                           147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     3  13
  AMP PEAK  3(2P24.3) WILD-TYPE  86 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      3   13
  AMP PEAK  3(2P24.3) WILD-TYPE   86  298
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NO                            3                            86
  YES                          13                           298
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(2P24.3) MUTATED                                  0     0
  AMP PEAK  3(2P24.3) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2P24.3) MUTATED                           0    15
  AMP PEAK  3(2P24.3) WILD-TYPE                        14   361
D3V7, multiclass
                                  clus
vv                                 AMP PEAK  3(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     15
                                  clus
vv                                 AMP PEAK  3(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      361
[1] 4 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(2P24.3) MUTATED     2  11
  AMP PEAK  3(2P24.3) WILD-TYPE  13 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      2   11
  AMP PEAK  3(2P24.3) WILD-TYPE   13  348
                        clus
vv                       AMP PEAK  3(2P24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK  3(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           348
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(3Q26.33) MUTATED    10   6
  AMP PEAK  4(3Q26.33) WILD-TYPE 314  65
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            16                            379 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                             6                             65 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-CS-4942 TCGA-CS-5395 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-DU-A5TW 
       43.89        21.01         1.22         8.84         5.10         5.65 
TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-HT-7606 TCGA-HT-7676 
       41.13        47.77        17.88        10.59        17.29         0.16 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-S9-A6WM TCGA-TM-A84B 
        0.23        14.70         9.30        12.00 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       11.41        26.76         7.13        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
      130.78        14.33        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 
       14.93        24.99        23.97        13.58        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.21         4.08        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        5.03        29.85        23.18       107.93         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       10.49         0.13         0.07         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       49.45        35.93        25.32        22.59        48.39        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                         47.77                         211.17 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                        11.295                         15.090 
[1] "0.2 - 47.8 (11.3)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.2"
D4V2, continuous
D4V3, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     9   8
  AMP PEAK  4(3Q26.33) WILD-TYPE 167 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      9    8
  AMP PEAK  4(3Q26.33) WILD-TYPE  167  216
        clus
vv       AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  FEMALE                            9                            167
  MALE                              8                            216
[1] 2 2
[1] FALSE
D4V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  4(3Q26.33) MUTATED            13                0                 4
  AMP PEAK  4(3Q26.33) WILD-TYPE         130              104               149
D4V5, multiclass
                   clus
vv                  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  ASTROCYTOMA                                 13                            130
  OLIGOASTROCYTOMA                             0                            104
  OLIGODENDROGLIOMA                            4                            149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     6  11
  AMP PEAK  4(3Q26.33) WILD-TYPE  83 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      6   11
  AMP PEAK  4(3Q26.33) WILD-TYPE   83  300
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                             6                             83
  YES                           11                            300
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(3Q26.33) MUTATED                                  0     0
  AMP PEAK  4(3Q26.33) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED                           3    14
  AMP PEAK  4(3Q26.33) WILD-TYPE                        11   362
D4V7, multiclass
                                  clus
vv                                 AMP PEAK  4(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      14
                                  clus
vv                                 AMP PEAK  4(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       362
[1] 4 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(3Q26.33) MUTATED     0  15
  AMP PEAK  4(3Q26.33) WILD-TYPE  15 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      0   15
  AMP PEAK  4(3Q26.33) WILD-TYPE   15  344
                        clus
vv                       AMP PEAK  4(3Q26.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       AMP PEAK  4(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            344
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    15   6
  AMP PEAK  5(4Q12) WILD-TYPE 309  65
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         21                         374 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                          6                          65 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 TCGA-DU-7010 TCGA-DU-7302 
       18.15        12.43         8.48        46.65        14.99        60.30 
TCGA-DU-7309 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-E1-5304 TCGA-E1-5307 TCGA-FG-A6J3 
        2.76        15.12         4.96        41.13        57.93        10.59 
TCGA-HT-7477 TCGA-HT-7856 TCGA-HT-7882 TCGA-S9-A6U0 TCGA-S9-A6WQ TCGA-S9-A7IS 
       24.26        39.09         1.71        16.37         3.39         7.92 
TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A84I 
        9.37         5.00        19.36 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.02        18.84        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 
       21.30       124.50        50.14        67.46        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        19.23         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        1.64         2.37         2.30         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        22.49        21.63        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
        9.04         7.59         6.15        14.27        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        4.21         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        24.26        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       1.71                        0.03 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      60.30                      211.17 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      14.99                       14.96 
[1] "1.7 - 60.3 (15.0)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.4"
D5V2, continuous
D5V3, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     9  12
  AMP PEAK  5(4Q12) WILD-TYPE 167 212
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      9   12
  AMP PEAK  5(4Q12) WILD-TYPE  167  212
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                         9                         167
  MALE                          12                         212
[1] 2 2
[1] FALSE
D5V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  5(4Q12) MUTATED            13                1                 7
  AMP PEAK  5(4Q12) WILD-TYPE         130              103               146
D5V5, multiclass
                   clus
vv                  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  ASTROCYTOMA                              13                         130
  OLIGOASTROCYTOMA                          1                         103
  OLIGODENDROGLIOMA                         7                         146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     4  17
  AMP PEAK  5(4Q12) WILD-TYPE  85 294
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      4   17
  AMP PEAK  5(4Q12) WILD-TYPE   85  294
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          4                          85
  YES                        17                         294
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(4Q12) MUTATED                                  0     0
  AMP PEAK  5(4Q12) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED                           1    20
  AMP PEAK  5(4Q12) WILD-TYPE                        13   356
D5V7, multiclass
                                  clus
vv                                 AMP PEAK  5(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   20
                                  clus
vv                                 AMP PEAK  5(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    356
[1] 4 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(4Q12) MUTATED     1  19
  AMP PEAK  5(4Q12) WILD-TYPE  14 340
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      1   19
  AMP PEAK  5(4Q12) WILD-TYPE   14  340
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          14
  NOT HISPANIC OR LATINO                        19                         340
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P11.2) MUTATED    66  34
  AMP PEAK  6(7P11.2) WILD-TYPE 258  37
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          100                           295 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                           34                            37 
$`AMP PEAK  6(7P11.2) MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        7.69        43.89        40.18        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        46.65 
TCGA-DB-A4X9 TCGA-DB-A4XE TCGA-DB-A64O TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66G 
       30.08        18.84        18.84        30.31        30.21         3.85 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6402 
        6.74         8.45       211.17        49.02         1.22         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       11.47       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
        7.96         5.10        23.74         3.98        20.68        19.13 
TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       16.96        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-6688 
       11.41        26.76        41.13       130.78        47.77        18.77 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-A4MU 
       23.97        13.58        15.35        20.09        13.68         0.59 
TCGA-FG-A4MW TCGA-FG-A70Z TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7688 TCGA-HT-7860 
        5.26        10.78        16.54        24.26        31.69         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 
        1.71        16.24        63.55        12.23         4.70        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
        0.23         0.13         0.07        14.70         5.33        16.14 
TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-QH-A6CS TCGA-QH-A6CV 
        7.89         4.73         2.30         4.11         4.18         2.96 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
        1.91         0.23         5.03        22.49        16.37         9.30 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-TM-A7C3 
       14.27        19.63         4.21         9.37        10.39        49.45 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       22.59        12.00        24.26        16.50 

$`AMP PEAK  6(7P11.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-6290 
        4.70        18.15        10.62        64.64         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       10.29        12.72        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       12.59        11.01        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        19.96        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 
       14.40         8.02        29.62        15.75         7.79        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       14.56        17.46        13.38         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       65.75        87.45       114.08         7.73        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 
      138.28        14.99        30.67        26.30        10.36        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       41.98         2.76        21.40        15.48        14.17        14.24 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       15.12         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5963 
       57.93       134.27        78.21        95.57        14.33        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 
       34.36        32.19        14.93        24.99        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.61        12.95        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       11.87        15.52        24.46         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 
        6.64         7.04         4.21         4.08        10.59        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.13         0.03         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33         2.93        11.28        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        9.40        21.50        33.01         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         3.95         0.23        29.59         3.88        16.04 
TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       10.49         0.10         2.70        13.02         1.81         5.33 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
        9.67         6.61        19.00        42.77         5.23         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        6.71         1.64         2.37         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        2.53         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.59         6.31         3.91         4.73        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.14        21.63        11.31        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
        6.15         3.39         7.92        12.59         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R3 
        8.12         3.58         4.04        18.21        13.02        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        83.80        31.59         5.00        35.93        25.32 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       48.39        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                        13.63                         15.12 
[1] "0.1 - 211.2 (13.6)" "0.0 - 182.3 (15.1)"
[1] "hr=" "3"  
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    50  51
  AMP PEAK  6(7P11.2) WILD-TYPE 126 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     50   51
  AMP PEAK  6(7P11.2) WILD-TYPE  126  173
        clus
vv       AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  FEMALE                          50                           126
  MALE                            51                           173
[1] 2 2
[1] FALSE
D6V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  6(7P11.2) MUTATED            46               26                29
  AMP PEAK  6(7P11.2) WILD-TYPE          97               78               124
D6V5, multiclass
                   clus
vv                  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  ASTROCYTOMA                                46                            97
  OLIGOASTROCYTOMA                           26                            78
  OLIGODENDROGLIOMA                          29                           124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    25  76
  AMP PEAK  6(7P11.2) WILD-TYPE  64 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     25   76
  AMP PEAK  6(7P11.2) WILD-TYPE   64  235
     clus
vv    AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  NO                           25                            64
  YES                          76                           235
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(7P11.2) MUTATED                                  1     1
  AMP PEAK  6(7P11.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P11.2) MUTATED                           6    93
  AMP PEAK  6(7P11.2) WILD-TYPE                         8   283
D6V7, multiclass
                                  clus
vv                                 AMP PEAK  6(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     93
                                  clus
vv                                 AMP PEAK  6(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED     4  92
  AMP PEAK  6(7P11.2) WILD-TYPE  11 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED      4   92
  AMP PEAK  6(7P11.2) WILD-TYPE   11  267
                        clus
vv                       AMP PEAK  6(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       AMP PEAK  6(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           267
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7Q31.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7Q31.2) MUTATED    98  38
  AMP PEAK  7(7Q31.2) WILD-TYPE 226  33
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          136                           259 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                           38                            33 
$`AMP PEAK  7(7Q31.2) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        4.70         7.69        43.89        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        46.65 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A64X 
       30.08        12.72        27.02        18.84        18.84        10.92 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5854 
        8.02        30.21        15.75         3.85        14.56         8.45 
TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 
        6.81        17.49       211.17        49.02        65.75         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96        11.47       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 
        6.54         8.84       117.40         7.96        25.91        41.98 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       23.74        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
        3.65         5.65        12.20        77.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 
        7.13        21.30       124.50        50.14        41.13       130.78 
TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       47.77        32.19        18.77        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW 
       15.35        20.09        13.68        16.01         0.59         5.26 
TCGA-FG-A60L TCGA-FG-A70Z TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 
        7.04        10.78        16.54        17.42        24.26       107.93 
TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 
       56.09        31.69        17.52         0.49         1.71        11.28 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8114 
       16.24        63.55        12.23         2.50         4.70         3.88 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC 
       15.72         0.23         0.13         0.07        14.70         5.33 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A7W1 
        1.81        16.14         4.31        17.82        10.55         4.73 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A6CS TCGA-QH-A6CV 
        0.23         2.30         4.11         5.88         4.18         2.96 
TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TY TCGA-S9-A6U0 
        0.59         1.91         0.23         5.03        22.49        16.37 
TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
        9.30         7.59        14.27        19.63         4.21         9.37 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
        3.58        18.21        10.39        49.45        35.93        22.59 
TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M 
       12.00        24.26        40.83        16.50 

$`AMP PEAK  7(7Q31.2) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 
       18.15        10.62        64.64        40.18         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       10.29        27.62        18.38        72.95        12.59        11.01 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B 
       13.64        19.96        31.82        30.31        14.40        29.62 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5870 
        7.79        18.02        17.46         6.74        13.38       182.33 
TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       18.94        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7015 TCGA-DU-7018 
       87.45       114.08         7.73        62.96        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36        94.32        18.94        44.02        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 
       60.30        23.31         2.76         5.10         3.98        21.40 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.48        14.17        14.24        15.12         8.65         2.70 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        7.23         5.98        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 
       78.21        95.57        14.33        17.98        34.36        14.93 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8187 
       17.88        22.55        20.61        12.95        14.24        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.96        11.87        15.52        24.46         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 
        7.04         6.64         4.21         4.08        10.59        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
        0.13         0.03         3.75         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
        0.33         0.13         3.68         5.33         2.93        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
        1.64         9.40        21.50        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-A4DV 
        0.46         3.95         0.23        29.59        16.04        10.49 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
        0.10         2.70        13.02         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18        35.90         8.61         8.94 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       19.59         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A65R 
        5.23         6.71         1.64         2.37         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        2.53         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        6.31         3.91         4.73        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ 
       22.92        70.65        10.88         9.04         6.15         3.39 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX 
        7.92        12.59         8.19         2.04         8.12         4.04 
TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       13.02        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       25.32        48.39        15.09        50.76        34.36        19.36 
TCGA-TM-A84J TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       17.49        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       14.845                        14.960 
[1] "0.1 - 211.2 (14.8)" "0.0 - 182.3 (15.0)"
[1] "hr=" "2.1"
D7V2, continuous
D7V3, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    69  69
  AMP PEAK  7(7Q31.2) WILD-TYPE 107 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     69   69
  AMP PEAK  7(7Q31.2) WILD-TYPE  107  155
        clus
vv       AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  FEMALE                          69                           107
  MALE                            69                           155
[1] 2 2
[1] FALSE
D7V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  7(7Q31.2) MUTATED            59               37                42
  AMP PEAK  7(7Q31.2) WILD-TYPE          84               67               111
D7V5, multiclass
                   clus
vv                  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  ASTROCYTOMA                                59                            84
  OLIGOASTROCYTOMA                           37                            67
  OLIGODENDROGLIOMA                          42                           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    33 105
  AMP PEAK  7(7Q31.2) WILD-TYPE  56 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     33  105
  AMP PEAK  7(7Q31.2) WILD-TYPE   56  206
     clus
vv    AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  NO                           33                            56
  YES                         105                           206
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(7Q31.2) MUTATED                                  1     1
  AMP PEAK  7(7Q31.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q31.2) MUTATED                           8   128
  AMP PEAK  7(7Q31.2) WILD-TYPE                         6   248
D7V7, multiclass
                                  clus
vv                                 AMP PEAK  7(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    128
                                  clus
vv                                 AMP PEAK  7(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      248
[1] 4 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(7Q31.2) MUTATED     5 129
  AMP PEAK  7(7Q31.2) WILD-TYPE  10 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED      5  129
  AMP PEAK  7(7Q31.2) WILD-TYPE   10  230
                        clus
vv                       AMP PEAK  7(7Q31.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         129
                        clus
vv                       AMP PEAK  7(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           230
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7Q32.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7Q32.3) MUTATED   104  38
  AMP PEAK  8(7Q32.3) WILD-TYPE 220  33
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          142                           253 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                           38                            33 
$`AMP PEAK  8(7Q32.3) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        4.70         7.69        43.89        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        46.65 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64O 
       78.28        30.08        12.72        27.02        18.84        18.84 
TCGA-DB-A64X TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5849 
       10.92         8.02        30.21        15.75         3.85        14.56 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 
        8.45         6.81        17.49       211.17        49.02        65.75 
TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
       94.52         7.96        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7292 
      105.21         6.54         8.84       117.40        90.77         7.96 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       25.91        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       19.13        16.96        12.59         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
       12.20        77.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5965 
      124.50        50.14        41.13       130.78        47.77        32.19 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 
       18.77        24.99        23.97        13.58        15.35        20.09 
TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60L TCGA-FG-A70Z 
       13.68        16.01         0.59         5.26         7.04        10.78 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7688 
       16.54        17.42        24.26       107.93        56.09        31.69 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 
        2.96        17.52         0.49         1.71        11.28        16.24 
TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-8564 
       63.55        12.23         2.50         4.70         3.88        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 
        0.23         0.13         0.07        14.70         5.33         1.81 
TCGA-HT-A617 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-KT-A7W1 
       16.14         4.31        17.82        10.55         6.61         4.73 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A6CS TCGA-QH-A6CV 
        0.23         2.30         4.11         5.88         4.18         2.96 
TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TY TCGA-S9-A6U0 
        0.59         1.91         0.23         5.03        22.49        16.37 
TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
        9.30         7.59        14.27        19.63         4.21         9.37 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 
        3.58         4.04        18.21        10.39        49.45        35.93 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       22.59        12.00        24.26        16.50 

$`AMP PEAK  8(7Q32.3) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 
       18.15        10.62        64.64        40.18         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4XA 
       47.93        72.92        50.17        44.52        36.56        10.29 
TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       27.62        18.38        72.95        12.59        11.01        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66F 
       19.96        31.82        30.31        14.40        29.62         7.79 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 
       18.02        17.46         6.74        13.38       182.33        18.94 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 
       15.16        52.11        22.42        75.16        46.06        87.45 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      114.08         7.73        62.96        30.67        26.30        10.36 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        62.01        60.30        23.31 
TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS 
        5.10        21.40        15.48        14.17        14.24        15.12 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5303 TCGA-E1-5305 
        8.65         2.70         7.23         5.98        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5963 
       57.93       134.27        78.21        95.57        14.33        17.98 
TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       34.36        14.93        17.88        22.55        20.61        12.95 
TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        20.09        14.96        11.87        15.52        24.46 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
        3.72         9.67         7.04         6.64         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.59        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 
        7.82         8.81         0.13         0.03         3.75         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 
        0.10        14.96         0.10         0.10         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       31.43         1.64         9.40        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 
        0.10         0.46         3.95         0.23        29.59        16.04 
TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 TCGA-HW-7486 
       10.49         0.10         2.70        13.02         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 
       13.45         8.32        19.23        40.18        35.90         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 
        8.94        19.59         7.89         9.67        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A65R 
        5.23         6.71         1.64         2.37         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        2.53         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        6.31         3.91         4.73        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ 
       22.92        70.65        10.88         9.04         6.15         3.39 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ 
        7.92        12.59         8.19         2.04         8.12        13.02 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C5 
       87.09        17.42        83.80        31.59         5.00        25.32 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       48.39        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                       14.415                        15.120 
[1] "0.1 - 211.2 (14.4)" "0.0 - 182.3 (15.1)"
[1] "hr=" "2"  
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    73  71
  AMP PEAK  8(7Q32.3) WILD-TYPE 103 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     73   71
  AMP PEAK  8(7Q32.3) WILD-TYPE  103  153
        clus
vv       AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  FEMALE                          73                           103
  MALE                            71                           153
[1] 2 2
[1] FALSE
D8V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  8(7Q32.3) MUTATED            61               39                44
  AMP PEAK  8(7Q32.3) WILD-TYPE          82               65               109
D8V5, multiclass
                   clus
vv                  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  ASTROCYTOMA                                61                            82
  OLIGOASTROCYTOMA                           39                            65
  OLIGODENDROGLIOMA                          44                           109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    35 109
  AMP PEAK  8(7Q32.3) WILD-TYPE  54 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     35  109
  AMP PEAK  8(7Q32.3) WILD-TYPE   54  202
     clus
vv    AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  NO                           35                            54
  YES                         109                           202
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7Q32.3) MUTATED                                  1     1
  AMP PEAK  8(7Q32.3) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7Q32.3) MUTATED                           8   134
  AMP PEAK  8(7Q32.3) WILD-TYPE                         6   242
D8V7, multiclass
                                  clus
vv                                 AMP PEAK  8(7Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    134
                                  clus
vv                                 AMP PEAK  8(7Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED     5 134
  AMP PEAK  8(7Q32.3) WILD-TYPE  10 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED      5  134
  AMP PEAK  8(7Q32.3) WILD-TYPE   10  225
                        clus
vv                       AMP PEAK  8(7Q32.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         134
                        clus
vv                       AMP PEAK  8(7Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           225
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8Q24.13) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.13) MUTATED    61  15
  AMP PEAK  9(8Q24.13) WILD-TYPE 263  56
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            76                            319 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            15                             56 
$`AMP PEAK  9(8Q24.13) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 
       18.15        40.18        17.95        12.43         8.48        46.65 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5143 
       78.28        12.72        27.02        18.84        10.92        14.40 
TCGA-DH-A669 TCGA-DH-A66G TCGA-DU-5871 TCGA-DU-6399 TCGA-DU-6407 TCGA-DU-6408 
       30.21         3.85        18.94        65.75        94.52       114.08 
TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7304 TCGA-DU-8158 
       14.99         8.84       117.40        90.77        23.31         5.10 
TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 
       20.68        15.48        15.12         5.65         7.23       124.50 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5962 TCGA-FG-5964 
       67.46        41.13        79.99        57.93        47.77        34.36 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A6J3 
       23.97        15.35        14.96        24.46         9.67        10.59 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 
       16.54        17.42         6.54        24.26         7.10        60.03 
TCGA-HT-7604 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8011 
      107.93        14.96        19.23        23.61         3.68        16.24 
TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A614 TCGA-HT-A616 TCGA-P5-A5F1 
       63.55         0.10         0.23         2.70         1.81         5.88 
TCGA-QH-A6XA TCGA-S9-A6TU TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WH 
        0.23        69.07        22.49         9.86        70.55        22.92 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7QW TCGA-S9-A7QX TCGA-TM-A7CF TCGA-TM-A84H 
        7.59         6.15         3.58         4.04        48.39        24.26 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.90        12.00        33.07        13.51 

$`AMP PEAK  9(8Q24.13) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6667 
       21.01         9.96         6.38        17.69        23.84         7.56 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        8.02         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 
       47.93        72.92        50.17        44.52        36.56        30.08 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       10.29        27.62        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 
       14.73        13.64        19.96        31.82        30.31         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         7.79        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       19.89        16.83         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7018 TCGA-DU-7019 
      156.23       138.28       105.21         6.54        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       25.91        60.30        41.98         2.76        23.74         3.98 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        14.17        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5302 
        5.98        11.41        26.76         7.13        21.30        50.14 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 
      134.27        78.21        95.57       130.78        14.33        17.98 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 
       32.19        18.77        14.93        24.99        13.58        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        20.09        11.87        15.52         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        3.72         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7478 
        7.82         8.81         0.13         0.03         3.75         6.38 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        59.18       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       39.48        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       31.43         1.64         9.40        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        6.25         0.46         2.50         3.95         4.70        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 
        0.07        14.70         0.10         5.33        13.02        16.14 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC 
        0.59         6.31         3.91         4.73         1.91         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        62.17        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.27        28.14        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       20.05        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WQ 
       72.59        70.65        10.88         9.30         9.04         3.39 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
        8.19         2.04         8.12        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        22.59        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        19.36        17.49        40.83        16.50        29.92 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
        9.44         4.57        30.08         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                        124.50                         211.17 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                         18.05                          14.24 
[1] "0.1 - 124.5 (18.0)" "0.0 - 211.2 (14.2)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    29  48
  AMP PEAK  9(8Q24.13) WILD-TYPE 147 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     29   48
  AMP PEAK  9(8Q24.13) WILD-TYPE  147  176
        clus
vv       AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  FEMALE                           29                            147
  MALE                             48                            176
[1] 2 2
[1] FALSE
D9V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  9(8Q24.13) MUTATED            37               24                16
  AMP PEAK  9(8Q24.13) WILD-TYPE         106               80               137
D9V5, multiclass
                   clus
vv                  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  ASTROCYTOMA                                 37                            106
  OLIGOASTROCYTOMA                            24                             80
  OLIGODENDROGLIOMA                           16                            137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    18  59
  AMP PEAK  9(8Q24.13) WILD-TYPE  71 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     18   59
  AMP PEAK  9(8Q24.13) WILD-TYPE   71  252
     clus
vv    AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  NO                            18                             71
  YES                           59                            252
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.13) MUTATED                                  0     0
  AMP PEAK  9(8Q24.13) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.13) MUTATED                           3    72
  AMP PEAK  9(8Q24.13) WILD-TYPE                        11   304
D9V7, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      72
                                  clus
vv                                 AMP PEAK  9(8Q24.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       304
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED     3  69
  AMP PEAK  9(8Q24.13) WILD-TYPE  12 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED      3   69
  AMP PEAK  9(8Q24.13) WILD-TYPE   12  290
                        clus
vv                       AMP PEAK  9(8Q24.13) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK  9(8Q24.13) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(9Q34.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(9Q34.3) MUTATED    32   7
  AMP PEAK 10(9Q34.3) WILD-TYPE 292  64
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           39                           356 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                            7                            64 
$`AMP PEAK 10(9Q34.3) MUTATED`
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DB-A64R 
        9.96         6.38        17.95        12.43        18.84        16.08 
TCGA-DB-A64X TCGA-DH-5142 TCGA-DU-7010 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 
       10.92        30.31        14.99        18.94         5.10        23.74 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 
       21.40        19.13        14.17         4.96         7.13        50.14 
TCGA-E1-5304 TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A6J3 TCGA-HT-7468 TCGA-HT-7477 
       41.13         9.67         6.64        10.59         6.67        24.26 
TCGA-HT-7478 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7686 TCGA-HT-7873 TCGA-HT-A5RB 
        6.38       154.19         5.03        42.74        23.61         0.10 
TCGA-HT-A617 TCGA-HW-8319 TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7QW 
       16.14         8.61        28.27        22.92         9.30         3.58 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84T 
       50.76        24.26        12.00 

