[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/11541557/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/10686104/transformed.cor.cli.txt"

nPatients in clinical file=433, in cluster file=289, common to both=286
[1] "Reduce the number of clustering variables from 38 to 37."
[1]  37 286
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           218             68 
  IDH1 MUTATED IDH1 WILD-TYPE 
           218             68 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           145            141 
  TP53 MUTATED TP53 WILD-TYPE 
           145            141 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
           118            168 
  ATRX MUTATED ATRX WILD-TYPE 
           118            168 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           53           233 
  CIC MUTATED CIC WILD-TYPE 
           53           233 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              29              257 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              29              257 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            12            274 
  IDH2 MUTATED IDH2 WILD-TYPE 
            12            274 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             26             260 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             26             260 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           19           267 
  NF1 MUTATED NF1 WILD-TYPE 
           19           267 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              273 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              273 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              8             278 
  STK19 MUTATED STK19 WILD-TYPE 
              8             278 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            273 
  PTEN MUTATED PTEN WILD-TYPE 
            13            273 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              261 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              261 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              274 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              274 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            16            270 
  EGFR MUTATED EGFR WILD-TYPE 
            16            270 
[1] "GAGE2B MUTATION ANALYSIS"
[1] 3
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               4              282 
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               4              282 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               5              281 
  CREBZF MUTATED CREBZF WILD-TYPE 
               5              281 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
              8             278 
  TCF12 MUTATED TCF12 WILD-TYPE 
              8             278 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               273 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               273 
[1] "VAV3 MUTATION ANALYSIS"
[1] 3
  VAV3 MUTATED VAV3 WILD-TYPE 
             8            278 
  VAV3 MUTATED VAV3 WILD-TYPE 
             8            278 
[1] "TMEM216 MUTATION ANALYSIS"
[1] 3
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               283 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               283 
[1] "ROBO3 MUTATION ANALYSIS"
[1] 3
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             282 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             282 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            281 
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            281 
[1] "HTRA2 MUTATION ANALYSIS"
[1] 3
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              4             282 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              4             282 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              282 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              282 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               7              279 
  FAM47C MUTATED FAM47C WILD-TYPE 
               7              279 
[1] "PLCG1 MUTATION ANALYSIS"
[1] 3
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4             282 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4             282 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            282 
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            282 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3              283 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3              283 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               3              283 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               3              283 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
             9            277 
  BCOR MUTATED BCOR WILD-TYPE 
             9            277 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             3            283 
  SRPX MUTATED SRPX WILD-TYPE 
             3            283 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              5             281 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              5             281 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              282 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              282 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
              5             281 
  NIPBL MUTATED NIPBL WILD-TYPE 
              5             281 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              13              273 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              13              273 
[1] "TRIP12 MUTATION ANALYSIS"
[1] 3
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5              281 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5              281 
[1] "KIAA0664 MUTATION ANALYSIS"
[1] 3
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                281 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                281 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 286 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
         225         2493         2289         1458         2218         1419 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
        1526         1354         1112         2381          915          313 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
         387          840          822          573          559         2219 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
         383          335          573          511          182          489 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
         469          846          448          415          332           NA 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66F 
         968          922          438          244         1279          523 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
         548          443          531           NA          407          257 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
         207         5546          576          532          461         1585 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