$`AMP PEAK 10(9Q34.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6666 
       40.18         0.10        21.01        17.69        23.84         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        46.65        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       27.02        18.38        72.95        12.59        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       16.80         5.98        15.42        27.81        14.73        13.64 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        14.40         8.02        30.21        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76         3.98 
TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       20.68        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 
        7.23         5.98        11.41        26.76        21.30       124.50 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L 
       24.46         0.59         5.26         3.72         7.04         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.21         4.08        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
       60.03         4.01        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 
        5.33         2.70        13.02         1.81         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       62.37        72.59        70.55        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59         5.00        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84I 
       22.59        48.39        12.00        15.09        34.36        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                       154.19                        211.17 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                        14.99                         14.96 
[1] "0.1 - 154.2 (15.0)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.3"
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED    22  17
  AMP PEAK 10(9Q34.3) WILD-TYPE 154 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED     22   17
  AMP PEAK 10(9Q34.3) WILD-TYPE  154  207
        clus
vv       AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  FEMALE                          22                           154
  MALE                            17                           207
[1] 2 2
[1] FALSE
D10V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 10(9Q34.3) MUTATED            21                9                 9
  AMP PEAK 10(9Q34.3) WILD-TYPE         122               95               144
D10V5, multiclass
                   clus
vv                  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  ASTROCYTOMA                                21                           122
  OLIGOASTROCYTOMA                            9                            95
  OLIGODENDROGLIOMA                           9                           144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED    10  29
  AMP PEAK 10(9Q34.3) WILD-TYPE  79 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED     10   29
  AMP PEAK 10(9Q34.3) WILD-TYPE   79  282
     clus
vv    AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  NO                           10                            79
  YES                          29                           282
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(9Q34.3) MUTATED                                  1     0
  AMP PEAK 10(9Q34.3) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(9Q34.3) MUTATED                           1    35
  AMP PEAK 10(9Q34.3) WILD-TYPE                        13   341
D10V7, multiclass
                                  clus
vv                                 AMP PEAK 10(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     35
                                  clus
vv                                 AMP PEAK 10(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED     3  34
  AMP PEAK 10(9Q34.3) WILD-TYPE  12 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED      3   34
  AMP PEAK 10(9Q34.3) WILD-TYPE   12  325
                        clus
vv                       AMP PEAK 10(9Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       AMP PEAK 10(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           325
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(10P15.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(10P15.3) MUTATED    41  11
  AMP PEAK 11(10P15.3) WILD-TYPE 283  60
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            52                            343 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            11                             60 
$`AMP PEAK 11(10P15.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5270 
       18.15        40.18        12.43         8.48         7.56       122.73 
TCGA-DB-5277 TCGA-DB-A4XE TCGA-DH-A66B TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6408 
       46.65        18.84        29.62        18.94        75.16       114.08 
TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS 
      117.40        26.30        44.02        23.31        12.59        15.12 
TCGA-DU-A5TW TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-6691 TCGA-FG-8185 
        5.65        67.46        41.13       130.78        23.97        14.24 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7479 
        9.67         7.04         8.81        16.54         6.54         7.10 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8106 
       60.03       154.19        31.69        23.61         3.68         0.10 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 
        0.23         3.88         8.32        35.90        19.59        19.00 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A6XA TCGA-S9-A6U0 TCGA-S9-A7IS TCGA-S9-A7J0 
        2.30         5.88         0.23        16.37         7.92         9.37 
TCGA-S9-A89Z TCGA-TM-A7CA TCGA-TM-A84H TCGA-VM-A8C8 
        5.00        22.59        24.26        33.07 

$`AMP PEAK 11(10P15.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        8.02         7.40         6.61        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       10.29        12.72        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        30.21        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83        94.52         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        10.36         7.96        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       15.48        14.17        14.24         4.96         3.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5305 
       26.76         7.13        21.30       124.50        50.14        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 
       57.93       134.27        78.21        95.57        14.33        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       15.52        24.46         0.59         5.26         3.72         7.04 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        6.64         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
        5.23         0.13         0.10         6.67         7.82         0.13 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 
        0.03         3.75        17.42        24.26         6.38        75.19 
TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
       59.18         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
       44.68         6.05        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        4.70        29.59        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 
       19.23        40.18         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67         6.61        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
        4.73         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        3.91         4.73         1.91         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        22.49        21.63        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
        9.04         7.59         6.15         3.39        14.27        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       12.59         4.21         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       83.80        31.59        49.45        35.93        25.32        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                        154.19                         211.17 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                        18.495                         14.700 
[1] "0.1 - 154.2 (18.5)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    19  33
  AMP PEAK 11(10P15.3) WILD-TYPE 157 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     19   33
  AMP PEAK 11(10P15.3) WILD-TYPE  157  191
        clus
vv       AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  FEMALE                           19                            157
  MALE                             33                            191
[1] 2 2
[1] FALSE
D11V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 11(10P15.3) MUTATED            25               19                 8
  AMP PEAK 11(10P15.3) WILD-TYPE         118               85               145
D11V5, multiclass
                   clus
vv                  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  ASTROCYTOMA                                 25                            118
  OLIGOASTROCYTOMA                            19                             85
  OLIGODENDROGLIOMA                            8                            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    18  34
  AMP PEAK 11(10P15.3) WILD-TYPE  71 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     18   34
  AMP PEAK 11(10P15.3) WILD-TYPE   71  277
     clus
vv    AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  NO                            18                             71
  YES                           34                            277
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(10P15.3) MUTATED                                  0     0
  AMP PEAK 11(10P15.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(10P15.3) MUTATED                           2    50
  AMP PEAK 11(10P15.3) WILD-TYPE                        12   326
D11V7, multiclass
                                  clus
vv                                 AMP PEAK 11(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      50
                                  clus
vv                                 AMP PEAK 11(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED     4  45
  AMP PEAK 11(10P15.3) WILD-TYPE  11 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED      4   45
  AMP PEAK 11(10P15.3) WILD-TYPE   11  314
                        clus
vv                       AMP PEAK 11(10P15.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       AMP PEAK 11(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            314
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(11Q24.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(11Q24.1) MUTATED    57  14
  AMP PEAK 12(11Q24.1) WILD-TYPE 267  57
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            71                            324 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            14                             57 
$`AMP PEAK 12(11Q24.1) MUTATED`
TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
        9.96        46.65        30.08        12.72        27.62        27.02 
TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V TCGA-DH-5144 TCGA-DH-A66D TCGA-DU-5852 
       11.01         5.98        14.73         8.02        15.75         6.74 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6397 
        6.81       182.33        18.94       211.17        52.11        46.06 
TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7298 TCGA-DU-7301 
        1.22        94.52        90.77        30.67        18.94        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S7 
       23.31        41.98         2.76         4.96         5.65         7.23 
TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5318 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-8191 
        5.98        41.13        78.21        47.77        15.35        15.52 
TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 
        7.04         8.81         3.75         5.03       107.93         3.16 
TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-8109 TCGA-HW-7490 
        0.16         6.05        31.69        17.52         3.95        19.23 
TCGA-HW-8319 TCGA-HW-8321 TCGA-P5-A5EV TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ 
        8.61        19.59         0.23         2.53         7.79         3.16 
TCGA-QH-A6X9 TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WD TCGA-S9-A6WH 
        1.91        69.07        28.27        22.49        62.37        22.92 
TCGA-S9-A6WN TCGA-S9-A7IZ TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R8 TCGA-S9-A89Z 
        9.04         4.21        18.21        13.02        31.59         5.00 
TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8C8 TCGA-VM-A8CA 
       12.00        19.36        17.49        33.07        13.51 

$`AMP PEAK 12(11Q24.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XE 
       50.17        44.52        36.56        78.28        10.29        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R 
       18.38        72.95        12.59        18.84        16.80        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       15.42        27.81        13.64        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G 
       30.31        14.40        30.21        29.62         7.79         3.85 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5872 
       18.02        14.56        17.46        13.38         8.45        17.49 
TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 
       15.16        22.42        49.02        75.16        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7019 
       14.99       105.21         6.54         8.84       117.40        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 
       10.36         7.96        94.32        44.02        62.01        60.30 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
        3.65        12.20         8.65         2.70        77.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99        57.93       134.27        95.57       130.78        14.33 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        13.58        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       11.87        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        7.04         6.64         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 
        4.01        29.85        23.18         4.57        17.29        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 
       45.99        56.09        57.60         0.23        14.27        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
        0.76        44.68        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        5.33        29.92        13.45         8.32        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        4.31         8.94        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW 
        6.61        19.00        42.77         5.23         4.73         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        1.64         2.37         2.30         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        5.75         4.83         4.11         4.18         2.96         2.20 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC 
        0.59         6.31         3.91         4.73         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        62.17        18.77 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE 
        9.86        94.62        83.70         5.85       103.76        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP 
       70.55        70.65        10.88         9.30         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        3.39        14.27         7.92        19.63        12.59         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 
        8.19         2.04         8.12         3.58         4.04        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       87.09        17.42        83.80        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       22.59        48.39        15.09        50.76        34.36        24.26 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08         0.10         7.89        26.79        10.95 

  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                        211.17                         156.23 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                        15.520                         14.945 
[1] "0.2 - 211.2 (15.5)" "0.0 - 156.2 (14.9)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    35  36
  AMP PEAK 12(11Q24.1) WILD-TYPE 141 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     35   36
  AMP PEAK 12(11Q24.1) WILD-TYPE  141  188
        clus
vv       AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  FEMALE                           35                            141
  MALE                             36                            188
[1] 2 2
[1] FALSE
D12V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 12(11Q24.1) MUTATED            24               15                32
  AMP PEAK 12(11Q24.1) WILD-TYPE         119               89               121
D12V5, multiclass
                   clus
vv                  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  ASTROCYTOMA                                 24                            119
  OLIGOASTROCYTOMA                            15                             89
  OLIGODENDROGLIOMA                           32                            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    13  58
  AMP PEAK 12(11Q24.1) WILD-TYPE  76 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     13   58
  AMP PEAK 12(11Q24.1) WILD-TYPE   76  253
     clus
vv    AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  NO                            13                             76
  YES                           58                            253
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(11Q24.1) MUTATED                                  0     0
  AMP PEAK 12(11Q24.1) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(11Q24.1) MUTATED                           3    66
  AMP PEAK 12(11Q24.1) WILD-TYPE                        11   310
D12V7, multiclass
                                  clus
vv                                 AMP PEAK 12(11Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      66
                                  clus
vv                                 AMP PEAK 12(11Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED     1  67
  AMP PEAK 12(11Q24.1) WILD-TYPE  14 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED      1   67
  AMP PEAK 12(11Q24.1) WILD-TYPE   14  292
                        clus
vv                       AMP PEAK 12(11Q24.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 12(11Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(12P13.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(12P13.32) MUTATED    40  16
  AMP PEAK 13(12P13.32) WILD-TYPE 284  55
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             56                             339 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             16                              55 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-CS-4943 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XB 
       18.15        81.96        47.93        46.65        78.28        12.72 
TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A64P TCGA-DH-A669 TCGA-DU-6395 TCGA-DU-6396 
       27.62        18.84        16.80        30.21        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 
       65.75         1.22        11.64       114.08        62.96       156.23 
TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       44.02        23.31        19.13        14.24        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-FG-5965 
        3.65        12.20       124.50        67.46        41.13        32.19 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8191 
       24.99        23.97        15.35        13.68        14.24        15.52 
TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7473 TCGA-HT-7478 TCGA-HT-7604 TCGA-HT-7686 
       10.59         7.82        16.54         6.38       107.93        42.74 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8018 TCGA-HT-A614 TCGA-HW-A5KM 
       23.61         3.68        11.28        21.50         2.70         6.61 
TCGA-QH-A6CV TCGA-S9-A6UA TCGA-S9-A6WO TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX 
        2.96         5.85         7.59         4.21         9.37         4.04 
TCGA-S9-A7R7 TCGA-TM-A84I 
       83.80        19.36 

$`AMP PEAK 13(12P13.32) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
        6.61       122.73        75.25        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       36.56        30.08        10.29        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       12.59        11.01        18.84         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 
      211.17        52.11        22.42        46.06        87.45         7.04 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83        94.52         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       94.32        18.94        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A6S2 
       16.96        15.48        14.17        12.59         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        7.13        21.30        50.14        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        47.77        17.98 
TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       34.36        18.77        14.93        13.58        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.61        20.09        12.95        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       11.87        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z 
        7.04         6.64         7.04         4.21         4.08        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       22.95         5.23         0.13         0.10         6.67         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03         3.75        17.42         6.54        24.26 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
        5.03        29.85        23.18         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
       50.63         0.49        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       63.55        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         5.33        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         4.18         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.30         9.04         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        7.92        19.63        12.59         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        3.58        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                           1.22                            0.03 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         156.23                          211.17 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         18.495                          14.530 
[1] "1.2 - 156.2 (18.5)" "0.0 - 211.2 (14.5)"
[1] "hr=" "1.3"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    18  38
  AMP PEAK 13(12P13.32) WILD-TYPE 158 186
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     18   38
  AMP PEAK 13(12P13.32) WILD-TYPE  158  186
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            18                             158
  MALE                              38                             186
[1] 2 2
[1] FALSE
D13V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  AMP PEAK 13(12P13.32) MUTATED            25               16
  AMP PEAK 13(12P13.32) WILD-TYPE         118               88
                                 vv
clus                              OLIGODENDROGLIOMA
  AMP PEAK 13(12P13.32) MUTATED                  15
  AMP PEAK 13(12P13.32) WILD-TYPE               138
D13V5, multiclass
                   clus
vv                  AMP PEAK 13(12P13.32) MUTATED
  ASTROCYTOMA                                  25
  OLIGOASTROCYTOMA                             16
  OLIGODENDROGLIOMA                            15
                   clus
vv                  AMP PEAK 13(12P13.32) WILD-TYPE
  ASTROCYTOMA                                   118
  OLIGOASTROCYTOMA                               88
  OLIGODENDROGLIOMA                             138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    18  38
  AMP PEAK 13(12P13.32) WILD-TYPE  71 273
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     18   38
  AMP PEAK 13(12P13.32) WILD-TYPE   71  273
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                             18                              71
  YES                            38                             273
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(12P13.32) MUTATED                                  0     1
  AMP PEAK 13(12P13.32) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(12P13.32) MUTATED                           2    53
  AMP PEAK 13(12P13.32) WILD-TYPE                        12   323
D13V7, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       53
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                     12
  WHITE                                                        323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     1  53
  AMP PEAK 13(12P13.32) WILD-TYPE  14 306
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      1   53
  AMP PEAK 13(12P13.32) WILD-TYPE   14  306
                        clus
vv                       AMP PEAK 13(12P13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       AMP PEAK 13(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  14
  NOT HISPANIC OR LATINO                             306
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q14.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q14.1) MUTATED    16  13
  AMP PEAK 14(12Q14.1) WILD-TYPE 308  58
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            29                            366 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            13                             58 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 
        7.69        12.43        30.21         1.22        11.64        14.99 
TCGA-DU-7013 TCGA-DU-7298 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-E1-5305 
        8.84        18.94        19.13         4.96        12.20        79.99 
TCGA-E1-5318 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-8563 
       78.21        15.35        17.88        10.59        10.78        16.04 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-IK-7675 TCGA-P5-A5EZ TCGA-QH-A6CV TCGA-S9-A6UA 
        5.33         2.70        19.00         2.30         2.96         5.85 
TCGA-S9-A7IZ TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
        4.21        10.39        49.45        12.00        19.36 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       46.06        65.75        87.45         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 
       62.96       156.23       138.28       105.21         6.54       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65         5.65         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 
       50.14        67.46        41.13        57.93       134.27        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 
       18.77        14.93        24.99        23.97        13.58        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
        4.21         4.08        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 
        3.95         4.70         0.23        29.59         3.88        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         0.07        14.70         0.10 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
        6.61        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        1.64         2.37         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62        83.70       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        14.27         7.92        19.63        12.59 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       18.21        13.02        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
        5.00        35.93        25.32        22.59        48.39        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        24.26        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          1.22                           0.03 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         79.99                         211.17 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         12.00                          15.14 
[1] "1.2 - 80.0 (12.0)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.8"
D14V2, continuous
D14V3, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    14  15
  AMP PEAK 14(12Q14.1) WILD-TYPE 162 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     14   15
  AMP PEAK 14(12Q14.1) WILD-TYPE  162  209
        clus
vv       AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  FEMALE                           14                            162
  MALE                             15                            209
[1] 2 2
[1] FALSE
D14V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 14(12Q14.1) MUTATED            18                4                 7
  AMP PEAK 14(12Q14.1) WILD-TYPE         125              100               146
D14V5, multiclass
                   clus
vv                  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  ASTROCYTOMA                                 18                            125
  OLIGOASTROCYTOMA                             4                            100
  OLIGODENDROGLIOMA                            7                            146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     4  25
  AMP PEAK 14(12Q14.1) WILD-TYPE  85 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      4   25
  AMP PEAK 14(12Q14.1) WILD-TYPE   85  286
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                             4                             85
  YES                           25                            286
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(12Q14.1) MUTATED                                  0     1
  AMP PEAK 14(12Q14.1) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q14.1) MUTATED                           2    26
  AMP PEAK 14(12Q14.1) WILD-TYPE                        12   350
D14V7, multiclass
                                  clus
vv                                 AMP PEAK 14(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      26
                                  clus
vv                                 AMP PEAK 14(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       350
[1] 4 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(12Q14.1) MUTATED     1  28
  AMP PEAK 14(12Q14.1) WILD-TYPE  14 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      1   28
  AMP PEAK 14(12Q14.1) WILD-TYPE   14  331
                        clus
vv                       AMP PEAK 14(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 14(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            331
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q34) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(13Q34) MUTATED    17   2
  AMP PEAK 15(13Q34) WILD-TYPE 307  69
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          19                          376 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                           2                           69 
$`AMP PEAK 15(13Q34) MUTATED`
TCGA-DB-5277 TCGA-DU-5853 TCGA-DU-7015 TCGA-DU-7301 TCGA-DU-A5TT TCGA-DU-A5TU 
       46.65        13.38        90.77        25.91         4.96         3.65 
TCGA-DU-A5TY TCGA-HT-7476 TCGA-HT-7604 TCGA-HT-7611 TCGA-HT-7688 TCGA-HT-7873 
       12.20         6.54       107.93        57.60        31.69        23.61 
TCGA-HT-8563 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84T 
       16.04         2.53         1.91         5.00        49.45        12.00 
TCGA-VM-A8CA 
       13.51 

$`AMP PEAK 15(13Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       17.46         6.74         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 
       14.99       105.21         6.54         8.84       117.40        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW 
       15.48        14.17        14.24        12.59        15.12         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      154.19         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
       17.29         3.16        22.06        45.99        56.09         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS 
        4.70         0.23        29.59         3.88        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        2.70        13.02         1.81        16.14         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        5.88         1.28         5.75         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        3.91         4.73         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 
       10.39        87.09        17.42        83.80        31.59        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 
       29.92        18.90         9.44         4.57        33.07        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10         7.89        26.79        10.95 

  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                        1.91                         0.03 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      107.93                       211.17 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      13.510                       14.975 
[1] "1.9 - 107.9 (13.5)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.9"
D15V2, continuous
D15V3, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     7  13
  AMP PEAK 15(13Q34) WILD-TYPE 169 211
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      7   13
  AMP PEAK 15(13Q34) WILD-TYPE  169  211
        clus
vv       AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  FEMALE                          7                          169
  MALE                           13                          211
[1] 2 2
[1] FALSE
D15V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 15(13Q34) MUTATED             9                5                 6
  AMP PEAK 15(13Q34) WILD-TYPE         134               99               147
D15V5, multiclass
                   clus
vv                  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  ASTROCYTOMA                                9                          134
  OLIGOASTROCYTOMA                           5                           99
  OLIGODENDROGLIOMA                          6                          147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     4  16
  AMP PEAK 15(13Q34) WILD-TYPE  85 295
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      4   16
  AMP PEAK 15(13Q34) WILD-TYPE   85  295
     clus
vv    AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  NO                           4                           85
  YES                         16                          295
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q34) MUTATED                                  0     0
  AMP PEAK 15(13Q34) WILD-TYPE                                1     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q34) MUTATED                           1    18
  AMP PEAK 15(13Q34) WILD-TYPE                        13   358
D15V7, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    18
                                  clus
vv                                 AMP PEAK 15(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     1  18
  AMP PEAK 15(13Q34) WILD-TYPE  14 341
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      1   18
  AMP PEAK 15(13Q34) WILD-TYPE   14  341
                        clus
vv                       AMP PEAK 15(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         18
                        clus
vv                       AMP PEAK 15(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          341
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(15Q26.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.3) MUTATED     9   5
  AMP PEAK 16(15Q26.3) WILD-TYPE 315  66
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            14                            381 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                             5                             66 
$`AMP PEAK 16(15Q26.3) MUTATED`
TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5277 TCGA-DU-5852 TCGA-DU-7306 TCGA-E1-5304 
       18.15         8.48        46.65         6.74        41.98        41.13 
TCGA-FG-A4MY TCGA-HT-7470 TCGA-HT-8108 TCGA-HW-8319 TCGA-S9-A6UA TCGA-S9-A7IS 
        9.67         8.81         2.50         8.61         5.85         7.92 
TCGA-S9-A7IZ TCGA-TM-A84B 
        4.21        12.00 