         682         1491         2286         1401           NA           NA 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 
        2660          214           NA           NA          605           NA 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
        3470          242          235           NA           NA         4752 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
        4206           NA           NA           NA         2761           NA 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
         800           NA           NA         2869           NA           NA 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
          NA           NA         1834           NA         1277           84 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
          NA           NA          121          629          651          582 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
         516          471          431          433          383          460 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 TCGA-E1-5303 
         151          111          172          371         1525         2052 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
        1251         2433         1762         4084         2379         2907 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        3978          436         1453          547         1045          979 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
         571          454          760          729          413          467 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
         544         1219          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          685 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
         472         1164          326          160          569          721 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
         449          542            4            3          203          238 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
         268            4            1          503          114          530 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
         199          738          194          216         2287         1800 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
        1826         4690          122          153          908          705 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
        3283          139          526           NA          671         1399 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
        1706         1752           NA          434            5          494 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
          23         1359          184         1300            3          964 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
         455            3            3           90          533          210 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
         442         1201          585         1189            7         1540 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
          15          718         1130           10            4          112 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
         162           89           52          343          956           50 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
         494          286           NA            3          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-8558 TCGA-HT-8563 
         143            7          900          118           52          488 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
         478            7          319            4          426            2 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
         447            3           NA           82          396           55 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
         491          162          194          910          409          253 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
         585         1222          131          660          657          596 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
         542          619          240          633          630           NA 
TCGA-IK-8125 TCGA-P5-A5ET TCGA-P5-A5EU TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
        1301           NA           NA            7          204           50 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
          72           70          125          179          232           23 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
          39           77          147          125 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=223,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=12,	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 286 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=56, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = IDH1 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED   184  32
  IDH1 WILD-TYPE  41  27
  IDH1 MUTATED IDH1 WILD-TYPE 
           216             68 
  IDH1 MUTATED IDH1 WILD-TYPE 
            32             27 
$`IDH1 MUTATED`
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-6665 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.95        12.43         8.48         7.56 
TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        8.02        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-A4XH 
       12.72        27.62        27.02        18.84        18.38        12.59 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       11.01        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       14.73        13.64        10.92        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
       42.05        17.19        17.46        13.38         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 
       75.16        46.06         1.22        87.45        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        62.96       156.23       138.28        14.99 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       90.77        30.67        26.30        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8163 
       62.01        25.91        60.30        23.31        41.98        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-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       15.12         3.65         5.65        50.14        67.46        41.13 
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-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       47.77        34.36        32.19        14.93        24.99        23.97 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8182 
       15.35        17.88        40.08        22.55        20.61        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        20.09        14.96        15.52        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 
       18.71        23.70        14.76        17.82         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42        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-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7855 TCGA-HT-7858 
        2.96        17.52         6.90        14.53        19.23        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-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 