$`AMP PEAK 16(15Q26.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        7.79         3.85        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        23.31         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       15.52        24.46         0.59         5.26         3.72         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18        35.90         4.31         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
        9.86        94.62        83.70       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       70.55        22.92        70.65        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
        7.59         6.15         3.39        14.27        19.63        12.59 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       48.39        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          2.50                           0.03 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         46.65                         211.17 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          8.71                          15.12 
[1] "2.5 - 46.6 (8.7)"   "0.0 - 211.2 (15.1)"
[1] "hr=" "3.9"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     6   8
  AMP PEAK 16(15Q26.3) WILD-TYPE 170 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      6    8
  AMP PEAK 16(15Q26.3) WILD-TYPE  170  216
        clus
vv       AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  FEMALE                            6                            170
  MALE                              8                            216
[1] 2 2
[1] FALSE
D16V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 16(15Q26.3) MUTATED             9                3                 2
  AMP PEAK 16(15Q26.3) WILD-TYPE         134              101               151
D16V5, multiclass
                   clus
vv                  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  ASTROCYTOMA                                  9                            134
  OLIGOASTROCYTOMA                             3                            101
  OLIGODENDROGLIOMA                            2                            151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     4  10
  AMP PEAK 16(15Q26.3) WILD-TYPE  85 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      4   10
  AMP PEAK 16(15Q26.3) WILD-TYPE   85  301
     clus
vv    AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  NO                             4                             85
  YES                           10                            301
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(15Q26.3) MUTATED                                  0     0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.3) MUTATED                           0    14
  AMP PEAK 16(15Q26.3) WILD-TYPE                        14   362
D16V7, multiclass
                                  clus
vv                                 AMP PEAK 16(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      14
                                  clus
vv                                 AMP PEAK 16(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       362
[1] 4 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(15Q26.3) MUTATED     1  12
  AMP PEAK 16(15Q26.3) WILD-TYPE  14 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      1   12
  AMP PEAK 16(15Q26.3) WILD-TYPE   14  347
                        clus
vv                       AMP PEAK 16(15Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       AMP PEAK 16(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17Q25.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(17Q25.1) MUTATED    23  10
  AMP PEAK 17(17Q25.1) WILD-TYPE 301  61
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            33                            362 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            10                             61 
$`AMP PEAK 17(17Q25.1) MUTATED`
TCGA-CS-6665 TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A64P TCGA-DB-A64Q TCGA-DH-5140 
       12.43        12.72        18.38        16.80         5.98        19.96 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-6399 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7304 
       30.21         7.79        65.75        14.99         8.84        23.31 
TCGA-DU-A6S7 TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A60J TCGA-HT-7477 
        7.23        41.13        47.77        15.35         7.04        24.26 
TCGA-HT-8010 TCGA-IK-7675 TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA 
        1.64        19.00         2.96        62.17        11.31         5.85 
TCGA-S9-A6WG TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84F TCGA-TM-A84H 
       70.55        10.88         9.30         9.37        50.76        24.26 
TCGA-TM-A84M TCGA-VM-A8CA TCGA-VM-A8CH 
       16.50        13.51        10.95 

$`AMP PEAK 17(17Q25.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH 
       10.29        27.62        27.02        18.84        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       11.01        18.84        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       13.64        10.92        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         3.85        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        13.58        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        3.72         9.67         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        2.70        13.02         1.81        16.14         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        4.18         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        59.38        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       22.49        21.63        16.37        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       94.62        83.70       103.76        62.37        72.59        22.92 
TCGA-S9-A6WI TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       70.65         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        19.63        12.59         4.21         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        48.39        12.00        15.09 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       34.36        19.36        17.49        40.83        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE 
        7.89        26.79 

  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                          1.64                           0.03 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         70.55                         211.17 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         14.99                          14.96 
[1] "1.6 - 70.5 (15.0)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.4"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED    14  19
  AMP PEAK 17(17Q25.1) WILD-TYPE 162 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED     14   19
  AMP PEAK 17(17Q25.1) WILD-TYPE  162  205
        clus
vv       AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  FEMALE                           14                            162
  MALE                             19                            205
[1] 2 2
[1] FALSE
D17V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 17(17Q25.1) MUTATED            16                6                11
  AMP PEAK 17(17Q25.1) WILD-TYPE         127               98               142
D17V5, multiclass
                   clus
vv                  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  ASTROCYTOMA                                 16                            127
  OLIGOASTROCYTOMA                             6                             98
  OLIGODENDROGLIOMA                           11                            142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED     6  27
  AMP PEAK 17(17Q25.1) WILD-TYPE  83 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED      6   27
  AMP PEAK 17(17Q25.1) WILD-TYPE   83  284
     clus
vv    AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  NO                             6                             83
  YES                           27                            284
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(17Q25.1) MUTATED                                  0     1
  AMP PEAK 17(17Q25.1) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q25.1) MUTATED                           0    30
  AMP PEAK 17(17Q25.1) WILD-TYPE                        14   346
D17V7, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      30
                                  clus
vv                                 AMP PEAK 17(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       346
[1] 4 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(17Q25.1) MUTATED     2  28
  AMP PEAK 17(17Q25.1) WILD-TYPE  13 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED      2   28
  AMP PEAK 17(17Q25.1) WILD-TYPE   13  331
                        clus
vv                       AMP PEAK 17(17Q25.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 17(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            331
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(19P13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(19P13.3) MUTATED    84  18
  AMP PEAK 18(19P13.3) WILD-TYPE 240  53
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           102                            293 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                            18                             53 
$`AMP PEAK 18(19P13.3) MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       50.17        27.02        72.95        12.59        11.01        16.80 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 
       16.08        27.81        13.64        31.82        30.31         8.02 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       30.21         7.79         8.45        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 
       46.06         1.22         7.04        16.83       138.28        90.77 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A6S2 
       26.30        18.94        62.01        41.98        21.40         8.65 
TCGA-DU-A6S6 TCGA-DU-A76K TCGA-E1-5304 TCGA-E1-5318 TCGA-FG-5962 TCGA-FG-6692 
       77.98        11.41        41.13        78.21        47.77        13.58 
TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MU 
       22.55        20.09        16.01        20.09        14.96         0.59 
TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7472 
        5.26         6.64        22.95         6.67         7.82         0.03 
TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7681 TCGA-HT-7687 
       75.19       154.19         4.57        22.06        44.68         0.10 
TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8012 
       14.53         0.49        23.61         0.33         1.71         9.40 
TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HW-7495 TCGA-HW-8322 
       12.23        14.70         5.33        13.02         4.31        17.82 
TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-QH-A6XC 
        4.73         4.11         7.79         2.96         3.16         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY 
       88.83        94.03        59.38        18.77        28.14        22.49 
TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7IZ 
       15.62       103.76        72.59        22.92         9.30         4.21 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-TM-A7C3 TCGA-TM-A7CF TCGA-TM-A84B 
        8.19         2.04        13.02        49.45        48.39        12.00 
TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84Q TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       34.36        16.50        18.90        13.51         0.10        26.79 

$`AMP PEAK 18(19P13.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        46.65        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O 
       10.29        12.72        27.62        18.84        18.38        18.84 
TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64V TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5143 
        5.98        15.42        14.73        10.92        19.96        14.40 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         3.85        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 
      211.17        49.02        75.16        65.75        87.45        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84       117.40        30.67        10.36         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       44.02        25.91        60.30        23.31         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
        5.65        12.20         2.70         7.23         5.98        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 
       57.93       134.27        95.57       130.78        14.33        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       15.35        17.88        20.61        12.95        13.68        14.24 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       11.87        15.52        24.46         3.72         9.67         7.04 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A713 
        7.04         4.21         4.08        10.59        10.78         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 
        0.13         0.10         8.81         0.13        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
       17.42         6.54        24.26         6.38         7.10        59.18 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
       60.03         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
       17.29         3.16        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       14.27         0.16        16.24         0.76         6.05        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
        6.90        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.13         3.68         5.33         2.93        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64        16.24        63.55        21.50        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 
       10.49         0.13         0.07         0.10         2.70         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ 
       40.18        35.90         8.61         8.94        19.59        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        19.00        42.77         5.23 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         2.30         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
        1.28         5.75         2.53         4.83         4.11         4.18 
TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TZ 
        0.23        32.65        62.17        69.07        28.27        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       16.37        11.31        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
        5.85        62.37        70.55        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
       12.59         9.37         8.12         3.58         4.04        18.21 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       35.93        25.32        22.59        15.09        50.76        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       19.36        17.49        40.83        29.92         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
       12.00        33.07        30.08         7.89        10.95 

  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                        154.19                         211.17 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                         16.65                          14.33 
[1] "0.0 - 154.2 (16.6)" "0.1 - 211.2 (14.3)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    44  59
  AMP PEAK 18(19P13.3) WILD-TYPE 132 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     44   59
  AMP PEAK 18(19P13.3) WILD-TYPE  132  165
        clus
vv       AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  FEMALE                           44                            132
  MALE                             59                            165
[1] 2 2
[1] FALSE
D18V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 18(19P13.3) MUTATED            19               25                59
  AMP PEAK 18(19P13.3) WILD-TYPE         124               79                94
D18V5, multiclass
                   clus
vv                  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  ASTROCYTOMA                                 19                            124
  OLIGOASTROCYTOMA                            25                             79
  OLIGODENDROGLIOMA                           59                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    21  82
  AMP PEAK 18(19P13.3) WILD-TYPE  68 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     21   82
  AMP PEAK 18(19P13.3) WILD-TYPE   68  229
     clus
vv    AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  NO                            21                             68
  YES                           82                            229
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(19P13.3) MUTATED                                  0     1
  AMP PEAK 18(19P13.3) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(19P13.3) MUTATED                           4    95
  AMP PEAK 18(19P13.3) WILD-TYPE                        10   281
D18V7, multiclass
                                  clus
vv                                 AMP PEAK 18(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      95
                                  clus
vv                                 AMP PEAK 18(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED     5  93
  AMP PEAK 18(19P13.3) WILD-TYPE  10 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED      5   93
  AMP PEAK 18(19P13.3) WILD-TYPE   10  266
                        clus
vv                       AMP PEAK 18(19P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       AMP PEAK 18(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            266
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(19P13.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(19P13.2) MUTATED    77  18
  AMP PEAK 19(19P13.2) WILD-TYPE 247  53
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            95                            300 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            18                             53 
$`AMP PEAK 19(19P13.2) MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       50.17        27.02        72.95        11.01        16.80        16.08 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5854 
       31.82        30.31         8.02        30.21         7.79         8.45 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 
       15.16        52.11        22.42        46.06         1.22         7.04 
TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7306 
       16.83       138.28        90.77        26.30        18.94        41.98 
TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-E1-5304 
       21.40         4.96         8.65        77.98        11.41        41.13 
TCGA-E1-5318 TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8186 
       78.21        47.77        13.58        22.55        20.09        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A710 
       20.09        14.96         0.59         5.26         6.64        22.95 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7480 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7681 
        6.67         7.82        75.19         4.57        22.06        44.68 
TCGA-HT-7687 TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8011 
        0.10        14.53         0.49         0.33         1.71        16.24 
TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HW-7495 
        9.40        12.23        14.70         5.33        13.02         4.31 
TCGA-HW-8322 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ 
       17.82         4.73         4.11         7.79         2.96         3.16 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TV TCGA-S9-A6TX 
        5.03        88.83        94.03        59.38        18.77        28.14 
TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WM 
       22.49        15.62       103.76        72.59        22.92         9.30 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84G 
        8.19         2.04        13.02        49.45        12.00        34.36 
TCGA-TM-A84L TCGA-TM-A84M TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       40.83        16.50        13.51         0.10        26.79 

$`AMP PEAK 19(19P13.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        46.65        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH 
       10.29        12.72        27.62        18.84        18.38        12.59 
TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       18.84         5.98        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       10.92        19.96        14.40        29.62        15.75         3.85 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 
       18.02        14.56        17.46         6.74        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49       211.17        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 
       65.75        87.45        11.64       133.74        19.89        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 
       14.99       105.21         6.54         8.84       117.40        30.67 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 
       12.59        15.12         3.65         5.65        12.20         2.70 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        7.23         5.98        26.76         7.13        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 
       50.14        67.46        79.99        57.93       134.27        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
      130.78        14.33        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7641 
       14.93        24.99        23.97        15.35        17.88        20.61 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       12.95        13.68        14.24        11.87        15.52        24.46 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        3.72         9.67         7.04         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 
       10.59        10.78         5.23         0.13         0.10         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38         7.10        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 
        4.01         5.03        29.85        23.18       107.93        17.29 
TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
        0.16        16.24         0.76         6.05        42.74        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.13         3.68         5.33         2.93        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       31.43         1.64        63.55        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
        0.13         0.07         0.10         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK 
       35.90         8.61         8.94        19.59        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
        9.67         6.61        19.00        42.77         5.23         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 
        6.71         1.64         2.37         2.30         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        5.75         2.53         4.83         4.11         4.18         2.20 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TZ TCGA-S9-A6U0 
       32.65        62.17        69.07        28.27        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       11.31        20.05         9.86        94.62        83.70         5.85 
TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       62.37        70.55        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        4.21         9.37         8.12         3.58         4.04        18.21 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        22.59        48.39        15.09        50.76 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.26        19.36        17.49        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
        4.57        12.00        33.07        30.08         7.89        10.95 

  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                        138.28                         211.17 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                        16.240                         14.365 
[1] "0.1 - 138.3 (16.2)" "0.0 - 211.2 (14.4)"
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    39  59
  AMP PEAK 19(19P13.2) WILD-TYPE 137 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     39   59
  AMP PEAK 19(19P13.2) WILD-TYPE  137  165
        clus
vv       AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  FEMALE                           39                            137
  MALE                             59                            165
[1] 2 2
[1] FALSE
D19V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 19(19P13.2) MUTATED            18               21                59
  AMP PEAK 19(19P13.2) WILD-TYPE         125               83                94
D19V5, multiclass
                   clus
vv                  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  ASTROCYTOMA                                 18                            125
  OLIGOASTROCYTOMA                            21                             83
  OLIGODENDROGLIOMA                           59                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    21  77
  AMP PEAK 19(19P13.2) WILD-TYPE  68 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     21   77
  AMP PEAK 19(19P13.2) WILD-TYPE   68  234
     clus
vv    AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  NO                            21                             68
  YES                           77                            234
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(19P13.2) MUTATED                                  0     1
  AMP PEAK 19(19P13.2) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(19P13.2) MUTATED                           4    90
  AMP PEAK 19(19P13.2) WILD-TYPE                        10   286
D19V7, multiclass
                                  clus
vv                                 AMP PEAK 19(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      90
                                  clus
vv                                 AMP PEAK 19(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED     5  88
  AMP PEAK 19(19P13.2) WILD-TYPE  10 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED      5   88
  AMP PEAK 19(19P13.2) WILD-TYPE   10  271
                        clus
vv                       AMP PEAK 19(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK 19(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(XP11.22) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(XP11.22) MUTATED    26   6
  AMP PEAK 20(XP11.22) WILD-TYPE 298  65
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            32                            363 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                             6                             65 
$`AMP PEAK 20(XP11.22) MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A66B TCGA-DU-5871 
       12.43         7.56        46.65        78.28        29.62        18.94 
TCGA-DU-6407 TCGA-DU-7014 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT TCGA-E1-5302 
       94.52       117.40        14.24        15.12         4.96        50.14 
TCGA-E1-5318 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A713 TCGA-HT-7475 TCGA-HT-7476 
       78.21        17.88        14.24         5.23        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-8013 TCGA-HT-8104 
       24.26        45.99        31.69        14.96        63.55        12.23 
TCGA-HT-8106 TCGA-HT-A616 TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ TCGA-QH-A6CV 
        0.10         1.81        35.90        19.59         2.30         2.96 
TCGA-S9-A7QX TCGA-VM-A8C8 
        4.04        33.07 

$`AMP PEAK 20(XP11.22) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.02        18.84        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        30.21        15.75         7.79         3.85 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TU 
       19.13        16.96        15.48        14.17        12.59         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 
       67.46        41.13        79.99        57.93       134.27        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FN-7833 
        4.21         4.08        10.59        10.78        22.95         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       16.54         3.75         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 
      107.93         4.57        17.29         3.16        22.06        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8018 
       11.28        31.43         1.64        16.24         9.40        21.50 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       33.01         6.25         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
        2.70        13.02        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31         8.61         8.94 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.37         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                        117.40                         211.17 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                         17.65                          14.73 
[1] "0.1 - 117.4 (17.6)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    13  19
  AMP PEAK 20(XP11.22) WILD-TYPE 163 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     13   19
  AMP PEAK 20(XP11.22) WILD-TYPE  163  205
        clus
vv       AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  FEMALE                           13                            163
  MALE                             19                            205
[1] 2 2
[1] FALSE
D20V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 20(XP11.22) MUTATED            17                7                 8
  AMP PEAK 20(XP11.22) WILD-TYPE         126               97               145
D20V5, multiclass
                   clus
vv                  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 17                            126
  OLIGOASTROCYTOMA                             7                             97
  OLIGODENDROGLIOMA                            8                            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    11  21
  AMP PEAK 20(XP11.22) WILD-TYPE  78 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     11   21
  AMP PEAK 20(XP11.22) WILD-TYPE   78  290
     clus
vv    AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  NO                            11                             78
  YES                           21                            290
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(XP11.22) MUTATED                                  0     1
  AMP PEAK 20(XP11.22) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(XP11.22) MUTATED                           1    30
  AMP PEAK 20(XP11.22) WILD-TYPE                        13   346
D20V7, multiclass
                                  clus
vv                                 AMP PEAK 20(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      30
                                  clus
vv                                 AMP PEAK 20(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       346
[1] 4 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(XP11.22) MUTATED     1  30
  AMP PEAK 20(XP11.22) WILD-TYPE  14 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED      1   30
  AMP PEAK 20(XP11.22) WILD-TYPE   14  329
                        clus
vv                       AMP PEAK 20(XP11.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       AMP PEAK 20(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            329
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(XP11.22) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(XP11.22) MUTATED    36  11
  AMP PEAK 21(XP11.22) WILD-TYPE 288  60
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            47                            348 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            11                             60 
$`AMP PEAK 21(XP11.22) MUTATED`
TCGA-CS-4938 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A66B 
        4.70        12.43         7.56        46.65        78.28        29.62 
TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7007 
       18.94        75.16        87.45        94.52         7.73        62.96 
TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       14.99       117.40        15.48        14.24        15.12         4.96 
TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5307 TCGA-E1-5318 TCGA-FG-7636 TCGA-FG-8185 
        3.65        50.14        57.93        78.21        17.88        14.24 
TCGA-FG-A4MY TCGA-FG-A713 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7688 
        9.67         5.23         6.54        24.26        45.99        31.69 
TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8104 
       14.96        19.23         0.23        31.43        63.55        12.23 
TCGA-HT-8106 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ 
        0.10         1.81         5.33        35.90        19.59         2.30 
TCGA-QH-A6CV TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-TM-A84Q TCGA-VM-A8C8 
        2.96         4.21         4.04        18.90        33.07 

$`AMP PEAK 21(XP11.22) WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       18.84        18.38        72.95        12.59        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       13.64        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
        8.02        30.21        15.75         7.79         3.85        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 
       49.02        46.06        65.75         1.22         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
      133.74        19.89        16.83       114.08         7.96        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A5TY 
       19.13        16.96        14.17        12.59         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 
       26.76         7.13        21.30       124.50        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
       79.99       134.27        95.57       130.78        14.33        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        13.58        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       15.52        24.46         0.59         5.26         3.72         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       22.95         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 
        0.13         0.03        16.54         3.75        17.42         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
        0.10         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       14.53        39.48        39.09        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8018 
        1.71        11.28         1.64        16.24         9.40        21.50 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       33.01         6.25         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        2.70        13.02        16.14        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 
       19.23        40.18         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         4.18         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        3.39        14.27         7.92        19.63        12.59         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04         8.12         3.58        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        16.50        29.92         9.44         4.57        12.00 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 