        2.93        11.28        31.43         1.64         9.40        63.55 
TCGA-HT-8018 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 
       21.50         6.25         0.10         2.50         3.95         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB 
        3.88        16.04        10.49         0.13        14.01         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
        2.70        13.02         1.81         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       13.45         8.32        19.23         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        20.35        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F0 
       42.77         0.23         6.71         1.64         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        5.88         7.63         0.76         2.53         4.83         4.11 

$`IDH1 WILD-TYPE`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6669 
        7.69        21.01         6.38        17.69        23.84         7.40 
TCGA-DB-A4XG TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-5141 TCGA-DU-5847 TCGA-DU-5849 
       72.95        18.84        19.96        31.82        18.02        14.56 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
        6.74         8.45        65.75         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 
       19.89        11.47         6.54         8.84        10.36         7.96 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT 
        2.76         5.10        23.74         3.98        19.13         4.96 
TCGA-DU-A5TY TCGA-E1-5318 TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 
       12.20        78.21        17.98        18.77        13.58        20.09 
TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-HT-7469 TCGA-HT-7476 
       12.95        22.52        10.72         5.26         7.82         6.54 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
        0.76        44.68         0.10        39.48        39.09         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
        0.49         1.71        16.24         0.10        33.01        12.23 
TCGA-HT-8107 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DS 
        0.46         4.70        29.59         1.71        15.72         0.23 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-7491 TCGA-HW-A5KK 
        0.07        14.70         5.33        16.14        40.18         7.89 
TCGA-P5-A5EY TCGA-P5-A5F6 
        2.37         1.28 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.03           0.07 
  IDH1 MUTATED IDH1 WILD-TYPE 
        182.33         133.74 
  IDH1 MUTATED IDH1 WILD-TYPE 
        17.075         11.555 
[1] "0.0 - 182.3 (17.1)" "0.1 - 133.7 (11.6)"
[1] "hr=" "4.7"
D1V2, continuous
D1V3, binary
                cls
clus               0   1
  IDH1 MUTATED    92 126
  IDH1 WILD-TYPE  35  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     92  126
  IDH1 WILD-TYPE   35   33
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE           92             35
  MALE            126             33
[1] 2 2
[1] FALSE
D1V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IDH1 MUTATED            65               64                89
  IDH1 WILD-TYPE          32               12                24
D1V5, multiclass
                   clus
vv                  IDH1 MUTATED IDH1 WILD-TYPE
  ASTROCYTOMA                 65             32
  OLIGOASTROCYTOMA            64             12
  OLIGODENDROGLIOMA           89             24
[1] 3 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
  IDH1 MUTATED    66 152
  IDH1 WILD-TYPE  19  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     66  152
  IDH1 WILD-TYPE   19   49
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            66             19
  YES          152             49
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  IDH1 MUTATED                                  0                         8
  IDH1 WILD-TYPE                                1                         4
                vv
clus             WHITE
  IDH1 MUTATED     206
  IDH1 WILD-TYPE    63
D1V7, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   8              4
  WHITE                                     206             63
[1] 3 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
  IDH1 MUTATED     9 197
  IDH1 WILD-TYPE   5  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      9  197
  IDH1 WILD-TYPE    5   58
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                9              5
  NOT HISPANIC OR LATINO          197             58
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   116  28
  TP53 WILD-TYPE 109  31
  TP53 MUTATED TP53 WILD-TYPE 
           144            140 
  TP53 MUTATED TP53 WILD-TYPE 
            28             31 
$`TP53 MUTATED`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5396 TCGA-CS-6290 
        4.70        43.89        18.15        40.18         9.96        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 
       12.43         8.48         7.56        81.96        47.93        46.65 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        78.28        30.08        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 
       18.84        18.38        15.42        10.92        19.96        30.31 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
       14.40        42.05        17.46        13.38         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       17.49        49.02        75.16        65.75        87.45        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7013 
      114.08         7.73        62.96       156.23        14.99         8.84 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       90.77        26.30        18.94        44.02        62.01        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
       23.31        41.98         2.76        20.68        19.13        16.96 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        14.24        12.59         4.96         3.65         5.65 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 
       50.14        67.46        41.13        79.99        57.93       130.78 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
       17.98        32.19        14.93        24.99        23.97        17.88 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX 
       13.68        14.24        14.96        15.52        38.27        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       23.70        14.76         0.13         7.82         8.81         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-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        7.10        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       23.18       107.93        17.29        45.99        56.09        57.60 
TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 
        0.16        42.74        31.69        14.96         0.10        17.52 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7884 
       19.23        50.63        23.61         3.68         5.33        11.28 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8108 
       31.43        63.55        21.50         6.25         0.10         2.50 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 