  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                        117.40                         211.17 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                        15.480                         14.715 
[1] "0.1 - 117.4 (15.5)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(XP11.22) MUTATED    25  22
  AMP PEAK 21(XP11.22) WILD-TYPE 151 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED     25   22
  AMP PEAK 21(XP11.22) WILD-TYPE  151  202
        clus
vv       AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  FEMALE                           25                            151
  MALE                             22                            202
[1] 2 2
[1] FALSE
D21V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 21(XP11.22) MUTATED            27               11                 9
  AMP PEAK 21(XP11.22) WILD-TYPE         116               93               144
D21V5, multiclass
                   clus
vv                  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 27                            116
  OLIGOASTROCYTOMA                            11                             93
  OLIGODENDROGLIOMA                            9                            144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(XP11.22) MUTATED    13  34
  AMP PEAK 21(XP11.22) WILD-TYPE  76 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED     13   34
  AMP PEAK 21(XP11.22) WILD-TYPE   76  277
     clus
vv    AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  NO                            13                             76
  YES                           34                            277
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(XP11.22) MUTATED                                  0     1
  AMP PEAK 21(XP11.22) WILD-TYPE                                1     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(XP11.22) MUTATED                           1    45
  AMP PEAK 21(XP11.22) WILD-TYPE                        13   331
D21V7, multiclass
                                  clus
vv                                 AMP PEAK 21(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      45
                                  clus
vv                                 AMP PEAK 21(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       331
[1] 4 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(XP11.22) MUTATED     2  44
  AMP PEAK 21(XP11.22) WILD-TYPE  13 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED      2   44
  AMP PEAK 21(XP11.22) WILD-TYPE   13  315
                        clus
vv                       AMP PEAK 21(XP11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       AMP PEAK 21(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            315
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED   140  24
  DEL PEAK  1(1P36.32) WILD-TYPE 184  47
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           164                            231 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            24                             47 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       47.93        50.17        44.52        10.29        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       11.01        18.84        16.80         5.98        16.08        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       14.73        13.64        31.82         8.02        30.21         7.79 
TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
       14.56         6.74       182.33        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6405 
       22.42        75.16        46.06         1.22         7.04        19.89 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 
        7.96        11.47       138.28       117.40        30.67        10.36 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8167 
       94.32        62.01        60.30         5.10        21.40        15.48 
TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R 
       14.17         8.65         2.70        77.98         5.98        21.30 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 
      134.27        78.21        95.57        14.33        47.77        34.36 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 TCGA-FG-8186 
       13.58        15.35        22.55        20.61        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 
       20.09        11.87         6.64         4.21         4.08        22.95 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7480 
        5.23         0.10         6.67         0.13        24.26        75.19 
TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 
       59.18         4.57         3.16        22.06         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       16.24        44.68         0.10         2.96         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 
       39.09         0.23        37.15         0.33         0.13         2.93 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV 
        1.64         9.40         6.25         3.95        29.59        10.49 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A615 TCGA-HT-A617 TCGA-HW-7486 TCGA-HW-7487 
        0.07        14.70        13.02        16.14        29.92        13.45 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X 
       40.18         4.31        17.82        10.55        42.77         5.23 
TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.64         4.11         5.75         4.83         7.79         4.11 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.96         2.20         3.16         6.31         3.91         4.73 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB 
       28.27        28.14        22.49        15.62        20.05       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       62.37        72.59        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 
        9.04         6.15         3.39        14.27        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G 
        2.04         8.12        18.21        13.02        25.32        34.36 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB 
       16.50        29.92         9.44         4.57        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE 
        7.89        26.79 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 
        8.48         7.56         7.40       122.73        81.96        72.92 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       46.65        36.56        78.28        30.08        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5140 
       27.02        18.84        18.38        15.42        10.92        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5847 
       30.31        14.40        29.62        15.75         3.85        18.02 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-6392 
       17.46        13.38         8.45         6.81        18.94       211.17 
TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 
       49.02        65.75        87.45        11.64       133.74        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
       94.52       114.08         7.73        62.96       156.23        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 
      105.21         6.54         8.84        90.77        26.30         7.96 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       18.94        44.02        25.91        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TP 
       23.74         3.98        20.68        19.13        16.96        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 
        7.23        11.41        26.76         7.13       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5963 
       67.46        41.13        79.99        57.93       130.78        17.98 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
       32.19        18.77        14.93        24.99        23.97        17.88 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       20.09        12.95        13.68        14.96        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
        0.59         5.26         3.72         9.67         7.04         7.04 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       10.59        10.78         0.13         7.82         8.81         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 
      107.93        17.29        45.99        56.09        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.76         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        0.10        17.52        39.48        19.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
       23.61         3.68         5.33         1.71        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       16.24        63.55        21.50        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
        0.46         2.50         4.70         0.23         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       15.72         0.23         0.13         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 
        1.81         5.33         8.32        19.23        35.90         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        8.94        19.59         7.89         9.67         6.61        19.00 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
        4.73         0.23         6.71         2.37         2.30         5.88 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
        1.28         2.53         4.18         0.59         1.91         0.23 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 
       69.07        18.77        21.63        16.37        11.31         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A7IS 
       94.62        83.70         5.85        70.55         7.59         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 
       19.63         4.21         9.37         3.58         4.04        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        22.59        48.39        12.00        15.09        50.76 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T 
       24.26        19.36        17.49        40.83        18.90        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH 
       33.07        30.08        10.95 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        182.33                         211.17 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         14.27                          15.72 
[1] "0.1 - 182.3 (14.3)" "0.0 - 211.2 (15.7)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    77  89
  DEL PEAK  1(1P36.32) WILD-TYPE  99 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     77   89
  DEL PEAK  1(1P36.32) WILD-TYPE   99  135
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           77                             99
  MALE                             89                            135
[1] 2 2
[1] FALSE
D22V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  1(1P36.32) MUTATED            18               36               112
  DEL PEAK  1(1P36.32) WILD-TYPE         125               68                41
D22V5, multiclass
                   clus
vv                  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  ASTROCYTOMA                                 18                            125
  OLIGOASTROCYTOMA                            36                             68
  OLIGODENDROGLIOMA                          112                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    28 138
  DEL PEAK  1(1P36.32) WILD-TYPE  61 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     28  138
  DEL PEAK  1(1P36.32) WILD-TYPE   61  173
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            28                             61
  YES                          138                            173
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.32) MUTATED                                  1     2
  DEL PEAK  1(1P36.32) WILD-TYPE                                0     0
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED                           5   153
  DEL PEAK  1(1P36.32) WILD-TYPE                         9   223
D22V7, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     153
                                  clus
vv                                 DEL PEAK  1(1P36.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         0
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     6 147
  DEL PEAK  1(1P36.32) WILD-TYPE   9 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      6  147
  DEL PEAK  1(1P36.32) WILD-TYPE    9  212
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          147
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  2(1P32.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P32.3) MUTATED   136  19
  DEL PEAK  2(1P32.3) WILD-TYPE 188  52
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          155                           240 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           19                            52 
$`DEL PEAK  2(1P32.3) MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       50.17        44.52        10.29        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       18.84        16.80         5.98        16.08        27.81        14.73 
TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5849 
       13.64        31.82         8.02        30.21         7.79        14.56 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        52.11        22.42        46.06         1.22 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7300 
        7.96       138.28       117.40        30.67        94.32        62.01 
TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
       60.30         5.10        23.74        21.40        15.48        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       21.30       134.27        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 
       47.77        34.36        15.35        22.55        20.61        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       16.01        20.09        11.87         6.64         4.21         4.08 
TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 
       22.95         5.23         0.10         6.67         0.13        75.19 
TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 
       59.18         4.57         3.16        22.06         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       16.24        44.68         0.10         2.96         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       39.09         0.23         0.49        37.15         0.33         0.13 
TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8110 
        2.93         1.64         9.40         6.25         3.95         4.70 
TCGA-HT-8113 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A617 
       29.59         0.23        10.49         0.07        13.02        16.14 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ 
       29.92        13.45        40.18         4.31        17.82        10.55 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A65V 
       42.77         5.23         1.64         4.11         5.75         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
        7.79         4.11         2.20         3.16         6.31         3.91 
TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW 
        4.73        88.83        94.03        32.65        59.38        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       28.14        22.49        15.62        20.05       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       72.59        22.92        70.65        10.88         9.04         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        3.39        14.27        12.59         8.19         2.04         8.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       18.21        13.02        25.32        34.36        16.50        29.92 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
        9.44         4.57        13.51         0.10        26.79 

$`DEL PEAK  2(1P32.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        8.48         7.56         7.40       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        46.65        36.56        78.28        30.08        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X 
       27.62        27.02        18.84        18.38        15.42        10.92 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       19.96        30.31        14.40        29.62        15.75         3.85 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       18.94        17.49       211.17        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.73        11.47        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 
       14.99       105.21         6.54         8.84        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 
       10.36         7.96        18.94        44.02        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
       41.98         2.76         3.98        20.68        19.13        16.96 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       12.20         7.23         7.13       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 
       41.13        79.99        57.93        17.98        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7643 
       14.93        24.99        23.97        13.58        17.88        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       12.95        13.68        14.96        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 
        5.26         3.72         9.67         7.04         7.04        10.59 
TCGA-FG-A70Z TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
       10.78         0.13         7.82         8.81         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 
      107.93        17.29        45.99        56.09        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.76         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 
        0.10        17.52        39.48        19.23        50.63        23.61 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 
        3.68         5.33         1.71        11.28        31.43        16.24 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
       63.55        21.50        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R5 
        2.50         0.23         3.88        16.04        15.72         0.13 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 
       14.70         0.10         5.33         2.70         1.81         5.33 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        19.23        35.90         8.61         8.94        19.59 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV 
        7.89         9.67         6.61        19.00         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S 
        6.71         2.37         2.30         5.88         1.28         2.53 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        4.18         2.96         0.59         1.91         0.23         5.03 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       62.17        69.07        18.77        21.63        16.37        11.31 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM 
        9.86        94.62        83.70         5.85        70.55         9.30 
TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
        7.59         7.92        19.63         4.21         9.37         3.58 
TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
        4.04        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
        5.00        49.45        35.93        22.59        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        24.26        19.36        17.49        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
       18.90        12.00        33.07        30.08         7.89        10.95 

  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       182.33                        211.17 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                        14.27                         15.47 
[1] "0.1 - 182.3 (14.3)" "0.0 - 211.2 (15.5)"
[1] "hr=" "1.8"
D23V2, continuous
D23V3, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    72  85
  DEL PEAK  2(1P32.3) WILD-TYPE 104 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     72   85
  DEL PEAK  2(1P32.3) WILD-TYPE  104  139
        clus
vv       DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  FEMALE                          72                           104
  MALE                            85                           139
[1] 2 2
[1] FALSE
D23V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  2(1P32.3) MUTATED            11               33               113
  DEL PEAK  2(1P32.3) WILD-TYPE         132               71                40
D23V5, multiclass
                   clus
vv                  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  ASTROCYTOMA                                11                           132
  OLIGOASTROCYTOMA                           33                            71
  OLIGODENDROGLIOMA                         113                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    23 134
  DEL PEAK  2(1P32.3) WILD-TYPE  66 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     23  134
  DEL PEAK  2(1P32.3) WILD-TYPE   66  177
     clus
vv    DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  NO                           23                            66
  YES                         134                           177
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P32.3) MUTATED                                  1     1
  DEL PEAK  2(1P32.3) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P32.3) MUTATED                           4   146
  DEL PEAK  2(1P32.3) WILD-TYPE                        10   230
D23V7, multiclass
                                  clus
vv                                 DEL PEAK  2(1P32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                    146
                                  clus
vv                                 DEL PEAK  2(1P32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED     6 139
  DEL PEAK  2(1P32.3) WILD-TYPE   9 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED      6  139
  DEL PEAK  2(1P32.3) WILD-TYPE    9  220
                        clus
vv                       DEL PEAK  2(1P32.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         139
                        clus
vv                       DEL PEAK  2(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    14   5
  DEL PEAK  3(1Q43) WILD-TYPE 310  66
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         19                         376 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          5                          66 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8161 
       18.94        75.16         7.73        90.77         5.10        23.74 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5322 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A6J3 
       15.12        50.14       130.78        17.88        14.24        10.59 
TCGA-HT-7857 TCGA-HT-8109 TCGA-HT-8113 TCGA-QH-A65S TCGA-S9-A6WI TCGA-TM-A84I 
        0.23         3.95        29.59         2.53        70.65        19.36 
TCGA-TM-A84T 
       12.00 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 
       26.76         7.13        21.30       124.50        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 
       79.99        57.93       134.27        78.21        95.57        14.33 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        13.58        15.35        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.10         0.46         2.50         4.70         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        1.64         2.37         2.30         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        5.75         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        70.55        22.92        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       18.90         9.44         4.57        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10         7.89        26.79        10.95 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.23                        0.03 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     130.78                      211.17 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     17.880                      14.945 
[1] "0.2 - 130.8 (17.9)" "0.0 - 211.2 (14.9)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    11   9
  DEL PEAK  3(1Q43) WILD-TYPE 165 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     11    9
  DEL PEAK  3(1Q43) WILD-TYPE  165  215
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        11                         165
  MALE                           9                         215
[1] 2 2
[1] FALSE
D24V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  3(1Q43) MUTATED             7                9                 4
  DEL PEAK  3(1Q43) WILD-TYPE         136               95               149
D24V5, multiclass
                   clus
vv                  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  ASTROCYTOMA                               7                         136
  OLIGOASTROCYTOMA                          9                          95
  OLIGODENDROGLIOMA                         4                         149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     5  15
  DEL PEAK  3(1Q43) WILD-TYPE  84 296
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      5   15
  DEL PEAK  3(1Q43) WILD-TYPE   84  296
     clus
vv    DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  NO                          5                          84
  YES                        15                         296
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q43) MUTATED                                  0     0
  DEL PEAK  3(1Q43) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED                           2    18
  DEL PEAK  3(1Q43) WILD-TYPE                        12   358
D24V7, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   18
                                  clus
vv                                 DEL PEAK  3(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     1  19
  DEL PEAK  3(1Q43) WILD-TYPE  14 340
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      1   19
  DEL PEAK  3(1Q43) WILD-TYPE   14  340
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             1                          14
  NOT HISPANIC OR LATINO                        19                         340
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    43  14
  DEL PEAK  4(2Q37.3) WILD-TYPE 281  57
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           57                           338 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           14                            57 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-5281 
       18.15         6.38         8.48       122.73        46.65        78.28 
TCGA-DB-A64P TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5855 TCGA-DU-6395 
       16.80        30.31        30.21        29.62         6.81        49.02 
TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       75.16        94.52       114.08         7.73        62.96       156.23 
TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8167 TCGA-DU-A5TR TCGA-DU-A5TS 
      117.40        23.31        41.98        15.48        12.59        15.12 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-E1-5304 TCGA-FG-A6J3 TCGA-HT-7473 TCGA-HT-7477 
        5.65         7.23        41.13        10.59        16.54        24.26 
TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7855 
        5.03        17.29         0.10         2.96        17.52        19.23 
TCGA-HT-8013 TCGA-HT-A5RB TCGA-HT-A618 TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 
       63.55         0.10         5.33        35.90        19.59        19.00 
TCGA-P5-A5EW TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-S9-A6U6 
        6.71         1.28         2.96         0.59         1.91         9.86 
TCGA-S9-A6WG TCGA-S9-A6WQ TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A7CA TCGA-TM-A84I 
       70.55         3.39         9.37         5.00        22.59        19.36 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       40.83        29.92        18.90 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 
       12.43         7.56         8.02         7.40         6.61        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q 
       18.38        72.95        12.59        11.01        18.84         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F 
       19.96        31.82        14.40         8.02        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        8.45       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       52.11        22.42        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 
        7.04        11.64       133.74        19.89        16.83         7.96 
TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7309 
       18.94        44.02        62.01        25.91        60.30         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       16.96        14.17        14.24         4.96         3.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.21         4.08        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 
       59.18        60.03       154.19         4.01        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      107.93         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
        0.10         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        1.64        16.24         9.40        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
       10.49         0.13         0.07        14.70         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       13.02         1.81        16.14        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 
       19.23        40.18         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67         6.61        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        4.73         0.23         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        5.88         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        4.18         2.20         3.16         6.31         3.91         4.73 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       21.63        16.37        11.31        15.62        20.05        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       83.70         5.85       103.76        62.37        72.59        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       14.27         7.92        19.63        12.59         4.21         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 
       10.39        87.09        17.42        83.80        31.59        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84R TCGA-TM-A84S 
       34.36        24.26        17.49        16.50         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       18.150                        14.465 
[1] "0.1 - 156.2 (18.1)" "0.0 - 211.2 (14.5)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    22  37
  DEL PEAK  4(2Q37.3) WILD-TYPE 154 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     22   37
  DEL PEAK  4(2Q37.3) WILD-TYPE  154  187
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          22                           154
  MALE                            37                           187
[1] 2 2
[1] FALSE
D25V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  4(2Q37.3) MUTATED            27               19                13
  DEL PEAK  4(2Q37.3) WILD-TYPE         116               85               140
D25V5, multiclass
                   clus
vv                  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  ASTROCYTOMA                                27                           116
  OLIGOASTROCYTOMA                           19                            85
  OLIGODENDROGLIOMA                          13                           140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    15  44
  DEL PEAK  4(2Q37.3) WILD-TYPE  74 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     15   44
  DEL PEAK  4(2Q37.3) WILD-TYPE   74  267
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           15                            74
  YES                          44                           267
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           2    56
  DEL PEAK  4(2Q37.3) WILD-TYPE                        12   320
D25V7, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     56
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3  55
  DEL PEAK  4(2Q37.3) WILD-TYPE  12 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3   55
  DEL PEAK  4(2Q37.3) WILD-TYPE   12  304
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          55
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED    23   9
  DEL PEAK  5(3P21.31) WILD-TYPE 301  62
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            32                            363 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             9                             62 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-DB-5275 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7010 
       47.93        46.65        15.75        75.16         7.73        14.99 
TCGA-DU-7300 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5304 
       62.01        14.17         4.96         3.65        21.30        41.13 
TCGA-E1-5322 TCGA-HT-7469 TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 
      130.78         7.82        16.54        24.26         6.38        60.03 
TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5RA TCGA-IK-7675 
       17.29         0.10         0.23        15.72        14.70        19.00 
TCGA-P5-A5F6 TCGA-QH-A6X9 TCGA-S9-A6WG TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-TM-A84H 
        1.28         1.91        70.55         4.21         9.37        24.26 
TCGA-TM-A84J TCGA-VM-A8C8 
       17.49        33.07 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        75.25        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        29.62 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       15.12         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
        7.23         5.98        11.41        26.76         7.13       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57        14.33        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       22.95         5.23         0.13         0.10         6.67         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.13         0.03         3.75        17.42         6.54         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        59.18       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       107.93         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        0.10         0.46         2.50         3.95         4.70        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
        3.88        16.04         0.23        10.49         0.13         0.07 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67         6.61        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        6.31         3.91         4.73         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
      103.76        62.37        72.59        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        7.92        19.63        12.59         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       34.36        19.36        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        16.145                         14.730 
[1] "0.1 - 130.8 (16.1)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.7"
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    15  18
  DEL PEAK  5(3P21.31) WILD-TYPE 161 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     15   18
  DEL PEAK  5(3P21.31) WILD-TYPE  161  206
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                           15                            161
  MALE                             18                            206
[1] 2 2
[1] FALSE
D26V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  5(3P21.31) MUTATED            13                9                11
  DEL PEAK  5(3P21.31) WILD-TYPE         130               95               142
D26V5, multiclass
                   clus
vv                  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  ASTROCYTOMA                                 13                            130
  OLIGOASTROCYTOMA                             9                             95
  OLIGODENDROGLIOMA                           11                            142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    11  22
  DEL PEAK  5(3P21.31) WILD-TYPE  78 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     11   22
  DEL PEAK  5(3P21.31) WILD-TYPE   78  289
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                            11                             78
  YES                           22                            289
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P21.31) MUTATED                                  0     0
  DEL PEAK  5(3P21.31) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED                           0    33
  DEL PEAK  5(3P21.31) WILD-TYPE                        14   343
D26V7, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       343
[1] 4 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  5(3P21.31) MUTATED     3  29
  DEL PEAK  5(3P21.31) WILD-TYPE  12 330
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      3   29
  DEL PEAK  5(3P21.31) WILD-TYPE   12  330
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            330
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  6(3Q29) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  6(3Q29) MUTATED    22  12
  DEL PEAK  6(3Q29) WILD-TYPE 302  59
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                         34                         361 
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                         12                          59 
$`DEL PEAK  6(3Q29) MUTATED`
TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DU-6395 TCGA-DU-7007 
       17.95         8.48        46.65        78.28        49.02        62.96 
TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-8161 TCGA-DU-8167 
       14.99       117.40        18.94        62.01        23.74        15.48 
TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5302 TCGA-FG-5963 TCGA-FG-6691 TCGA-FG-A6J3 
        3.65        21.30        50.14        17.98        23.97        10.59 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7688 TCGA-HT-8111 
        8.81         0.03        24.26       107.93        31.69         0.23 
TCGA-HT-8564 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-S9-A7IZ TCGA-S9-A7J0 
       15.72        19.00         1.28         2.53         4.21         9.37 
TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84J TCGA-VM-A8C8 
        5.00        12.00        17.49        33.07 

$`DEL PEAK  6(3Q29) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.02        18.84        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 
        3.98        20.68        21.40        19.13        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         4.96         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       26.76         7.13       124.50        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        7.82         0.13        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        3.95         4.70        29.59         3.88        16.04         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        2.70        13.02         1.81        16.14         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        5.75         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       19.63        12.59         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80        31.59        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       48.39        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                     117.40                      211.17 
  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE 
                     17.965                      14.560 
[1] "0.0 - 117.4 (18.0)" "0.1 - 211.2 (14.6)"
[1] "hr=" "2"  
D27V2, continuous
D27V3, binary
                             cls
clus                            0   1
  DEL PEAK  6(3Q29) MUTATED    12  22
  DEL PEAK  6(3Q29) WILD-TYPE 164 202
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(3Q29) MUTATED     12   22
  DEL PEAK  6(3Q29) WILD-TYPE  164  202
        clus
vv       DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE
  FEMALE                        12                         164
  MALE                          22                         202
[1] 2 2
[1] FALSE
D27V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  6(3Q29) MUTATED            17                6                11
  DEL PEAK  6(3Q29) WILD-TYPE         126               98               142
D27V5, multiclass
                   clus
vv                  DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE
  ASTROCYTOMA                              17                         126
  OLIGOASTROCYTOMA                          6                          98
  OLIGODENDROGLIOMA                        11                         142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                             cls
clus                            0   1
  DEL PEAK  6(3Q29) MUTATED     9  25
  DEL PEAK  6(3Q29) WILD-TYPE  80 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(3Q29) MUTATED      9   25
  DEL PEAK  6(3Q29) WILD-TYPE   80  286
     clus
vv    DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE
  NO                          9                          80
  YES                        25                         286
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3Q29) MUTATED                                  0     0
  DEL PEAK  6(3Q29) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q29) MUTATED                           2    31
  DEL PEAK  6(3Q29) WILD-TYPE                        12   345
D27V7, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   31
                                  clus
vv                                 DEL PEAK  6(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                             cls
clus                            0   1
  DEL PEAK  6(3Q29) MUTATED     2  30
  DEL PEAK  6(3Q29) WILD-TYPE  13 329
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(3Q29) MUTATED      2   30
  DEL PEAK  6(3Q29) WILD-TYPE   13  329
                        clus
vv                       DEL PEAK  6(3Q29) MUTATED DEL PEAK  6(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             2                          13
  NOT HISPANIC OR LATINO                        30                         329
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED    86  23
  DEL PEAK  7(4Q34.3) WILD-TYPE 238  48
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          109                           286 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           23                            48 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5274 TCGA-DB-5275 
       18.15        64.64         8.48         7.56        75.25        47.93 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A4XH 
       46.65        44.52        78.28        10.29        18.84        12.59 
TCGA-DB-A64W TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66G TCGA-DU-5851 TCGA-DU-5853 
       13.64        30.21        29.62         3.85        17.46        13.38 
TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6410 
       18.94        15.16        65.75         1.22        19.89         7.96 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 
       62.96       156.23        14.99        30.67        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TR 
       25.91        60.30         2.76        19.13        14.17        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R 
       15.12         3.65         5.65         2.70         5.98        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
      134.27       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J 
       17.88        22.55        14.24        14.96         9.67         7.04 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A713 TCGA-HT-7467 
        7.04         4.21         4.08        10.59         5.23         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 
        6.67         7.82         0.13        16.54         6.54        24.26 
TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 
       75.19        16.24        31.69         2.96        39.09         6.25 
TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A616 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
        0.07         5.33         1.81        13.45         8.32        40.18 
TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EZ 
       35.90        19.59        19.00        42.77         0.23         2.30 
TCGA-QH-A6X4 TCGA-QH-A6XA TCGA-S9-A6TW TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP 
        6.31         0.23        28.27        62.37        10.88         6.15 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QY TCGA-S9-A89Z 
        7.92        12.59         4.21         9.37        18.21         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-TM-A84T 
       35.93        25.32        22.59        48.39         9.44        12.00 
TCGA-VM-A8C8 
       33.07 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        40.18         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
       12.43         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       72.92        50.17        36.56        30.08        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       27.02        18.38        72.95        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X 
        5.98        16.08        15.42        27.81        14.73        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       19.96        31.82        30.31        14.40         8.02        15.75 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
        7.79        18.02        14.56         6.74         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
      182.33        17.49       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        46.06        87.45         7.04        11.64       133.74 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 
       16.83        94.52       114.08         7.73        11.47       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7304 TCGA-DU-7306 
       10.36         7.96        18.94        62.01        23.31        41.98 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74         3.98        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 
       15.48        14.24         4.96        12.20         8.65        77.98 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5318 TCGA-E1-5319 
        7.23        11.41        26.76         7.13        78.21        95.57 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       15.35        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A70Z TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7470 
        3.72         6.64        10.78        22.95         0.13         8.81 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
        0.03         3.75        17.42         6.38         7.10        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 
       56.09        57.60         0.23        14.27         0.16         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
       44.68         6.05        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 
        0.23        10.49         0.13        14.70         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7490 TCGA-HW-7495 
       13.02        16.14         5.33        29.92        19.23         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.61         8.94        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        6.61         5.23         4.73         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-R8-A6MK 
        0.59         3.91         4.73         1.91         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        70.55        22.92        70.65         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.59         3.39        14.27        19.63         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        8.12         3.58         4.04        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C 
       17.42        83.80        31.59        49.45        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-VM-A8C9 TCGA-VM-A8CA 
       16.50        29.92        18.90         4.57        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10         7.89        26.79        10.95 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        16.24                         14.63 
[1] "0.1 - 156.2 (16.2)" "0.0 - 211.2 (14.6)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    46  63
  DEL PEAK  7(4Q34.3) WILD-TYPE 130 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     46   63
  DEL PEAK  7(4Q34.3) WILD-TYPE  130  161
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                          46                           130
  MALE                            63                           161
[1] 2 2
[1] FALSE
D28V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  7(4Q34.3) MUTATED            36               28                45
  DEL PEAK  7(4Q34.3) WILD-TYPE         107               76               108
D28V5, multiclass
                   clus
vv                  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  ASTROCYTOMA                                36                           107
  OLIGOASTROCYTOMA                           28                            76
  OLIGODENDROGLIOMA                          45                           108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    29  80
  DEL PEAK  7(4Q34.3) WILD-TYPE  60 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     29   80
  DEL PEAK  7(4Q34.3) WILD-TYPE   60  231
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           29                            60
  YES                          80                           231
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q34.3) MUTATED                                  0     0
  DEL PEAK  7(4Q34.3) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED                           2   106
  DEL PEAK  7(4Q34.3) WILD-TYPE                        12   270
D28V7, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                    106
                                  clus
vv                                 DEL PEAK  7(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      270
[1] 4 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  7(4Q34.3) MUTATED     4 100
  DEL PEAK  7(4Q34.3) WILD-TYPE  11 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      4  100
  DEL PEAK  7(4Q34.3) WILD-TYPE   11  259
                        clus
vv                       DEL PEAK  7(4Q34.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       DEL PEAK  7(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           259
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  8(5P15.33) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(5P15.33) MUTATED    31   6
  DEL PEAK  8(5P15.33) WILD-TYPE 293  65
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                            37                            358 
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                             6                             65 
$`DEL PEAK  8(5P15.33) MUTATED`
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5281 TCGA-DB-A4XC TCGA-DB-A4XE 
       18.15        47.93        72.92        78.28        27.62        18.84 
TCGA-DB-A4XH TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 
       12.59        10.92        19.96        15.75         3.85        65.75 
TCGA-DU-7007 TCGA-DU-7306 TCGA-DU-8165 TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-5962 
       62.96        41.98        19.13        50.14        41.13        47.77 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-HT-7474 
       32.19        14.93         5.26         9.67        10.59         3.75 
TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
       17.42        31.69        14.96        23.61         3.68        11.28 
TCGA-HT-8106 TCGA-HT-A614 TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R7 
        0.10         2.70        18.77         9.30        19.63        83.80 
TCGA-TM-A84I 
       19.36 