        0.23         3.88        16.04        15.72         0.23         0.13 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-8319 
        0.10         2.70         5.33         8.32        19.23        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV 
       21.60        19.59        20.81        20.71        19.00         0.23 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65S 
        6.71         2.30         5.88         7.63         0.76         2.53 

$`TP53 WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 
        7.69        10.62        64.64         0.10        21.01         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5274 TCGA-DB-5276 
       17.69        23.84         8.02         7.40        75.25        72.92 
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-A66F TCGA-DU-5847 TCGA-DU-5849 
       13.64        31.82         8.02        17.19        18.02        14.56 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
        6.74         8.45       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       46.06         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7012 TCGA-DU-7018 TCGA-DU-7290 
        7.96        11.47       138.28         6.54        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
        7.96        94.32        60.30         5.10        23.74         3.98 
TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A5TY TCGA-E1-5311 TCGA-E1-5318 
       21.40        14.17        15.12        12.20       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6692 
       95.57        14.33        47.77        34.36        18.77        13.58 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        40.08        22.55        20.61        20.09        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K 
       16.01        20.09        22.52        10.72         5.26        17.82 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 
        0.10         6.67         0.13        75.19        59.18         4.57 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 
        3.16        22.06         0.23        14.27        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
       44.68         6.05         0.10         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 
       14.53        39.48        39.09         0.23         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 
        0.33         0.13         2.93         1.71         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8107 TCGA-HT-8109 
        9.40         0.10        33.01        12.23         0.46         3.95 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 
        4.70        29.59         1.71        10.49        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61A 
       14.70         5.33        13.02         1.81        16.14         6.38 
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        20.35 
TCGA-HW-A5KK TCGA-IK-8125 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F6 
        7.89        42.77         1.64         2.37         4.11         1.28 
TCGA-QH-A65V TCGA-QH-A65Z 
        4.83         4.11 

  TP53 MUTATED TP53 WILD-TYPE 
          0.03           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        156.23         182.33 
  TP53 MUTATED TP53 WILD-TYPE 
        17.965         13.825 
[1] "0.0 - 156.2 (18.0)" "0.1 - 182.3 (13.8)"
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  TP53 MUTATED   58 87
  TP53 WILD-TYPE 69 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     58   87
  TP53 WILD-TYPE   69   72
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           58             69
  MALE             87             72
[1] 2 2
[1] FALSE
D2V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TP53 MUTATED            65               50                30
  TP53 WILD-TYPE          32               26                83
D2V5, multiclass
                   clus
vv                  TP53 MUTATED TP53 WILD-TYPE
  ASTROCYTOMA                 65             32
  OLIGOASTROCYTOMA            50             26
  OLIGODENDROGLIOMA           30             83
[1] 3 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
  TP53 MUTATED    52  93
  TP53 WILD-TYPE  33 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     52   93
  TP53 WILD-TYPE   33  108
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            52             33
  YES           93            108
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  TP53 MUTATED                                  0                         5
  TP53 WILD-TYPE                                1                         7
                vv
clus             WHITE
  TP53 MUTATED     139
  TP53 WILD-TYPE   130
D2V7, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   5              7
  WHITE                                     139            130
[1] 3 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
  TP53 MUTATED     7 132
  TP53 WILD-TYPE   7 123
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7  132
  TP53 WILD-TYPE    7  123
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                7              7
  NOT HISPANIC OR LATINO          132            123
[1] 2 2
[1] FALSE

Clustering(3) Variable = ATRX MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  ATRX MUTATED    95  22
  ATRX WILD-TYPE 130  37
  ATRX MUTATED ATRX WILD-TYPE 
           117            167 
  ATRX MUTATED ATRX WILD-TYPE 
            22             37 
$`ATRX MUTATED`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5273 TCGA-DB-5275 
        4.70        43.89        18.15         8.48        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       72.92        36.56        78.28        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A64S TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B TCGA-DU-5851 
       18.84        15.42        30.31         8.02        42.05        17.46 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 
       13.38         6.81        18.94        17.49        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 
       65.75        87.45        94.52       114.08        62.96       156.23 
TCGA-DU-7015 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       90.77        18.94        25.91        23.31        41.98         2.76 
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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        3.65         5.65        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       57.93       130.78        17.98        32.19        14.93        24.99 
TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 
       23.97        17.88        22.55        13.68        14.24        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FN-7833 TCGA-HT-7469 
       15.52        38.27        18.71        23.70         0.13         7.82 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7603 
       24.26         6.38        60.03       154.19         4.01        23.18 
TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7688 
      107.93        56.09        57.60         0.16        42.74        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 
       14.96         0.10        17.52        19.23         0.23        50.63 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8013 