$`DEL PEAK  8(5P15.33) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       44.52        36.56        30.08        10.29        12.72        27.02 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       18.38        72.95        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 
       16.08        15.42        27.81        14.73        13.64        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        29.62         7.79 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       52.11        22.42        49.02        75.16        46.06         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       21.30       124.50        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 
       78.21        95.57       130.78        14.33        17.98        34.36 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        0.59         3.72         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
        4.08        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 
        0.33         0.13         5.33         2.93         1.71        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
       94.03        32.65        59.38        62.17        69.07        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        14.27         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        31.59         5.00        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10         7.89        26.79        10.95 

  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                         83.80                         211.17 
  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE 
                        18.840                         14.465 
[1] "0.1 - 83.8 (18.8)"  "0.0 - 211.2 (14.5)"
[1] "hr=" "1.1"
D29V2, continuous
D29V3, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.33) MUTATED    13  24
  DEL PEAK  8(5P15.33) WILD-TYPE 163 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.33) MUTATED     13   24
  DEL PEAK  8(5P15.33) WILD-TYPE  163  200
        clus
vv       DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           13                            163
  MALE                             24                            200
[1] 2 2
[1] FALSE
D29V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  8(5P15.33) MUTATED            14               17                 6
  DEL PEAK  8(5P15.33) WILD-TYPE         129               87               147
D29V5, multiclass
                   clus
vv                  DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE
  ASTROCYTOMA                                 14                            129
  OLIGOASTROCYTOMA                            17                             87
  OLIGODENDROGLIOMA                            6                            147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.33) MUTATED    15  22
  DEL PEAK  8(5P15.33) WILD-TYPE  74 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.33) MUTATED     15   22
  DEL PEAK  8(5P15.33) WILD-TYPE   74  289
     clus
vv    DEL PEAK  8(5P15.33) MUTATED DEL PEAK  8(5P15.33) WILD-TYPE
  NO                            15                             74
  YES                           22                            289
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(5P15.33) MUTATED                                  0     0
  DEL PEAK  8(5P15.33) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P15.33) MUTATED                           0    37
  DEL PEAK  8(5P15.33) WILD-TYPE                        14   339
D29V7, multiclass
                                  clus
vv                                 DEL PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      37
                                  clus
vv                                 DEL PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.33) MUTATED     1  35
  DEL PEAK  8(5P15.33) WILD-TYPE  14 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.33) MUTATED      1   35
  DEL PEAK  8(5P15.33) WILD-TYPE   14  324
                        clus
vv                       DEL PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            324
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  9(5Q34) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  9(5Q34) MUTATED    35  16
  DEL PEAK  9(5Q34) WILD-TYPE 289  55
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                         51                         344 
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                         16                          55 
$`DEL PEAK  9(5Q34) MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XH 
       12.43         8.48        72.92        46.65        78.28        12.59 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 
       10.92        19.96        29.62        15.75         3.85        65.75 
TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TU 
       87.45       114.08        62.96        14.99        19.13         3.65 
TCGA-DU-A6S7 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5963 
        7.23        50.14        41.13        79.99        57.93        17.98 
TCGA-FG-7636 TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7609 
       17.88        10.59         7.82         8.81        24.26        45.99 
TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-A614 TCGA-HT-A618 
        3.68        11.28        31.43         0.10         2.70         5.33 
TCGA-HW-7489 TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A65S TCGA-S9-A6TS 
        8.32        19.00         2.30         5.88         2.53        62.17 
TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7R7 
       18.77         9.30         7.59         6.15         7.92        83.80 
TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84I 
        5.00        48.39        19.36 

$`DEL PEAK  9(5Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 
      122.73        81.96        75.25        47.93        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.84        18.38        72.95        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       31.82        30.31        14.40         8.02        30.21         7.79 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       52.11        22.42        49.02        75.16        46.06         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.96         7.73        11.47       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5311 
       26.76         7.13        21.30       124.50        67.46       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 
       78.21        95.57       130.78        14.33        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 
        6.64         7.04         4.21         4.08        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 
        5.23         0.13         0.10         6.67         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        5.33         2.93         1.71         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
       63.55        21.50        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         5.33        13.02         1.81        16.14 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        13.45        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F6 TCGA-QH-A65R 
        6.71         1.64         2.37         4.11         1.28         5.75 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        88.83        94.03        32.65        59.38 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
       70.65        10.88         9.04         3.39        14.27        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       17.42        31.59        49.45        35.93        25.32        22.59 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        24.26        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                     114.08                      211.17 
  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE 
                     15.750                      14.945 
[1] "0.1 - 114.1 (15.8)" "0.0 - 211.2 (14.9)"
[1] "hr=" "1.9"
D30V2, continuous
D30V3, binary
                             cls
clus                            0   1
  DEL PEAK  9(5Q34) MUTATED    22  29
  DEL PEAK  9(5Q34) WILD-TYPE 154 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(5Q34) MUTATED     22   29
  DEL PEAK  9(5Q34) WILD-TYPE  154  195
        clus
vv       DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE
  FEMALE                        22                         154
  MALE                          29                         195
[1] 2 2
[1] FALSE
D30V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  9(5Q34) MUTATED            31               12                 8
  DEL PEAK  9(5Q34) WILD-TYPE         112               92               145
D30V5, multiclass
                   clus
vv                  DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE
  ASTROCYTOMA                              31                         112
  OLIGOASTROCYTOMA                         12                          92
  OLIGODENDROGLIOMA                         8                         145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                             cls
clus                            0   1
  DEL PEAK  9(5Q34) MUTATED    16  35
  DEL PEAK  9(5Q34) WILD-TYPE  73 276
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(5Q34) MUTATED     16   35
  DEL PEAK  9(5Q34) WILD-TYPE   73  276
     clus
vv    DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE
  NO                         16                          73
  YES                        35                         276
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(5Q34) MUTATED                                  0     0
  DEL PEAK  9(5Q34) WILD-TYPE                                1     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q34) MUTATED                           0    51
  DEL PEAK  9(5Q34) WILD-TYPE                        14   325
D30V7, multiclass
                                  clus
vv                                 DEL PEAK  9(5Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                   51
                                  clus
vv                                 DEL PEAK  9(5Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                             cls
clus                            0   1
  DEL PEAK  9(5Q34) MUTATED     1  50
  DEL PEAK  9(5Q34) WILD-TYPE  14 309
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(5Q34) MUTATED      1   50
  DEL PEAK  9(5Q34) WILD-TYPE   14  309
                        clus
vv                       DEL PEAK  9(5Q34) MUTATED DEL PEAK  9(5Q34) WILD-TYPE
  HISPANIC OR LATINO                             1                          14
  NOT HISPANIC OR LATINO                        50                         309
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 10(6P25.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P25.3) MUTATED    24  13
  DEL PEAK 10(6P25.3) WILD-TYPE 300  58
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           37                           358 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           13                            58 
$`DEL PEAK 10(6P25.3) MUTATED`
TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O 
        6.38         8.48        46.65        18.38        12.59        18.84 
TCGA-DH-A669 TCGA-DH-A66G TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6407 TCGA-DU-8158 
       30.21         3.85         1.22         7.04        94.52         5.10 
TCGA-DU-8161 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-HT-7692 TCGA-HT-7855 
       23.74        17.98        32.19        24.99         2.96        19.23 
TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A614 TCGA-HT-A617 
       23.61        11.28        15.72         0.23         2.70        16.14 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8322 TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F6 
       19.23        35.90        17.82        19.00         2.30         1.28 
TCGA-QH-A6CS TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A7IS TCGA-TM-A7CF TCGA-VM-A8C8 
        4.18        18.77        21.63         7.92        48.39        33.07 
TCGA-VM-A8CD 
        7.89 

$`DEL PEAK 10(6P25.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P 
       27.62        27.02        18.84        72.95        11.01        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         7.79        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 
       75.16        46.06        65.75        87.45        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 
      130.78        14.33        47.77        34.36        18.77        14.93 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93         1.71        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       29.59         3.88        16.04        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       14.70         0.10         5.33        13.02         1.81         5.33 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       29.92        13.45         8.32        40.18         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
        8.94        19.59        10.55         7.89         9.67         6.61 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.37         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.27        28.14        22.49        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        22.59        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 
       29.92        18.90         9.44         4.57        12.00        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10        26.79        10.95 

  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                        94.52                        211.17 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                        17.82                         14.83 
[1] "0.2 - 94.5 (17.8)"  "0.0 - 211.2 (14.8)"
[1] "hr=" "3.5"
D31V2, continuous
D31V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    16  23
  DEL PEAK 10(6P25.3) WILD-TYPE 160 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     16   23
  DEL PEAK 10(6P25.3) WILD-TYPE  160  201
        clus
vv       DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  FEMALE                          16                           160
  MALE                            23                           201
[1] 2 2
[1] FALSE
D31V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 10(6P25.3) MUTATED            21                8                10
  DEL PEAK 10(6P25.3) WILD-TYPE         122               96               143
D31V5, multiclass
                   clus
vv                  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  ASTROCYTOMA                                21                           122
  OLIGOASTROCYTOMA                            8                            96
  OLIGODENDROGLIOMA                          10                           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"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED     9  30
  DEL PEAK 10(6P25.3) WILD-TYPE  80 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED      9   30
  DEL PEAK 10(6P25.3) WILD-TYPE   80  281
     clus
vv    DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  NO                            9                            80
  YES                          30                           281
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(6P25.3) MUTATED                                  1     0
  DEL PEAK 10(6P25.3) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.3) MUTATED                           0    38
  DEL PEAK 10(6P25.3) WILD-TYPE                        14   338
D31V7, multiclass
                                  clus
vv                                 DEL PEAK 10(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     38
                                  clus
vv                                 DEL PEAK 10(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED     2  34
  DEL PEAK 10(6P25.3) WILD-TYPE  13 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED      2   34
  DEL PEAK 10(6P25.3) WILD-TYPE   13  325
                        clus
vv                       DEL PEAK 10(6P25.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK 10(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           325
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 11(6Q22.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED    38  18
  DEL PEAK 11(6Q22.31) WILD-TYPE 286  53
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                            56                            339 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                            18                             53 
$`DEL PEAK 11(6Q22.31) MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        18.38        12.59 
TCGA-DB-A64O TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 TCGA-DU-5872 
       18.84        30.21        29.62        18.02         6.81        17.49 
TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7014 
        1.22        19.89         7.73        11.47         6.54       117.40 
TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       18.94         5.10        23.74        41.13        79.99        57.93 
TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-FN-7833 
       17.98        17.88        15.52        24.46        10.59         0.13 
TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.42        17.29        31.69        14.96         2.96        19.23 
TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-A5KK 
       11.28        15.72         0.23         0.10        16.14         7.89 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6TZ TCGA-S9-A6U6 
        0.23         2.30         1.28         4.18        21.63         9.86 
TCGA-S9-A7IS TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q 
        7.92        10.39        87.09        31.59        48.39        18.90 
TCGA-VM-A8C8 TCGA-VM-A8CD 
       33.07         7.89 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       27.02        18.84        72.95        11.01        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       19.96        31.82        30.31        14.40         8.02        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79         3.85        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        8.45       182.33        18.94        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 
       21.30       124.50        50.14        67.46       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        14.33        47.77        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        20.09        14.96        11.87         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 
        4.08        10.78        22.95         5.23         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      107.93         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33         2.93         1.71        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59         3.88        16.04        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07        14.70         5.33         2.70        13.02         1.81 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         9.67         6.61        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        4.73         6.71         1.64         2.37         4.11         5.88 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV 
        5.75         2.53         4.83         7.79         4.11         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       22.49        16.37        11.31        15.62        20.05        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        6.15         3.39        14.27        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 
       18.21        13.02        17.42        83.80         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        22.59        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA 
       29.92         9.44         4.57        12.00        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10        26.79        10.95 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        117.40                         211.17 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         15.93                          14.73 
[1] "0.1 - 117.4 (15.9)" "0.0 - 211.2 (14.7)"
[1] "hr=" "2.9"
D32V2, continuous
D32V3, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    26  32
  DEL PEAK 11(6Q22.31) WILD-TYPE 150 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     26   32
  DEL PEAK 11(6Q22.31) WILD-TYPE  150  192
        clus
vv       DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  FEMALE                           26                            150
  MALE                             32                            192
[1] 2 2
[1] FALSE
D32V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 11(6Q22.31) MUTATED            38               10                10
  DEL PEAK 11(6Q22.31) WILD-TYPE         105               94               143
D32V5, multiclass
                   clus
vv                  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  ASTROCYTOMA                                 38                            105
  OLIGOASTROCYTOMA                            10                             94
  OLIGODENDROGLIOMA                           10                            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"
D32V6, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    16  42
  DEL PEAK 11(6Q22.31) WILD-TYPE  73 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     16   42
  DEL PEAK 11(6Q22.31) WILD-TYPE   73  269
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                            16                             73
  YES                           42                            269
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6Q22.31) MUTATED                                  1     0
  DEL PEAK 11(6Q22.31) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q22.31) MUTATED                           3    54
  DEL PEAK 11(6Q22.31) WILD-TYPE                        11   322
D32V7, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 11(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     2  51
  DEL PEAK 11(6Q22.31) WILD-TYPE  13 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      2   51
  DEL PEAK 11(6Q22.31) WILD-TYPE   13  308
                        clus
vv                       DEL PEAK 11(6Q22.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       DEL PEAK 11(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            308
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 12(6Q24.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6Q24.3) MUTATED    41  18
  DEL PEAK 12(6Q24.3) WILD-TYPE 283  53
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                           59                           336 
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                           18                            53 
$`DEL PEAK 12(6Q24.3) MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        18.38        12.59 
TCGA-DB-A64O TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 TCGA-DU-5872 
       18.84        30.21        29.62        18.02         6.81        17.49 
TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7014 
        1.22        19.89         7.73        11.47         6.54       117.40 
TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       18.94         5.10        23.74        41.13        79.99        57.93 
TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A6J3 
      130.78        17.98        17.88        15.52        24.46        10.59 
TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 
        0.13         0.03        17.42        17.29        31.69        14.96 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7884 TCGA-HT-8108 TCGA-HT-8563 TCGA-HT-8564 
        2.96        19.23        11.28         2.50        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EZ 
        0.23         0.10        16.14         7.89         0.23         2.30 
TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6TZ TCGA-S9-A6U6 TCGA-S9-A7IS TCGA-S9-A7R3 
        1.28         4.18        21.63         9.86         7.92        87.09 
TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CD 
       31.59        48.39        18.90        33.07         7.89 

$`DEL PEAK 12(6Q24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       27.02        18.84        72.95        11.01        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       19.96        31.82        30.31        14.40         8.02        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79         3.85        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        8.45       182.33        18.94        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 
       21.30       124.50        50.14        67.46       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       95.57        14.33        47.77        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 
       14.93        24.99        23.97        13.58        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       20.09        14.96        11.87         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       10.78        22.95         5.23         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
        8.81         0.13        16.54         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
       42.74         0.10         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
       10.49         0.13         0.07        14.70         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       13.02         1.81         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        10.55         9.67         6.61        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77         5.23         4.73         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.27        28.14        22.49        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       20.05        94.62        83.70         5.85       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
        9.04         7.59         6.15         3.39        14.27        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 
        3.58         4.04        18.21        13.02        10.39        17.42 
TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80         5.00        49.45        35.93        25.32        22.59 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       17.49        40.83        16.50        29.92         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08        13.51         0.10        26.79        10.95 

  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                       130.78                        211.17 
  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE 
                       16.040                        14.715 
[1] "0.0 - 130.8 (16.0)" "0.1 - 211.2 (14.7)"
[1] "hr=" "2.4"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q24.3) MUTATED    29  32
  DEL PEAK 12(6Q24.3) WILD-TYPE 147 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q24.3) MUTATED     29   32
  DEL PEAK 12(6Q24.3) WILD-TYPE  147  192
        clus
vv       DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE
  FEMALE                          29                           147
  MALE                            32                           192
[1] 2 2
[1] FALSE
D33V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 12(6Q24.3) MUTATED            38               11                12
  DEL PEAK 12(6Q24.3) WILD-TYPE         105               93               141
D33V5, multiclass
                   clus
vv                  DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE
  ASTROCYTOMA                                38                           105
  OLIGOASTROCYTOMA                           11                            93
  OLIGODENDROGLIOMA                          12                           141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q24.3) MUTATED    17  44
  DEL PEAK 12(6Q24.3) WILD-TYPE  72 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q24.3) MUTATED     17   44
  DEL PEAK 12(6Q24.3) WILD-TYPE   72  267
     clus
vv    DEL PEAK 12(6Q24.3) MUTATED DEL PEAK 12(6Q24.3) WILD-TYPE
  NO                           17                            72
  YES                          44                           267
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q24.3) MUTATED                                  1     0
  DEL PEAK 12(6Q24.3) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q24.3) MUTATED                           3    57
  DEL PEAK 12(6Q24.3) WILD-TYPE                        11   319
D33V7, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     57
                                  clus
vv                                 DEL PEAK 12(6Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      319
[1] 4 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 12(6Q24.3) MUTATED     2  54
  DEL PEAK 12(6Q24.3) WILD-TYPE  13 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q24.3) MUTATED      2   54
  DEL PEAK 12(6Q24.3) WILD-TYPE   13  305
                        clus
vv                       DEL PEAK 12(6Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK 12(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           305
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 13(7P22.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7P22.3) MUTATED    10   5
  DEL PEAK 13(7P22.3) WILD-TYPE 314  66
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                           15                           380 
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                            5                            66 
$`DEL PEAK 13(7P22.3) MUTATED`
TCGA-CS-5393 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-7304 TCGA-DU-A6S7 TCGA-DU-A76R 
       40.18        46.06        65.75        23.31         7.23        21.30 
TCGA-FG-8188 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7477 TCGA-HW-A5KL TCGA-P5-A5F6 
       14.96         0.13         8.81        24.26         9.67         1.28 
TCGA-S9-A6TS TCGA-S9-A7R3 TCGA-TM-A84H 
       62.17        87.09        24.26 

$`DEL PEAK 13(7P22.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       49.02        75.16         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 
        5.98        11.41        26.76         7.13       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
       22.95         5.23         0.10         6.67         7.82         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        10.55         7.89         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        5.03        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       18.21        13.02        10.39        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                        87.09                        211.17 
  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE 
                        23.31                         14.83 
[1] "0.1 - 87.1 (23.3)"  "0.0 - 211.2 (14.8)"
[1] "hr=" "1.7"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.3) MUTATED     5  11
  DEL PEAK 13(7P22.3) WILD-TYPE 171 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.3) MUTATED      5   11
  DEL PEAK 13(7P22.3) WILD-TYPE  171  213
        clus
vv       DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE
  FEMALE                           5                           171
  MALE                            11                           213
[1] 2 2
[1] FALSE
D34V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 13(7P22.3) MUTATED             7                4                 5
  DEL PEAK 13(7P22.3) WILD-TYPE         136              100               148
D34V5, multiclass
                   clus
vv                  DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE
  ASTROCYTOMA                                 7                           136
  OLIGOASTROCYTOMA                            4                           100
  OLIGODENDROGLIOMA                           5                           148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.3) MUTATED     4  12
  DEL PEAK 13(7P22.3) WILD-TYPE  85 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.3) MUTATED      4   12
  DEL PEAK 13(7P22.3) WILD-TYPE   85  299
     clus
vv    DEL PEAK 13(7P22.3) MUTATED DEL PEAK 13(7P22.3) WILD-TYPE
  NO                            4                            85
  YES                          12                           299
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(7P22.3) MUTATED                                  0     0
  DEL PEAK 13(7P22.3) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7P22.3) MUTATED                           0    16
  DEL PEAK 13(7P22.3) WILD-TYPE                        14   360
D34V7, multiclass
                                  clus
vv                                 DEL PEAK 13(7P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     16
                                  clus
vv                                 DEL PEAK 13(7P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      360
[1] 4 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 13(7P22.3) MUTATED     0  14
  DEL PEAK 13(7P22.3) WILD-TYPE  15 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.3) MUTATED      0   14
  DEL PEAK 13(7P22.3) WILD-TYPE   15  345
                        clus
vv                       DEL PEAK 13(7P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       DEL PEAK 13(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 14(8Q24.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8Q24.3) MUTATED    17   4
  DEL PEAK 14(8Q24.3) WILD-TYPE 307  67
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                           21                           374 
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                            4                            67 
$`DEL PEAK 14(8Q24.3) MUTATED`
TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-7301 TCGA-DU-8165 
       78.28        10.92        19.96        11.47        25.91        19.13 
TCGA-FG-5965 TCGA-FG-8185 TCGA-FG-A4MY TCGA-HT-7473 TCGA-HT-7610 TCGA-HT-7688 
       32.19        14.24         9.67        16.54        56.09        31.69 
TCGA-HT-7879 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HW-8321 TCGA-P5-A5F6 
        3.68         0.23        15.72         0.23        19.59         1.28 
TCGA-QH-A6CV TCGA-S9-A6WM TCGA-VM-A8C8 
        2.96         9.30        33.07 

$`DEL PEAK 14(8Q24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 
       72.92        46.65        50.17        44.52        36.56        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 
       16.08        15.42        27.81        14.73        13.64        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       11.41        26.76         7.13        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        0.59         5.26         3.72         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.03         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       29.59         3.88        16.04        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 
       40.18        35.90         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         4.18         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       70.65        10.88         9.04         7.59         6.15         3.39 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        12.00        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                        78.28                        211.17 
  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE 
                        15.72                         14.96 
[1] "0.2 - 78.3 (15.7)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.5"
D35V2, continuous
D35V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(8Q24.3) MUTATED    10  11
  DEL PEAK 14(8Q24.3) WILD-TYPE 166 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q24.3) MUTATED     10   11
  DEL PEAK 14(8Q24.3) WILD-TYPE  166  213
        clus
vv       DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE
  FEMALE                          10                           166
  MALE                            11                           213
[1] 2 2
[1] FALSE
D35V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 14(8Q24.3) MUTATED             7                9                 5
  DEL PEAK 14(8Q24.3) WILD-TYPE         136               95               148
D35V5, multiclass
                   clus
vv                  DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE
  ASTROCYTOMA                                 7                           136
  OLIGOASTROCYTOMA                            9                            95
  OLIGODENDROGLIOMA                           5                           148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(8Q24.3) MUTATED     6  15
  DEL PEAK 14(8Q24.3) WILD-TYPE  83 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q24.3) MUTATED      6   15
  DEL PEAK 14(8Q24.3) WILD-TYPE   83  296
     clus
vv    DEL PEAK 14(8Q24.3) MUTATED DEL PEAK 14(8Q24.3) WILD-TYPE
  NO                            6                            83
  YES                          15                           296
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8Q24.3) MUTATED                                  0     1
  DEL PEAK 14(8Q24.3) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8Q24.3) MUTATED                           0    20
  DEL PEAK 14(8Q24.3) WILD-TYPE                        14   356
D35V7, multiclass
                                  clus
vv                                 DEL PEAK 14(8Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK 14(8Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      356
[1] 4 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 14(8Q24.3) MUTATED     3  17
  DEL PEAK 14(8Q24.3) WILD-TYPE  12 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q24.3) MUTATED      3   17
  DEL PEAK 14(8Q24.3) WILD-TYPE   12  342
                        clus
vv                       DEL PEAK 14(8Q24.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK 14(8Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           342
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(9P23) MUTATED    79  29
  DEL PEAK 15(9P23) WILD-TYPE 245  42
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        108                         287 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         29                          42 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
       18.15        40.18        21.01         9.96         6.38        23.84 
TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB 
        8.48         6.61        46.65        44.52        78.28        12.72 
TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V 
       27.62        18.38        12.59        11.01         5.98        14.73 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6395 
       18.02        17.46         6.74         8.45         6.81        49.02 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6542 
       46.06        65.75         7.04        11.64        19.89         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 
       11.47        62.96       117.40        90.77        26.30         7.96 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8162 
       18.94        25.91        23.31        41.98        23.74         3.98 
TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5305 
       14.17        12.20         7.23         5.98        41.13        79.99 
TCGA-E1-5307 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 
       57.93        14.33        17.98        34.36        32.19        24.99 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       13.58        17.88        14.24         5.26         3.72         9.67 
TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
       10.59         8.81         0.13        17.42         6.54        24.26 
TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.29         0.10        31.69        14.96         2.96        19.23 
TCGA-HT-7902 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 
       31.43        12.23         2.50        14.70         0.10         2.70 
TCGA-HT-A618 TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KM 
        5.33        19.23         8.61         8.94        17.82         6.61 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-QH-A6CZ 
        4.73         0.23         2.30         1.28         2.96         3.16 
TCGA-QH-A6X9 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7IS 
        1.91        62.17        28.27        22.92         6.15         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF 
       19.63         4.21         9.37        87.09        31.59        48.39 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-VM-A8CD 
       24.26        17.49        18.90        33.07         0.10         7.89 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        17.95        12.43         7.56         8.02         7.40 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG 
       36.56        30.08        10.29        27.02        18.84        72.95 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W 
       18.84        16.80        16.08        15.42        27.81        13.64 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 
       30.21        29.62        15.75         7.79         3.85        14.56 
TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
       13.38       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 
       52.11        22.42        75.16         1.22        87.45       133.74 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       16.83        94.52       114.08         7.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7290 
       14.99       105.21         6.54         8.84        30.67        10.36 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8158 
       94.32        44.02        62.01        60.30         2.76         5.10 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        2.70        77.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
      124.50        50.14        67.46       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 
      130.78        47.77        18.77        14.93        23.97        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z 
        7.04         6.64         7.04         4.21         4.08        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03        16.54         3.75         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       107.93         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33         2.93         1.71        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       16.24         9.40        63.55        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7486 
        0.07         5.33        13.02         1.81        16.14        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8321 
       13.45         8.32        40.18        35.90         4.31        19.59 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67        19.00        42.77         5.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R 
        6.71         1.64         2.37         4.11         5.88         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         2.20 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC 
        0.59         6.31         3.91         4.73         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       62.37        72.59        70.55        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 
        9.04         7.59         3.39        14.27        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       10.39        17.42        83.80         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       25.32        22.59        12.00        15.09        50.76        34.36 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       19.36        40.83        16.50        29.92         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08        13.51        26.79        10.95 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     117.40                      211.17 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     14.515                      15.120 
[1] "0.1 - 117.4 (14.5)" "0.0 - 211.2 (15.1)"
[1] "hr=" "2.7"
D36V2, continuous
D36V3, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    48  62
  DEL PEAK 15(9P23) WILD-TYPE 128 162
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     48   62
  DEL PEAK 15(9P23) WILD-TYPE  128  162
        clus
vv       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  FEMALE                        48                         128
  MALE                          62                         162
[1] 2 2
[1] FALSE
D36V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 15(9P23) MUTATED            52               27                31
  DEL PEAK 15(9P23) WILD-TYPE          91               77               122
D36V5, multiclass
                   clus
vv                  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  ASTROCYTOMA                              52                          91
  OLIGOASTROCYTOMA                         27                          77
  OLIGODENDROGLIOMA                        31                         122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    34  76
  DEL PEAK 15(9P23) WILD-TYPE  55 235
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     34   76
  DEL PEAK 15(9P23) WILD-TYPE   55  235
     clus
vv    DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  NO                         34                          55
  YES                        76                         235
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(9P23) MUTATED                                  0     1
  DEL PEAK 15(9P23) WILD-TYPE                                1     1
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED                           2   104
  DEL PEAK 15(9P23) WILD-TYPE                        12   272
D36V7, multiclass
                                  clus
vv                                 DEL PEAK 15(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                  104
                                  clus
vv                                 DEL PEAK 15(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    272
[1] 4 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 15(9P23) MUTATED     3  98
  DEL PEAK 15(9P23) WILD-TYPE  12 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      3   98
  DEL PEAK 15(9P23) WILD-TYPE   12  261
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             3                          12
  NOT HISPANIC OR LATINO                        98                         261
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(9P21.3) MUTATED    89  41
  DEL PEAK 16(9P21.3) WILD-TYPE 235  30
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          130                           265 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           41                            30 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       18.15        40.18        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 
       23.84         8.48         6.61        47.93        46.65        44.52 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L 
       78.28        12.72        27.62        18.38        12.59        11.01 
TCGA-DB-A64V TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 
       14.73        19.96        18.02        17.46         6.74         8.45 
TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 
        6.81        49.02        46.06        65.75         7.04        11.64 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       19.89        16.83        94.52         7.73        11.47        62.96 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        6.54       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 
       18.94        25.91        60.30        23.31        41.98         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 
       23.74         3.98        14.17        12.20         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-E1-5307 TCGA-EZ-7264 TCGA-FG-5963 
       11.41        26.76        41.13        57.93        14.33        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 
       34.36        32.19        24.99        13.58        17.88        14.24 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A70Z 
        0.59         5.26         3.72         9.67        10.59        10.78 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        7.82         8.81         0.13        17.42         6.54        24.26 
TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.29         0.10        31.69        14.96         2.96        19.23 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8108 
        0.23         0.49        31.43        16.24        12.23         2.50 
TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        4.70         0.23        14.70         0.10         5.33         2.70 
TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KM 
       19.23         8.61         8.94        17.82         7.89         6.61 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A6CV 
       19.00         4.73         0.23         2.30         1.28         2.96 
TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6U0 
        3.16         1.91         5.03        62.17        28.27        16.37 
TCGA-S9-A6UA TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ 
        5.85        22.92         9.30         7.92        19.63         4.21 
TCGA-S9-A7J0 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H 
        9.37        87.09        31.59         5.00        48.39        24.26 
TCGA-TM-A84J TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-VM-A8CD 
       17.49        33.07         0.10         7.89 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       17.95        12.43         7.56         8.02         7.40       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 
       81.96        75.25        72.92        50.17        36.56        30.08 
TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P 
       10.29        27.02        18.84        72.95        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X 
        5.98        16.08        15.42        27.81        13.64        10.92 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5853 TCGA-DU-5870 
       15.75         7.79         3.85        14.56        13.38       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6408 TCGA-DU-6410 
       75.16         1.22        87.45       133.74       114.08         7.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7290 
      156.23       138.28        14.99       105.21         8.84        10.36 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8164 
       94.32        44.02        62.01         2.76        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65         5.65         8.65         2.70        77.98 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        50.14        67.46        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-6688 
      134.27        78.21        95.57       130.78        47.77        18.77 
TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       14.93        23.97        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       15.52        24.46         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        4.08        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03        16.54         3.75         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       107.93         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 
       17.52         6.90        14.53        39.48        39.09        50.63 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 
        2.93         1.71        11.28         1.64         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       21.50        33.01         6.25         0.10         0.46         3.95 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04        15.72        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.13         0.07        13.02         1.81        16.14         5.33 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        13.45         8.32        40.18        35.90         4.31 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW 
       19.59        10.55         9.67        42.77         5.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S 
        1.64         2.37         4.11         5.88         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6X3 
        4.83         7.79         4.11         4.18         2.20         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-R8-A6MK TCGA-R8-A6ML 
        6.31         3.91         4.73         0.23        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY 
       32.65        59.38        69.07        18.77        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
       83.70       103.76        62.37        72.59        70.55        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       12.59         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-TM-A7C3 
       18.21        13.02        10.39        17.42        83.80        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        25.32        22.59        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       34.36        19.36        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
        9.44         4.57        12.00        30.08        13.51        26.79 
TCGA-VM-A8CH 
       10.95 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       117.40                        211.17 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       14.205                        15.350 
[1] "0.1 - 117.4 (14.2)" "0.0 - 211.2 (15.3)"
[1] "hr=" "4.8"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    59  73
  DEL PEAK 16(9P21.3) WILD-TYPE 117 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     59   73
  DEL PEAK 16(9P21.3) WILD-TYPE  117  151
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          59                           117
  MALE                            73                           151
[1] 2 2
[1] FALSE
D37V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 16(9P21.3) MUTATED            63               31                38
  DEL PEAK 16(9P21.3) WILD-TYPE          80               73               115
D37V5, multiclass
                   clus
vv                  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  ASTROCYTOMA                                63                            80
  OLIGOASTROCYTOMA                           31                            73
  OLIGODENDROGLIOMA                          38                           115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    40  92
  DEL PEAK 16(9P21.3) WILD-TYPE  49 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     40   92
  DEL PEAK 16(9P21.3) WILD-TYPE   49  219
     clus
vv    DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  NO                           40                            49
  YES                          92                           219
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P21.3) MUTATED                                  0     1
  DEL PEAK 16(9P21.3) WILD-TYPE                                1     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED                           4   125
  DEL PEAK 16(9P21.3) WILD-TYPE                        10   251
D37V7, multiclass
                                  clus
vv                                 DEL PEAK 16(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                    125
                                  clus
vv                                 DEL PEAK 16(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     4 119
  DEL PEAK 16(9P21.3) WILD-TYPE  11 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      4  119
  DEL PEAK 16(9P21.3) WILD-TYPE   11  240
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 17(10Q26.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(10Q26.3) MUTATED    71  43
  DEL PEAK 17(10Q26.3) WILD-TYPE 253  28
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           114                            281 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                            43                             28 
$`DEL PEAK 17(10Q26.3) MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        7.69        21.01         6.38        17.69        23.84        12.43 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 
       46.65        44.52        18.38        11.01        18.84        19.96 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 
       30.21        29.62        15.75        18.02         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
        8.45        17.49        75.16        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 
       11.64        19.89        16.83        94.52       114.08        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       156.23        14.99         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-8158 
       90.77        10.36         7.96        18.94        25.91         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K 
       23.74         3.98        19.13        15.48        12.20        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5311 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 
       26.76        21.30       134.27        18.77        13.58        20.09 
TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 
       14.96         0.59         5.26        10.59        10.78         7.82 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7606 
        0.13        16.54         6.54       154.19         4.01        17.29 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7873 
       31.69         0.10        17.52         0.23         0.49        23.61 
TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8108 
        3.68         1.71        31.43        16.24        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC 
        4.70        16.04        15.72         0.23        14.70         5.33 
TCGA-HT-A617 TCGA-HW-8321 TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EZ 
       16.14        19.59         7.89        19.00         4.73         2.30 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-S9-A6TS 
        4.18         2.96         0.59         1.91         5.03        62.17 
TCGA-S9-A6U0 TCGA-S9-A6UB TCGA-S9-A6WM TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IX 
       16.37       103.76         9.30         3.39         7.92        19.63 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A89Z 
        9.37         3.58         4.04        10.39        87.09         5.00 
TCGA-TM-A7C3 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CD 
       49.45        48.39        12.00        19.36        17.49         7.89 

$`DEL PEAK 17(10Q26.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH 
       12.72        27.62        27.02        18.84        72.95        12.59 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       13.64        10.92        31.82        30.31        14.40         8.02 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-5870 
        7.79         3.85        14.56        17.46         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6404 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 
       46.06         1.22       133.74         7.96         7.73       138.28 
TCGA-DU-7011 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
      105.21        30.67        26.30        94.32        44.02        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8164 
       60.30        23.31        41.98         2.76        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65         5.65         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        5.98         7.13       124.50        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99        57.93        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       47.77        17.98        34.36        32.19        14.93        24.99 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       23.97        15.35        17.88        22.55        20.61        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       24.46         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
        4.21         4.08        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 
        6.67         8.81         0.03         3.75        17.42        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7601 
        6.38         7.10        75.19        59.18        60.03         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18       107.93         4.57         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       19.23        39.09        50.63        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 
        5.33         2.93        11.28         1.64         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       21.50        33.01         6.25         0.10         0.46         3.95 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
        0.23        29.59         3.88        10.49         0.13         0.07 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 
        0.10         2.70        13.02         1.81         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
        8.61         8.94        17.82        10.55         9.67         6.61 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77         5.23         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
        7.79         4.11         2.20         3.16         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        4.73         0.23        88.83        94.03        32.65        59.38 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        28.27        28.14        22.49        21.63 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
        5.85        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IY 
       10.88         9.04         7.59         6.15        14.27        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
        4.21         8.19         2.04         8.12        18.21        13.02 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       17.42        83.80        31.59        35.93        25.32        22.59 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M 
       15.09        50.76        34.36        24.26        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10        26.79        10.95 

  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                        14.975                         14.960 
[1] "0.1 - 156.2 (15.0)" "0.0 - 211.2 (15.0)"
[1] "hr=" "4"  
D38V2, continuous
D38V3, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q26.3) MUTATED    58  58
  DEL PEAK 17(10Q26.3) WILD-TYPE 118 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED     58   58
  DEL PEAK 17(10Q26.3) WILD-TYPE  118  166
        clus
vv       DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  FEMALE                           58                            118
  MALE                             58                            166
[1] 2 2
[1] FALSE
D38V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 17(10Q26.3) MUTATED            60               26                30
  DEL PEAK 17(10Q26.3) WILD-TYPE          83               78               123
D38V5, multiclass
                   clus
vv                  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  ASTROCYTOMA                                 60                             83
  OLIGOASTROCYTOMA                            26                             78
  OLIGODENDROGLIOMA                           30                            123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q26.3) MUTATED    26  90
  DEL PEAK 17(10Q26.3) WILD-TYPE  63 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED     26   90
  DEL PEAK 17(10Q26.3) WILD-TYPE   63  221
     clus
vv    DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  NO                            26                             63
  YES                           90                            221
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(10Q26.3) MUTATED                                  1     1
  DEL PEAK 17(10Q26.3) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q26.3) MUTATED                           6   107
  DEL PEAK 17(10Q26.3) WILD-TYPE                         8   269
D38V7, multiclass
                                  clus
vv                                 DEL PEAK 17(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                     107
                                  clus
vv                                 DEL PEAK 17(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       269
[1] 4 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 17(10Q26.3) MUTATED     5 106
  DEL PEAK 17(10Q26.3) WILD-TYPE  10 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED      5  106
  DEL PEAK 17(10Q26.3) WILD-TYPE   10  253
                        clus
vv                       DEL PEAK 17(10Q26.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 17(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 18(11P15.5) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(11P15.5) MUTATED    61  16
  DEL PEAK 18(11P15.5) WILD-TYPE 263  55
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                            77                            318 
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                            16                             55 
$`DEL PEAK 18(11P15.5) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6665 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-A64X 
       18.15        17.95        12.43        47.93        46.65        10.92 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5851 TCGA-DU-5853 
       19.96        30.31        15.75         3.85        17.46        13.38 
TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
       75.16       114.08        11.47        62.96       156.23        14.99 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7298 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8165 
      117.40        90.77        18.94         2.76         5.10        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S7 
       16.96        15.48        12.59        15.12         3.65         7.23 
TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-8188 TCGA-FG-A4MW 
       50.14        41.13        32.19        14.93        14.96         5.26 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 
        9.67         7.04         8.81        24.26         6.38         5.03 
TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7693 
       23.18         3.16         0.16        42.74         0.10        17.52 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8114 
       23.61        31.43        63.55        21.50         0.23         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7493 
       16.04        15.72         2.70         1.81         5.33        35.90 
TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A6XA TCGA-S9-A6TV 
        8.61        19.00         1.28         2.53         0.23        18.77 
TCGA-S9-A6WM TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 
        9.30         4.21         9.37         4.04        17.42        83.80 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J 
        5.00        49.45        35.93        19.36        17.49 

$`DEL PEAK 18(11P15.5) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       81.96        75.25        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       18.84        18.38        72.95        12.59        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       13.64        31.82        14.40         8.02        30.21        29.62 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
        7.79        18.02        14.56         6.74         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        7.96         7.73       138.28       105.21         6.54         8.84 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8161 
       62.01        25.91        60.30        23.31        41.98        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT 
        3.98        20.68        21.40        14.17        14.24         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
        5.65        12.20         8.65         2.70        77.98         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5303 
       11.41        26.76         7.13        21.30       124.50        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 
       14.33        47.77        17.98        34.36        18.77        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J 
       11.87        15.52        24.46         0.59         3.72         7.04 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        6.64         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
        5.23         0.13         0.10         6.67         7.82         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.54         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 
       75.19        59.18        60.03       154.19         4.01        29.85 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      107.93         4.57        17.29        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 
        6.05         0.10        31.69        14.96         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93         1.71        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        9.40        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-A4DS TCGA-HT-A4DV 
        2.50         3.95         4.70        29.59         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
        0.13         0.07        14.70         0.10         5.33        13.02 
TCGA-HT-A617 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       16.14        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        5.75         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        1.91         5.03        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        69.07        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 
        3.39        14.27         7.92        19.63        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
        2.04         8.12         3.58        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       87.09        31.59        25.32        22.59        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M 
       15.09        50.76        34.36        24.26        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 

  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE 
                        15.720                         14.545 
[1] "0.1 - 156.2 (15.7)" "0.0 - 211.2 (14.5)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P15.5) MUTATED    43  35
  DEL PEAK 18(11P15.5) WILD-TYPE 133 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P15.5) MUTATED     43   35
  DEL PEAK 18(11P15.5) WILD-TYPE  133  189
        clus
vv       DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE
  FEMALE                           43                            133
  MALE                             35                            189
[1] 2 2
[1] FALSE
D39V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 18(11P15.5) MUTATED            39               23                16
  DEL PEAK 18(11P15.5) WILD-TYPE         104               81               137
D39V5, multiclass
                   clus
vv                  DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE
  ASTROCYTOMA                                 39                            104
  OLIGOASTROCYTOMA                            23                             81
  OLIGODENDROGLIOMA                           16                            137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P15.5) MUTATED    20  58
  DEL PEAK 18(11P15.5) WILD-TYPE  69 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P15.5) MUTATED     20   58
  DEL PEAK 18(11P15.5) WILD-TYPE   69  253
     clus
vv    DEL PEAK 18(11P15.5) MUTATED DEL PEAK 18(11P15.5) WILD-TYPE
  NO                            20                             69
  YES                           58                            253
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11P15.5) MUTATED                                  0     0
  DEL PEAK 18(11P15.5) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11P15.5) MUTATED                           2    75
  DEL PEAK 18(11P15.5) WILD-TYPE                        12   301
D39V7, multiclass
                                  clus
vv                                 DEL PEAK 18(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      75
                                  clus
vv                                 DEL PEAK 18(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P15.5) MUTATED     3  73
  DEL PEAK 18(11P15.5) WILD-TYPE  12 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P15.5) MUTATED      3   73
  DEL PEAK 18(11P15.5) WILD-TYPE   12  286
                        clus
vv                       DEL PEAK 18(11P15.5) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           73
                        clus
vv                       DEL PEAK 18(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            286
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 19(12P13.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(12P13.1) MUTATED    21   9
  DEL PEAK 19(12P13.1) WILD-TYPE 303  62
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                            30                            365 
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                             9                             62 
$`DEL PEAK 19(12P13.1) MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DU-5855 TCGA-DU-6403 
       18.15        12.43        44.52        12.59         6.81        11.64 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-A6S6 TCGA-DU-A76R 
        7.73        62.96        44.02        23.31        77.98        21.30 
TCGA-E1-5302 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7690 
       50.14        32.19        24.99        10.59         8.81         0.10 
TCGA-HT-7879 TCGA-HT-8106 TCGA-HT-8108 TCGA-HW-A5KM TCGA-P5-A5EW TCGA-S9-A6U1 
        3.68         0.10         2.50         6.61         6.71        11.31 
TCGA-S9-A6UA TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-TM-A84I 
        5.85         9.37         4.04        10.39        17.42        19.36 

$`DEL PEAK 19(12P13.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L 
       27.62        27.02        18.84        18.38        72.95        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        8.45       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22        87.45         7.04       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 
       94.52       114.08         7.96        11.47       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 
        3.65         5.65        12.20         8.65         2.70         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 
        5.98        11.41        26.76         7.13       124.50        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 
      130.78        14.33        47.77        17.98        34.36        18.77 
TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.21         4.08        10.78        22.95         5.23         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67         7.82         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        31.69        14.96         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.46         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 
       19.59        17.82        10.55         7.89         9.67        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY 
       42.77         5.23         4.73         0.23         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       83.70       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04         8.12         3.58        18.21        13.02 
TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       87.09        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                         77.98                         211.17 
  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE 
                        11.475                         15.120 
[1] "0.1 - 78.0 (11.5)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "2.7"
D40V2, continuous
D40V3, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P13.1) MUTATED    12  19
  DEL PEAK 19(12P13.1) WILD-TYPE 164 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P13.1) MUTATED     12   19
  DEL PEAK 19(12P13.1) WILD-TYPE  164  205
        clus
vv       DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE
  FEMALE                           12                            164
  MALE                             19                            205
[1] 2 2
[1] FALSE
D40V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 19(12P13.1) MUTATED            16                9                 6
  DEL PEAK 19(12P13.1) WILD-TYPE         127               95               147
D40V5, multiclass
                   clus
vv                  DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE
  ASTROCYTOMA                                 16                            127
  OLIGOASTROCYTOMA                             9                             95
  OLIGODENDROGLIOMA                            6                            147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P13.1) MUTATED     9  22
  DEL PEAK 19(12P13.1) WILD-TYPE  80 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P13.1) MUTATED      9   22
  DEL PEAK 19(12P13.1) WILD-TYPE   80  289
     clus
vv    DEL PEAK 19(12P13.1) MUTATED DEL PEAK 19(12P13.1) WILD-TYPE
  NO                             9                             80
  YES                           22                            289
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(12P13.1) MUTATED                                  0     0
  DEL PEAK 19(12P13.1) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(12P13.1) MUTATED                           0    30
  DEL PEAK 19(12P13.1) WILD-TYPE                        14   346
D40V7, multiclass
                                  clus
vv                                 DEL PEAK 19(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      30
                                  clus
vv                                 DEL PEAK 19(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       346
[1] 4 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 19(12P13.1) MUTATED     0  28
  DEL PEAK 19(12P13.1) WILD-TYPE  15 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P13.1) MUTATED      0   28
  DEL PEAK 19(12P13.1) WILD-TYPE   15  331
                        clus
vv                       DEL PEAK 19(12P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 19(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            331
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 20(12Q12) MUTATION ANALYSIS
D41V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 20(12Q12) MUTATED    41   9
  DEL PEAK 20(12Q12) WILD-TYPE 283  62
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                          50                          345 
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                           9                           62 
$`DEL PEAK 20(12Q12) MUTATED`
TCGA-CS-4941 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DH-A66B 
        7.69        46.65        44.52        18.38        12.59        29.62 
TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
       18.94        87.45         7.73        62.96       156.23        14.99 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76O 
       16.96        15.48         3.65        12.20        77.98         7.13 
TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-6689 TCGA-FG-6690 TCGA-HT-7470 
       21.30        50.14        41.13        14.93        24.99         8.81 
TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7884 
        3.75         6.38        42.74        31.69         0.10        11.28 
TCGA-HT-7902 TCGA-HT-8018 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8563 TCGA-HT-A618 
       31.43        21.50         0.10         2.50        16.04         5.33 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WQ 
        6.71         2.30        18.77        11.31         5.85         3.39 
TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-TM-A84G TCGA-TM-A84I 
        4.04        87.09        17.42        83.80        34.36        19.36 
TCGA-VM-A8C8 TCGA-VM-A8CB 
       33.07         0.10 

$`DEL PEAK 20(12Q12) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       27.62        27.02        18.84        72.95        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       13.64        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
        8.02        30.21        15.75         7.79         3.85        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 
       49.02        75.16        46.06        65.75         1.22         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        7.96        11.47       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        21.40        19.13        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 
       15.12         4.96         5.65         8.65         2.70         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5305 
        5.98        11.41        26.76       124.50        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6691 
       47.77        17.98        34.36        32.19        18.77        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 
        6.67         7.82         0.13         0.03        16.54        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54        24.26         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 
       44.68         6.05         0.10        14.96         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 
        0.13         3.68         5.33         2.93         1.71         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       16.24         9.40        63.55        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        4.73         0.23         1.64         2.37         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
       94.03        32.65        59.38        62.17        69.07        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        22.49        21.63        16.37        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
        9.86        94.62        83.70       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       70.55        22.92        70.65        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        7.59         6.15        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       18.21        13.02        10.39        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       50.76        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA 
       18.90         9.44         4.57        12.00        30.08        13.51 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                      156.23                       211.17 
  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE 
                        16.5                         14.7 
[1] "0.1 - 156.2 (16.5)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1"  
D41V2, continuous
D41V3, binary
                              cls
clus                             0   1
  DEL PEAK 20(12Q12) MUTATED    25  26
  DEL PEAK 20(12Q12) WILD-TYPE 151 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 20(12Q12) MUTATED     25   26
  DEL PEAK 20(12Q12) WILD-TYPE  151  198
        clus
vv       DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE
  FEMALE                         25                          151
  MALE                           26                          198
[1] 2 2
[1] FALSE
D41V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 20(12Q12) MUTATED            28               12                11
  DEL PEAK 20(12Q12) WILD-TYPE         115               92               142
D41V5, multiclass
                   clus
vv                  DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE
  ASTROCYTOMA                               28                          115
  OLIGOASTROCYTOMA                          12                           92
  OLIGODENDROGLIOMA                         11                          142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                              cls
clus                             0   1
  DEL PEAK 20(12Q12) MUTATED    10  41
  DEL PEAK 20(12Q12) WILD-TYPE  79 270
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 20(12Q12) MUTATED     10   41
  DEL PEAK 20(12Q12) WILD-TYPE   79  270
     clus
vv    DEL PEAK 20(12Q12) MUTATED DEL PEAK 20(12Q12) WILD-TYPE
  NO                          10                           79
  YES                         41                          270
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(12Q12) MUTATED                                  0     0
  DEL PEAK 20(12Q12) WILD-TYPE                                1     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q12) MUTATED                           0    49
  DEL PEAK 20(12Q12) WILD-TYPE                        14   327
D41V7, multiclass
                                  clus
vv                                 DEL PEAK 20(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    49
                                  clus
vv                                 DEL PEAK 20(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                              cls
clus                             0   1
  DEL PEAK 20(12Q12) MUTATED     0  48
  DEL PEAK 20(12Q12) WILD-TYPE  15 311
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 20(12Q12) MUTATED      0   48
  DEL PEAK 20(12Q12) WILD-TYPE   15  311
                        clus
vv                       DEL PEAK 20(12Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         48
                        clus
vv                       DEL PEAK 20(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                          311
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 21(13Q14.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.2) MUTATED    80  30
  DEL PEAK 21(13Q14.2) WILD-TYPE 244  41
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           110                            285 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            30                             41 
$`DEL PEAK 21(13Q14.2) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        46.65 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 
       10.29        18.84        10.92        19.96        30.31        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6392 
       15.75         7.79        18.02         6.74        13.38       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       14.99        10.36         7.96        18.94        44.02        25.91 
TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS 
        5.10        19.13        15.48        14.17        14.24        15.12 
TCGA-DU-A5TU TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
        3.65         2.70         7.23        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 
       67.46        41.13        57.93       130.78        47.77        17.98 
TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 
       34.36        18.77        14.93        13.58        20.61        14.96 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Z 
        9.67         7.04         7.04         4.21        10.59        10.78 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        7.82         8.81         0.13        17.42         6.54        24.26 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7616 
       60.03       154.19       107.93         4.57        17.29         0.23 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 
       31.69        14.96         0.10         2.96        39.09         0.23 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A614 
       23.61        31.43         0.10        16.04        15.72         2.70 
TCGA-HT-A617 TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-QH-A65S 
       16.14         8.32        40.18         5.23         2.30         2.53 
TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-S9-A6TV TCGA-S9-A6UA 
        4.11         2.96         2.20         4.73        18.77         5.85 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 
        7.92        19.63        12.59         4.21         9.37         8.12 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84R 
        5.00        49.45        50.76        19.36        40.83         9.44 
TCGA-TM-A84S TCGA-VM-A8CD 
        4.57         7.89 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       30.08        12.72        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5143 
       15.42        27.81        14.73        13.64        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 
        8.02        29.62         3.85        14.56        17.46         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        46.06        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 
       11.64       133.74        19.89        16.83         7.96         7.73 
TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       138.28       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
       90.77        30.67        26.30        94.32        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       21.40        16.96        12.59         4.96         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65        77.98         5.98        11.41        26.76         7.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5965 
       79.99       134.27        78.21        95.57        14.33        32.19 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 
       24.99        23.97        15.35        17.88        22.55        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        20.09        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60K 
       15.52        24.46         0.59         5.26         3.72         6.64 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        4.08        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03        16.54         3.75         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 
       59.18         4.01         5.03        29.85        23.18         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09        57.60        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93         1.71        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
        3.88         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 
        0.10         5.33        13.02         1.81         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       13.45        19.23        35.90         4.31         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V 
        2.37         4.11         5.88         1.28         5.75         4.83 
TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        7.79         4.18         3.16         0.59         6.31         3.91 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       59.38        62.17        69.07        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62        83.70       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW 
        6.15         3.39        14.27         8.19         2.04         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80        31.59        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84M 
       12.00        15.09        34.36        24.26        17.49        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       29.92        18.90        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10        26.79        10.95 

  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                        211.17                         182.33 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                         14.96                          15.09 
[1] "0.1 - 211.2 (15.0)" "0.0 - 182.3 (15.1)"
[1] "hr=" "1.8"
D42V2, continuous
D42V3, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    43  69
  DEL PEAK 21(13Q14.2) WILD-TYPE 133 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     43   69
  DEL PEAK 21(13Q14.2) WILD-TYPE  133  155
        clus
vv       DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  FEMALE                           43                            133
  MALE                             69                            155
[1] 2 2
[1] FALSE
D42V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 21(13Q14.2) MUTATED            47               30                35
  DEL PEAK 21(13Q14.2) WILD-TYPE          96               74               118
D42V5, multiclass
                   clus
vv                  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  ASTROCYTOMA                                 47                             96
  OLIGOASTROCYTOMA                            30                             74
  OLIGODENDROGLIOMA                           35                            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    31  81
  DEL PEAK 21(13Q14.2) WILD-TYPE  58 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     31   81
  DEL PEAK 21(13Q14.2) WILD-TYPE   58  230
     clus
vv    DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  NO                            31                             58
  YES                           81                            230
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(13Q14.2) MUTATED                                  1     1
  DEL PEAK 21(13Q14.2) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.2) MUTATED                           5   104
  DEL PEAK 21(13Q14.2) WILD-TYPE                         9   272
D42V7, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     104
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       272
[1] 4 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 21(13Q14.2) MUTATED     3 104
  DEL PEAK 21(13Q14.2) WILD-TYPE  12 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      3  104
  DEL PEAK 21(13Q14.2) WILD-TYPE   12  255
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 22(13Q14.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(13Q14.2) MUTATED    82  30
  DEL PEAK 22(13Q14.2) WILD-TYPE 242  41
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                           112                            283 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            30                             41 
$`DEL PEAK 22(13Q14.2) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        46.65 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 
       10.29        18.84        10.92        19.96        30.31        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6392 
       15.75         7.79        18.02         6.74        13.38       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       14.99        10.36         7.96        18.94        44.02        25.91 
TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS 
        5.10        19.13        15.48        14.17        14.24        15.12 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 
        3.65        12.20         2.70         7.23        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5962 
       50.14        67.46        41.13        57.93       130.78        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 
       17.98        34.36        18.77        14.93        13.58        20.61 
TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 
       14.96         9.67         7.04         7.04         4.21        10.59 
TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 
       10.78         7.82         8.81         0.13        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
       24.26        60.03       154.19       107.93         4.57        17.29 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 
       57.60         0.23        31.69        14.96         0.10         2.96 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8563 
       39.09         0.23        23.61        31.43         0.10        16.04 
TCGA-HT-8564 TCGA-HT-A614 TCGA-HT-A617 TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X 
       15.72         2.70        16.14         8.32        40.18         5.23 
TCGA-P5-A5EZ TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X8 
        2.30         2.53         4.11         2.96         2.20         4.73 
TCGA-S9-A6TV TCGA-S9-A6UA TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.77         5.85         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I 
        9.37         8.12         5.00        49.45        50.76        19.36 
TCGA-TM-A84L TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CD 
       40.83         9.44         4.57         7.89 

$`DEL PEAK 22(13Q14.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       30.08        12.72        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5143 
       15.42        27.81        14.73        13.64        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 
        8.02        29.62         3.85        14.56        17.46         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        46.06        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 
       11.64       133.74        19.89        16.83         7.96         7.73 
TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       138.28       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
       90.77        30.67        26.30        94.32        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S2 
       21.40        16.96        12.59         4.96         5.65         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5305 
       77.98         5.98        11.41        26.76         7.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5965 TCGA-FG-6690 
      134.27        78.21        95.57        14.33        32.19        24.99 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 
       23.97        15.35        17.88        22.55        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A6J1 
       24.46         0.59         5.26         3.72         6.64         4.08 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 
       22.95         5.23         0.13         0.10         6.67         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       16.54         3.75         6.38         7.10        75.19        59.18 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 
        4.01         5.03        29.85        23.18         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       45.99        56.09        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7693 
       44.68         6.05        42.74         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        6.90        14.53        39.48        19.23        50.63         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        11.28         1.64        16.24         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS 
        3.95         4.70         0.23        29.59         3.88         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 
       13.02         1.81         5.33        29.92        13.45        19.23 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
        4.73         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        5.88         1.28         5.75         4.83         7.79         4.18 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA 
        3.16         0.59         6.31         3.91         1.91         0.23 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
       14.27         8.19         2.04         3.58         4.04        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        48.39        12.00        15.09 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       34.36        24.26        17.49        16.50        29.92        18.90 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       12.00        33.07        30.08        13.51         0.10        26.79 
TCGA-VM-A8CH 
       10.95 

  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                        211.17                         182.33 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                         14.96                          15.09 
[1] "0.1 - 211.2 (15.0)" "0.0 - 182.3 (15.1)"
[1] "hr=" "1.8"
D43V2, continuous
D43V3, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED    44  70
  DEL PEAK 22(13Q14.2) WILD-TYPE 132 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED     44   70
  DEL PEAK 22(13Q14.2) WILD-TYPE  132  154
        clus
vv       DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  FEMALE                           44                            132
  MALE                             70                            154
[1] 2 2
[1] FALSE
D43V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 22(13Q14.2) MUTATED            48               31                35
  DEL PEAK 22(13Q14.2) WILD-TYPE          95               73               118
D43V5, multiclass
                   clus
vv                  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  ASTROCYTOMA                                 48                             95
  OLIGOASTROCYTOMA                            31                             73
  OLIGODENDROGLIOMA                           35                            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(13Q14.2) MUTATED    31  83
  DEL PEAK 22(13Q14.2) WILD-TYPE  58 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED     31   83
  DEL PEAK 22(13Q14.2) WILD-TYPE   58  228
     clus
vv    DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE
  NO                            31                             58
  YES                           83                            228
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(13Q14.2) MUTATED                                  1     1
  DEL PEAK 22(13Q14.2) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(13Q14.2) MUTATED                           5   106
  DEL PEAK 22(13Q14.2) WILD-TYPE                         9   270
D43V7, multiclass
                                  clus
vv                                 DEL PEAK 22(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     106
                                  clus
vv                                 DEL PEAK 22(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       270
[1] 4 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 22(13Q14.2) MUTATED     3 106
  DEL PEAK 22(13Q14.2) WILD-TYPE  12 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(13Q14.2) MUTATED      3  106
  DEL PEAK 22(13Q14.2) WILD-TYPE   12  253
                        clus
vv                       DEL PEAK 22(13Q14.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 22(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 23(13Q34) MUTATION ANALYSIS
D44V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(13Q34) MUTATED    62  23
  DEL PEAK 23(13Q34) WILD-TYPE 262  48
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          85                          310 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          23                           48 
$`DEL PEAK 23(13Q34) MUTATED`
TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DH-5140 TCGA-DH-A669 
       17.95         8.48        10.29        18.84        19.96        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6399 
       15.75         7.79        18.02        18.94       211.17        65.75 
TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 
        1.22        94.52       114.08        11.47       156.23        14.99 
TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 
       10.36        18.94        44.02         5.10        19.13        15.48 
TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 
       14.17        15.12         2.70         7.23        21.30       124.50 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       67.46        41.13       130.78        47.77        17.98        34.36 
TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L 
       14.93        13.58        20.61        14.96         7.04         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        4.21        10.59        10.78         7.82         8.81         0.13 
TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7611 TCGA-HT-7689 
       24.26        60.03         4.57        17.29        57.60        14.96 
TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7882 
        0.10         2.96         6.90        39.09         0.23         1.71 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A617 TCGA-HW-7489 TCGA-HW-7491 
       31.43         0.10        15.72        16.14         8.32        40.18 
TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY 
       19.00         5.23         2.30         4.11         2.96         2.20 
TCGA-QH-A6X8 TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 
        4.73         5.85        19.63        12.59         9.37         8.12 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84R TCGA-TM-A84S 
        5.00        49.45        50.76        19.36         9.44         4.57 
TCGA-VM-A8CD 
        7.89 

$`DEL PEAK 23(13Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        30.08        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.62        27.02        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       14.73        13.64        10.92        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        8.02        29.62         3.85        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 
       52.11        22.42        49.02        75.16        46.06        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 
        7.04        11.64       133.74        19.89        16.83         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        7.73        62.96       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        26.30         7.96        94.32 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP 
       23.74         3.98        20.68        21.40        16.96        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5302 
       77.98         5.98        11.41        26.76         7.13        50.14 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 
       79.99        57.93       134.27        78.21        95.57        14.33 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 
       32.19        18.77        24.99        23.97        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 
        3.72         9.67         6.64         4.08        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        0.13         0.10         6.67         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        56.09         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 
        0.10        31.69         0.10        17.52        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       19.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 
        0.13         3.68         5.33         2.93        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        16.04         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 
        1.81         5.33        29.92        13.45        19.23        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV 
        7.89         9.67         6.61        42.77         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        6.71         1.64         2.37         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CZ 
        5.75         2.53         4.83         7.79         4.18         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        0.59         6.31         3.91         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW 
       14.27         7.92         4.21         8.19         2.04         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80        31.59        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       12.00        15.09        34.36        24.26        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       16.50        29.92        18.90        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10        26.79        10.95 

  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      211.17                       182.33 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      14.960                       15.125 
[1] "0.1 - 211.2 (15.0)" "0.0 - 182.3 (15.1)"
[1] "hr=" "1.8"
D44V2, continuous
D44V3, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    34  52
  DEL PEAK 23(13Q34) WILD-TYPE 142 172
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     34   52
  DEL PEAK 23(13Q34) WILD-TYPE  142  172
        clus
vv       DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  FEMALE                         34                          142
  MALE                           52                          172
[1] 2 2
[1] FALSE
D44V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 23(13Q34) MUTATED            31               21                34
  DEL PEAK 23(13Q34) WILD-TYPE         112               83               119
D44V5, multiclass
                   clus
vv                  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  ASTROCYTOMA                               31                          112
  OLIGOASTROCYTOMA                          21                           83
  OLIGODENDROGLIOMA                         34                          119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    23  63
  DEL PEAK 23(13Q34) WILD-TYPE  66 248
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     23   63
  DEL PEAK 23(13Q34) WILD-TYPE   66  248
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                          23                           66
  YES                         63                          248
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(13Q34) MUTATED                                  1     1
  DEL PEAK 23(13Q34) WILD-TYPE                                0     1
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(13Q34) MUTATED                           3    80
  DEL PEAK 23(13Q34) WILD-TYPE                        11   296
D44V7, multiclass
                                  clus
vv                                 DEL PEAK 23(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    80
                                  clus
vv                                 DEL PEAK 23(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     296
[1] 4 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 23(13Q34) MUTATED     3  79
  DEL PEAK 23(13Q34) WILD-TYPE  12 280
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED      3   79
  DEL PEAK 23(13Q34) WILD-TYPE   12  280
                        clus
vv                       DEL PEAK 23(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         79
                        clus
vv                       DEL PEAK 23(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          280
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 24(14Q24.3) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(14Q24.3) MUTATED    62  30
  DEL PEAK 24(14Q24.3) WILD-TYPE 262  41
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                            92                            303 
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                            30                             41 
$`DEL PEAK 24(14Q24.3) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-6668 TCGA-DB-5279 
        4.70         7.69        43.89        10.62         8.02        44.52 
TCGA-DB-A4XA TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       10.29        11.01        18.84        19.96        30.31        14.40 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6397 
       18.02         6.74         6.81        17.49        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6403 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       65.75        11.64       114.08         7.73        11.47        62.96 
TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7302 
       14.99         6.54        26.30        10.36        18.94        60.30 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R 
        5.10        23.74        19.13         5.98        26.76        21.30 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       41.13        79.99        57.93        95.57       130.78        14.33 
TCGA-FG-5963 TCGA-FG-7643 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A6J3 
       17.98        20.09        15.52        24.46         9.67        10.59 
TCGA-HT-7477 TCGA-HT-7603 TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7689 
       24.26        23.18        17.29         0.23        31.69        14.96 
TCGA-HT-7858 TCGA-HT-7902 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       50.63        31.43         4.70        16.04        15.72         0.23 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-A5KK TCGA-IK-8125 
       13.02        16.14         5.33         8.32         7.89        42.77 
TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CZ 
        0.23         1.64         2.30         4.18         2.96         3.16 
TCGA-QH-A6X4 TCGA-R8-A6MK TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6WD TCGA-S9-A6WM 
        6.31        88.83        59.38        62.17        62.37         9.30 
TCGA-S9-A6WP TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7QX TCGA-S9-A7QZ 
        6.15        19.63         9.37         8.19         4.04        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A84I TCGA-TM-A84Q 
       10.39        87.09        31.59        49.45        19.36        18.90 
TCGA-VM-A8CB TCGA-VM-A8CD 
        0.10         7.89 

$`DEL PEAK 24(14Q24.3) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       18.15        64.64        40.18         0.10        21.01         9.96 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        6.38        17.69        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        7.56         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        46.65        50.17        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       30.08        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        12.59        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5144 
       27.81        14.73        13.64        10.92        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 
       30.21        29.62        15.75         7.79         3.85        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 
       17.46        13.38         8.45       182.33        18.94        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6401 
      211.17        52.11        22.42        49.02         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
        7.04       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      156.23       138.28       105.21         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       30.67         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       23.31        41.98         2.76         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 
       77.98         7.23        11.41         7.13       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       67.46       134.27        78.21        47.77        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        20.09        14.96        11.87         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        3.72         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
       60.03       154.19         4.01         5.03        29.85       107.93 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       42.74         0.10         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93         1.71        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50         3.95         0.23        29.59 
TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        3.88        10.49         0.13         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 
        5.33         2.70         1.81        29.92        13.45        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       17.82        10.55         9.67         6.61        19.00         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        4.73         6.71         2.37         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY 
        5.75         2.53         4.83         7.79         4.11         2.20 
TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        0.59         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       94.03        32.65        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE 
        9.86        94.62        83.70         5.85       103.76        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        70.65        10.88         9.04         7.59 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J2 
        3.39        14.27         7.92        12.59         4.21         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z 
        8.12         3.58        18.21        17.42        83.80         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        24.26        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       29.92         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51        26.79        10.95 

  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE 
                         15.88                          14.70 
[1] "0.1 - 130.8 (15.9)" "0.0 - 211.2 (14.7)"
[1] "hr=" "2.6"
D45V2, continuous
D45V3, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q24.3) MUTATED    46  48
  DEL PEAK 24(14Q24.3) WILD-TYPE 130 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q24.3) MUTATED     46   48
  DEL PEAK 24(14Q24.3) WILD-TYPE  130  176
        clus
vv       DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE
  FEMALE                           46                            130
  MALE                             48                            176
[1] 2 2
[1] FALSE
D45V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 24(14Q24.3) MUTATED            42               23                29
  DEL PEAK 24(14Q24.3) WILD-TYPE         101               81               124
D45V5, multiclass
                   clus
vv                  DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE
  ASTROCYTOMA                                 42                            101
  OLIGOASTROCYTOMA                            23                             81
  OLIGODENDROGLIOMA                           29                            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q24.3) MUTATED    22  72
  DEL PEAK 24(14Q24.3) WILD-TYPE  67 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q24.3) MUTATED     22   72
  DEL PEAK 24(14Q24.3) WILD-TYPE   67  239
     clus
vv    DEL PEAK 24(14Q24.3) MUTATED DEL PEAK 24(14Q24.3) WILD-TYPE
  NO                            22                             67
  YES                           72                            239
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(14Q24.3) MUTATED                                  1     1
  DEL PEAK 24(14Q24.3) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(14Q24.3) MUTATED                           4    86
  DEL PEAK 24(14Q24.3) WILD-TYPE                        10   290
D45V7, multiclass
                                  clus
vv                                 DEL PEAK 24(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 24(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q24.3) MUTATED     2  84
  DEL PEAK 24(14Q24.3) WILD-TYPE  13 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q24.3) MUTATED      2   84
  DEL PEAK 24(14Q24.3) WILD-TYPE   13  275
                        clus
vv                       DEL PEAK 24(14Q24.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 24(14Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            275
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 25(15Q21.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q21.3) MUTATED    34  13
  DEL PEAK 25(15Q21.3) WILD-TYPE 290  58
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                            47                            348 
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                            13                             58 
$`DEL PEAK 25(15Q21.3) MUTATED`
TCGA-CS-5397 TCGA-DB-5274 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XH 
        6.38        75.25        44.52        78.28        10.29        12.59 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DU-6393 TCGA-DU-6396 TCGA-DU-6400 
       19.96        30.31        30.21        52.11        75.16         1.22 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-8158 TCGA-DU-A6S3 TCGA-DU-A76R TCGA-E1-5311 
       62.96        14.99         5.10         2.70        21.30       134.27 
TCGA-FG-6688 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-HT-7468 
       18.77        15.35        17.88         5.26        10.59         6.67 
TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7875 TCGA-HT-8011 
       75.19        17.29        45.99         0.23         0.33        16.24 
TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-8563 TCGA-HT-A618 TCGA-HW-7489 TCGA-P5-A5EZ 
        9.40        12.23        16.04         5.33         8.32         2.30 
TCGA-QH-A65S TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-S9-A6TS TCGA-S9-A6U2 TCGA-S9-A6WD 
        2.53         4.73        88.83        62.17        15.62        62.37 
TCGA-S9-A6WI TCGA-S9-A7J0 TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84F 
       70.65         9.37        13.02        25.32        50.76 

$`DEL PEAK 25(15Q21.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        6.61       122.73        81.96        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       50.17        36.56        30.08        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.84        18.38        72.95        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       10.92        31.82        14.40         8.02        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
       15.16       211.17        22.42        49.02        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      138.28       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 
        4.96         3.65         5.65        12.20         8.65        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
        7.23         5.98        11.41        26.76         7.13       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
       50.14        67.46        41.13        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 
       32.19        14.93        24.99        23.97        13.58        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
        4.08        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
       17.42         6.54        24.26         6.38         7.10        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 
      107.93         4.57         3.16        22.06        56.09        57.60 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       31.43         1.64        63.55        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 
        1.81        16.14        29.92        13.45        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         1.28         5.75         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6ML 
        6.31         3.91         1.91         0.23         5.03        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        59.38        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 
       22.49        21.63        16.37        11.31        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62        83.70         5.85       103.76        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        18.21 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        35.93        22.59        48.39        12.00        15.09 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 

  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                          0.23                           0.03 
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                        134.27                         211.17 
  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE 
                        16.040                         14.715 
[1] "0.2 - 134.3 (16.0)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q21.3) MUTATED    21  27
  DEL PEAK 25(15Q21.3) WILD-TYPE 155 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.3) MUTATED     21   27
  DEL PEAK 25(15Q21.3) WILD-TYPE  155  197
        clus
vv       DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE
  FEMALE                           21                            155
  MALE                             27                            197
[1] 2 2
[1] FALSE
D46V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 25(15Q21.3) MUTATED            17               12                19
  DEL PEAK 25(15Q21.3) WILD-TYPE         126               92               134
D46V5, multiclass
                   clus
vv                  DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE
  ASTROCYTOMA                                 17                            126
  OLIGOASTROCYTOMA                            12                             92
  OLIGODENDROGLIOMA                           19                            134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q21.3) MUTATED    12  36
  DEL PEAK 25(15Q21.3) WILD-TYPE  77 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.3) MUTATED     12   36
  DEL PEAK 25(15Q21.3) WILD-TYPE   77  275
     clus
vv    DEL PEAK 25(15Q21.3) MUTATED DEL PEAK 25(15Q21.3) WILD-TYPE
  NO                            12                             77
  YES                           36                            275
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(15Q21.3) MUTATED                                  0     0
  DEL PEAK 25(15Q21.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(15Q21.3) MUTATED                           1    46
  DEL PEAK 25(15Q21.3) WILD-TYPE                        13   330
D46V7, multiclass
                                  clus
vv                                 DEL PEAK 25(15Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      46
                                  clus
vv                                 DEL PEAK 25(15Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q21.3) MUTATED     0  47
  DEL PEAK 25(15Q21.3) WILD-TYPE  15 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q21.3) MUTATED      0   47
  DEL PEAK 25(15Q21.3) WILD-TYPE   15  312
                        clus
vv                       DEL PEAK 25(15Q21.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 25(15Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            312
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 26(18Q23) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(18Q23) MUTATED    52  12
  DEL PEAK 26(18Q23) WILD-TYPE 272  59
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          64                          331 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          12                           59 
$`DEL PEAK 26(18Q23) MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 
        9.96        12.43         7.56        47.93        44.52        36.56 
TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 
       27.02        72.95        12.59        11.01        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5870 
       30.21        29.62        14.56        17.46         8.45       182.33 
TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7300 
       52.11        94.52       138.28         6.54       117.40        62.01 
TCGA-DU-8158 TCGA-DU-A5TT TCGA-E1-5307 TCGA-FG-8185 TCGA-FG-8188 TCGA-HT-7476 
        5.10         4.96        57.93        14.24        14.96         6.54 
TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 
       75.19        17.29         0.23        31.69         2.96         0.23 
TCGA-HT-7873 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-7489 
       23.61         3.88        15.72         0.10        16.14         8.32 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-P5-A5EX TCGA-QH-A65R 
       40.18         8.94        10.55         6.61         1.64         5.75 
TCGA-QH-A65Z TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6WD TCGA-S9-A6WH 
        4.11        62.17        28.27        28.14        62.37        22.92 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 
       10.88         9.30         9.04         6.15        18.21        10.39 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CA 
       34.36        19.36        17.49        13.51 

$`DEL PEAK 26(18Q23) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 
       81.96        75.25        72.92        46.65        50.17        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF 
       30.08        10.29        12.72        27.62        18.84        18.38 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       14.73        13.64        10.92        31.82        14.40         8.02 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 
       15.75         7.79         3.85        18.02         6.74        13.38 
TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 
        6.81        18.94        17.49        15.16       211.17        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
        7.96         7.73        11.47        62.96       156.23        14.99 
TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      105.21         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 
        7.96        94.32        18.94        44.02        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13        21.30       124.50        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99       134.27        78.21        95.57       130.78        14.33 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        16.01        20.09 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
        3.75        17.42        24.26         6.38         7.10        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      107.93         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59        16.04         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07        14.70         5.33         2.70        13.02         1.81 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 
        5.33        29.92        13.45        19.23        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 
        8.61        19.59        17.82         7.89         9.67        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       42.77         5.23         4.73         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         1.28         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.18         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE 
        9.86        94.62        83.70         5.85       103.76        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       70.55        70.65         7.59         3.39        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 
        8.12         3.58         4.04        13.02        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59         5.00        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       22.59        48.39        12.00        15.09        50.76        24.26 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        33.07        30.08         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                      182.33                       211.17 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                       15.93                        14.93 
[1] "0.1 - 182.3 (15.9)" "0.0 - 211.2 (14.9)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED    25  39
  DEL PEAK 26(18Q23) WILD-TYPE 151 185
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED     25   39
  DEL PEAK 26(18Q23) WILD-TYPE  151  185
        clus
vv       DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  FEMALE                         25                          151
  MALE                           39                          185
[1] 2 2
[1] FALSE
D47V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 26(18Q23) MUTATED            23               13                28
  DEL PEAK 26(18Q23) WILD-TYPE         120               91               125
D47V5, multiclass
                   clus
vv                  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  ASTROCYTOMA                               23                          120
  OLIGOASTROCYTOMA                          13                           91
  OLIGODENDROGLIOMA                         28                          125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED    15  49
  DEL PEAK 26(18Q23) WILD-TYPE  74 262
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED     15   49
  DEL PEAK 26(18Q23) WILD-TYPE   74  262
     clus
vv    DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  NO                          15                           74
  YES                         49                          262
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(18Q23) MUTATED                                  1     0
  DEL PEAK 26(18Q23) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(18Q23) MUTATED                           1    60
  DEL PEAK 26(18Q23) WILD-TYPE                        13   316
D47V7, multiclass
                                  clus
vv                                 DEL PEAK 26(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    60
                                  clus
vv                                 DEL PEAK 26(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED     3  55
  DEL PEAK 26(18Q23) WILD-TYPE  12 304
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED      3   55
  DEL PEAK 26(18Q23) WILD-TYPE   12  304
                        clus
vv                       DEL PEAK 26(18Q23) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         55
                        clus
vv                       DEL PEAK 26(18Q23) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          304
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 27(19Q13.42) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(19Q13.42) MUTATED   182  31
  DEL PEAK 27(19Q13.42) WILD-TYPE 142  40
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            213                             182 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                             31                              40 
$`DEL PEAK 27(19Q13.42) MUTATED`
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 
       43.89        18.15        10.62        64.64         0.10         9.96 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
       17.95         8.48         8.02         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA 
       75.25        47.93        46.65        50.17        44.52        10.29 
TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       12.72        72.95        12.59        11.01        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5140 TCGA-DH-5141 
       16.08        27.81        14.73        13.64        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        3.85        14.56        17.46         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        52.11        22.42        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 
        1.22       114.08         7.96         7.73        62.96       138.28 
TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 
       14.99       117.40        90.77        30.67        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8166 
       62.01        60.30        41.98         2.76        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       14.17        14.24        15.12         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 
        5.98        21.30       124.50        50.14        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       34.36        32.19        24.99        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MX 
       20.61        16.01        20.09        14.96        24.46         3.72 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A713 
        6.64         4.21         4.08        10.59        22.95         5.23 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7475 
        0.10         6.67         7.82         0.13         0.03        17.42 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7605 TCGA-HT-7606 
       75.19        59.18       154.19         5.03         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        56.09         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 
       16.24        44.68         0.10        31.69        14.96         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 
        6.90        14.53        39.09         0.23        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 
        0.13         2.93         1.64         9.40         6.25         3.95 
TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 
        0.23        16.04        15.72        10.49         0.07        13.02 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 
        5.33        29.92        13.45        40.18         4.31         8.94 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EX 
       17.82        10.55        42.77         5.23         0.23         1.64 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        2.30         4.11         1.28         5.75         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        4.11         2.20         3.16         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TV 
        1.91        88.83        94.03        32.65        59.38        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 
       28.27        28.14        22.49        21.63        16.37        15.62 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI 
       20.05       103.76        62.37        72.59        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
       10.88         9.04         6.15        14.27         7.92        12.59 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04         8.12         3.58        18.21        13.02 
TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84J TCGA-TM-A84M 
       31.59        25.32        12.00        34.36        17.49        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       13.51         0.10        26.79 

$`DEL PEAK 27(19Q13.42) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 
        4.70         7.69        40.18        21.01         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5276 TCGA-DB-5280 
       23.84        12.43         7.56         7.40        72.92        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        30.08        27.62        27.02        18.84        18.38 
TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5143 TCGA-DU-5847 TCGA-DU-5852 
       18.84        15.42        10.92        14.40        18.02         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6401 
       13.38         8.45        18.94       211.17        49.02        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7019 
       11.47       156.23       105.21         6.54         8.84        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-8158 
       10.36         7.96        44.02        25.91        23.31         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TR 
       23.74         3.98        20.68        19.13        15.48        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K 
        4.96         3.65         5.65        12.20         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5303 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-6688 
       26.76         7.13        67.46        57.93        17.98        18.77 
TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       14.93        23.97        13.58        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MY 
       14.24        11.87        15.52         0.59         5.26         9.67 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Z TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7473 
        7.04         7.04        10.78         0.13         8.81        16.54 
TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 
        3.75         6.54        24.26         6.38         7.10        60.03 
TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7611 TCGA-HT-7676 
        4.01        29.85        23.18       107.93        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
        0.76         6.05        42.74         0.10         0.10        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 
       39.48        19.23        50.63         0.49        23.61         3.68 
TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 
        5.33         1.71        11.28        31.43        16.24        63.55 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01        12.23         0.10         0.46         2.50 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5RA 
        4.70        29.59         3.88         0.23         0.13        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7489 
        0.10         5.33         2.70         1.81        16.14         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       19.23        35.90         8.61        19.59         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F1 
        6.61        19.00         4.73         6.71         2.37         5.88 
TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A6XC 
        2.53         4.18         2.96         0.59         0.23         5.03 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       62.17        69.07        11.31         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IX 
        5.85        70.55         9.30         7.59         3.39        19.63 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.21         9.37         4.04        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80         5.00        49.45        35.93        22.59        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-VM-A8C9 
       15.09        50.76        24.26        19.36        40.83        30.08 
TCGA-VM-A8CD TCGA-VM-A8CH 
        7.89        10.95 

  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                         182.33                          211.17 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                         15.750                          13.165 
[1] "0.0 - 182.3 (15.8)" "0.1 - 211.2 (13.2)"
[1] "hr=" "1.9"
D48V2, continuous
D48V3, binary
                                 cls
clus                                0   1
  DEL PEAK 27(19Q13.42) MUTATED    94 122
  DEL PEAK 27(19Q13.42) WILD-TYPE  82 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED     94  122
  DEL PEAK 27(19Q13.42) WILD-TYPE   82  102
        clus
vv       DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE
  FEMALE                            94                              82
  MALE                             122                             102
[1] 2 2
[1] FALSE
D48V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 27(19Q13.42) MUTATED            43               49
  DEL PEAK 27(19Q13.42) WILD-TYPE         100               55
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 27(19Q13.42) MUTATED                 124
  DEL PEAK 27(19Q13.42) WILD-TYPE                29
D48V5, multiclass
                   clus
vv                  DEL PEAK 27(19Q13.42) MUTATED
  ASTROCYTOMA                                  43
  OLIGOASTROCYTOMA                             49
  OLIGODENDROGLIOMA                           124
                   clus
vv                  DEL PEAK 27(19Q13.42) WILD-TYPE
  ASTROCYTOMA                                   100
  OLIGOASTROCYTOMA                               55
  OLIGODENDROGLIOMA                              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                                 cls
clus                                0   1
  DEL PEAK 27(19Q13.42) MUTATED    48 168
  DEL PEAK 27(19Q13.42) WILD-TYPE  41 143
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED     48  168
  DEL PEAK 27(19Q13.42) WILD-TYPE   41  143
     clus
vv    DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE
  NO                             48                              41
  YES                           168                             143
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(19Q13.42) MUTATED                                  0     1
  DEL PEAK 27(19Q13.42) WILD-TYPE                                1     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(19Q13.42) MUTATED                           7   202
  DEL PEAK 27(19Q13.42) WILD-TYPE                         7   174
D48V7, multiclass
                                  clus
vv                                 DEL PEAK 27(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                      202
                                  clus
vv                                 DEL PEAK 27(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                      7
  WHITE                                                        174
[1] 4 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 27(19Q13.42) MUTATED     7 193
  DEL PEAK 27(19Q13.42) WILD-TYPE   8 166
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED      7  193
  DEL PEAK 27(19Q13.42) WILD-TYPE    8  166
                        clus
vv                       DEL PEAK 27(19Q13.42) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           193
                        clus
vv                       DEL PEAK 27(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             166
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 28(22Q13.31) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(22Q13.31) MUTATED    37  22
  DEL PEAK 28(22Q13.31) WILD-TYPE 287  49
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             59                             336 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             22                              49 
$`DEL PEAK 28(22Q13.31) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6186 TCGA-DB-5273 TCGA-DB-5277 
       18.15        40.18         6.38        17.69        81.96        46.65 
TCGA-DB-A4XB TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 
       12.72        11.01        18.84        30.21        18.02         6.74 
TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-7007 TCGA-DU-7008 
       13.38        65.75         7.04       133.74        62.96       156.23 
TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
       10.36        18.94        41.98         5.10        23.74        19.13 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76K 
       15.48        14.24         4.96         3.65        12.20        11.41 
TCGA-DU-A76L TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-7643 TCGA-FG-A4MY 
       26.76        67.46        41.13       130.78        20.09         9.67 
TCGA-FG-A60L TCGA-HT-7477 TCGA-HT-7611 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 
        7.04        24.26        57.60        42.74        31.69         0.10 
TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK TCGA-P5-A5F6 
        0.49         2.70        16.14         5.33         7.89         1.28 
TCGA-QH-A6CS TCGA-S9-A6TS TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7R2 
        4.18        62.17         5.85        19.63         9.37        10.39 
TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84G TCGA-VM-A8CD 
       83.80         5.00        12.00        34.36         7.89 

$`DEL PEAK 28(22Q13.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       21.01         9.96        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 
        7.56         8.02         7.40         6.61       122.73        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       30.08        10.29        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        12.59        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
        3.85        14.56        17.46         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 
       49.02        75.16        46.06         1.22        87.45        11.64 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        26.30         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       44.02        62.01        25.91        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TR 
        3.98        20.68        21.40        16.96        14.17        12.59 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       15.12         5.65         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5305 
        5.98         7.13        21.30       124.50        50.14        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 
       57.93       134.27        78.21        95.57        14.33        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        7.04         6.64         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        6.05         0.10        14.96         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       13.02         1.81        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        10.55         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       15.62        20.05         9.86        94.62        83.70       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        14.27 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        7.92        12.59         4.21         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 
        3.58         4.04        18.21        13.02        87.09        17.42 
TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       33.07        30.08        13.51         0.10        26.79        10.95 

  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                         156.23                          211.17 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                         16.140                          14.945 
[1] "0.1 - 156.2 (16.1)" "0.0 - 211.2 (14.9)"
[1] "hr=" "2.2"
D49V2, continuous
D49V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(22Q13.31) MUTATED    24  35
  DEL PEAK 28(22Q13.31) WILD-TYPE 152 189
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED     24   35
  DEL PEAK 28(22Q13.31) WILD-TYPE  152  189
        clus
vv       DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE
  FEMALE                            24                             152
  MALE                              35                             189
[1] 2 2
[1] FALSE
D49V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 28(22Q13.31) MUTATED            32               13
  DEL PEAK 28(22Q13.31) WILD-TYPE         111               91
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 28(22Q13.31) MUTATED                  14
  DEL PEAK 28(22Q13.31) WILD-TYPE               139
D49V5, multiclass
                   clus
vv                  DEL PEAK 28(22Q13.31) MUTATED
  ASTROCYTOMA                                  32
  OLIGOASTROCYTOMA                             13
  OLIGODENDROGLIOMA                            14
                   clus
vv                  DEL PEAK 28(22Q13.31) WILD-TYPE
  ASTROCYTOMA                                   111
  OLIGOASTROCYTOMA                               91
  OLIGODENDROGLIOMA                             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(22Q13.31) MUTATED    14  45
  DEL PEAK 28(22Q13.31) WILD-TYPE  75 266
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED     14   45
  DEL PEAK 28(22Q13.31) WILD-TYPE   75  266
     clus
vv    DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE
  NO                             14                              75
  YES                            45                             266
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(22Q13.31) MUTATED                                  1     0
  DEL PEAK 28(22Q13.31) WILD-TYPE                                0     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(22Q13.31) MUTATED                           1    57
  DEL PEAK 28(22Q13.31) WILD-TYPE                        13   319
D49V7, multiclass
                                  clus
vv                                 DEL PEAK 28(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       57
                                  clus
vv                                 DEL PEAK 28(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        319
[1] 4 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 28(22Q13.31) MUTATED     1  53
  DEL PEAK 28(22Q13.31) WILD-TYPE  14 306
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED      1   53
  DEL PEAK 28(22Q13.31) WILD-TYPE   14  306
                        clus
vv                       DEL PEAK 28(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 28(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  14
  NOT HISPANIC OR LATINO                             306
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 29(XQ21.1) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 29(XQ21.1) MUTATED    38  15
  DEL PEAK 29(XQ21.1) WILD-TYPE 286  56
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           53                           342 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           15                            56 
$`DEL PEAK 29(XQ21.1) MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF 
       12.43         7.56        47.93        46.65        44.52        18.38 
TCGA-DB-A4XH TCGA-DB-A64W TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-6404 TCGA-DU-6410 
       12.59        13.64        19.96        18.02       133.74         7.96 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8158 
       11.47       156.23        14.99        30.67        94.32         5.10 
TCGA-DU-8168 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-5311 TCGA-EZ-7264 
       14.17         5.98        21.30        50.14       134.27        14.33 
TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7616 
       34.36         4.21        10.59         7.82         0.13         0.23 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7692 TCGA-HW-7491 TCGA-HW-8321 TCGA-IK-7675 
       31.69         0.10         2.96        40.18        19.59        19.00 
TCGA-KT-A74X TCGA-P5-A5F6 TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-QH-A6X9 
        5.23         1.28         4.11         6.31         4.73         1.91 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7QW TCGA-S9-A89Z 
       69.07        18.77         6.15         7.92         3.58         5.00 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84I TCGA-VM-A8C8 TCGA-VM-A8CD 
       25.32        48.39        19.36        33.07         7.89 

$`DEL PEAK 29(XQ21.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
      122.73        81.96        75.25        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       18.84        72.95        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DH-5141 
       16.08        15.42        27.81        14.73        10.92        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79         3.85        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 
       65.75         1.22        87.45         7.04        11.64        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 
       16.83        94.52       114.08         7.73        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         7.23        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        7.13       124.50        67.46        41.13        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 
       78.21        95.57       130.78        47.77        17.98        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        6.64         7.04         4.08        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.13         0.10         6.67         8.81         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09        57.60        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 
       19.23        35.90         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 
       10.55         7.89         9.67         6.61        42.77         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        5.88         5.75         2.53         4.83         7.79         4.18 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6XA 
        2.96         2.20         3.16         0.59         3.91         0.23 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.30         9.04         7.59         3.39        14.27 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
        8.12         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       17.42        83.80        31.59        49.45        35.93        22.59 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        24.26        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08        13.51         0.10        26.79        10.95 

  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                       14.170                        15.105 
[1] "0.1 - 156.2 (14.2)" "0.0 - 211.2 (15.1)"
[1] "hr=" "1.6"
D50V2, continuous
D50V3, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED    25  30
  DEL PEAK 29(XQ21.1) WILD-TYPE 151 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED     25   30
  DEL PEAK 29(XQ21.1) WILD-TYPE  151  194
        clus
vv       DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  FEMALE                          25                           151
  MALE                            30                           194
[1] 2 2
[1] FALSE
D50V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 29(XQ21.1) MUTATED            20               11                24
  DEL PEAK 29(XQ21.1) WILD-TYPE         123               93               129
D50V5, multiclass
                   clus
vv                  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  ASTROCYTOMA                                20                           123
  OLIGOASTROCYTOMA                           11                            93
  OLIGODENDROGLIOMA                          24                           129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED    12  43
  DEL PEAK 29(XQ21.1) WILD-TYPE  77 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED     12   43
  DEL PEAK 29(XQ21.1) WILD-TYPE   77  268
     clus
vv    DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  NO                           12                            77
  YES                          43                           268
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(XQ21.1) MUTATED                                  0     0
  DEL PEAK 29(XQ21.1) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(XQ21.1) MUTATED                           0    54
  DEL PEAK 29(XQ21.1) WILD-TYPE                        14   322
D50V7, multiclass
                                  clus
vv                                 DEL PEAK 29(XQ21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK 29(XQ21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED     1  50
  DEL PEAK 29(XQ21.1) WILD-TYPE  14 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED      1   50
  DEL PEAK 29(XQ21.1) WILD-TYPE   14  309
                        clus
vv                       DEL PEAK 29(XQ21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK 29(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           309
[1] 2 2
[1] FALSE