       23.61         3.68         5.33        11.28        31.43        63.55 
TCGA-HT-8018 TCGA-HT-8108 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R5 TCGA-HT-A5R7 
       21.50         2.50         3.88        16.04         0.13        14.01 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-7490 
        0.10         2.70         1.81         5.33         8.32        19.23 
TCGA-HW-8319 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW 
       21.70        20.81        20.71        19.00         0.23         6.71 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-QH-A65S 
        5.88         7.63         2.53 

$`ATRX WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
        7.69        10.62        64.64        40.18         0.10        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        9.96         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 
        7.56         8.02         7.40        75.25        46.65        50.17 
TCGA-DB-5279 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       44.52        30.08        10.29        18.38        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-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 
       14.73        13.64        10.92        19.96        31.82        14.40 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5870 
       17.19        18.02        14.56         6.74         8.45       182.33 
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-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       11.64       133.74        19.89         7.96         7.73        11.47 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 
      138.28        14.99         6.54         8.84        30.67        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-8164 TCGA-DU-8165 TCGA-DU-8168 
        5.10        23.74         3.98        21.40        19.13        14.17 
TCGA-DU-A5TT TCGA-DU-A5TY TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 
        4.96        12.20       134.27        78.21        95.57        14.33 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7637 
       47.77        34.36        18.77        13.58        15.35        40.08 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       20.61        20.09        12.95        16.01        20.09        22.52 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60J TCGA-FG-A60K TCGA-HT-7467 TCGA-HT-7468 
       10.72         5.26        14.76        17.82         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7601 TCGA-HT-7602 
        0.13         7.10        75.19        59.18         5.03        29.85 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 
        4.57        17.29         3.16        22.06        45.99         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
       14.27        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10         2.96         6.90        14.53        39.48        39.09 
TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-7882 
        0.49        37.15         0.33         0.13         2.93         1.71 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
        1.64        16.24         9.40         0.10        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.10         0.46         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R9 
       29.59         1.71        15.72         0.23        10.49         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A61A TCGA-HW-7486 
       14.70         5.33        13.02        16.14         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       13.45        40.18         4.31        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-IK-8125 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       20.35         7.89        42.77         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65V TCGA-QH-A65Z 
        4.11         0.76         1.28         4.83         4.11 

  ATRX MUTATED ATRX WILD-TYPE 
          0.03           0.07 
  ATRX MUTATED ATRX WILD-TYPE 
        156.23         182.33 
  ATRX MUTATED ATRX WILD-TYPE 
         18.71          14.27 
[1] "0.0 - 156.2 (18.7)" "0.1 - 182.3 (14.3)"
[1] "hr=" "1.7"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  ATRX MUTATED   48 70
  ATRX WILD-TYPE 79 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     48   70
  ATRX WILD-TYPE   79   89
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           48             79
  MALE             70             89
[1] 2 2
[1] FALSE
D3V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ATRX MUTATED            49               43                26
  ATRX WILD-TYPE          48               33                87
D3V5, multiclass
                   clus
vv                  ATRX MUTATED ATRX WILD-TYPE
  ASTROCYTOMA                 49             48
  OLIGOASTROCYTOMA            43             33
  OLIGODENDROGLIOMA           26             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus               0   1
  ATRX MUTATED    42  76
  ATRX WILD-TYPE  43 125
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     42   76
  ATRX WILD-TYPE   43  125
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            42             43
  YES           76            125
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  ATRX MUTATED                                  0                         6
  ATRX WILD-TYPE                                1                         6
                vv
clus             WHITE
  ATRX MUTATED     112
  ATRX WILD-TYPE   157
D3V7, multiclass
                                  clus
vv                                 ATRX MUTATED ATRX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   6              6
  WHITE                                     112            157
[1] 3 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
  ATRX MUTATED     6 108
  ATRX WILD-TYPE   8 147
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      6  108
  ATRX WILD-TYPE    8  147
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                6              8
  NOT HISPANIC OR LATINO          108            147
[1] 2 2
[1] FALSE

Clustering(4) Variable = CIC MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  CIC MUTATED    46   7
  CIC WILD-TYPE 179  52
  CIC MUTATED CIC WILD-TYPE 
           53           231 
  CIC MUTATED CIC WILD-TYPE 
            7            52 
$`CIC MUTATED`
TCGA-CS-5394 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-A4XA TCGA-DB-A64L 
        0.10         8.02        75.25        50.17        10.29        11.01 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       16.80         5.98        16.08        27.81        14.73        13.64 
TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A66F TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6400 
       31.82         8.02        17.19       182.33        52.11         1.22 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8168 TCGA-E1-5311 TCGA-E1-5318 
       30.67        94.32        60.30        14.17       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 
       95.57        14.33        47.77        34.36        15.35        22.55 
TCGA-FG-7641 TCGA-FG-A60K TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7608 
       20.61        17.82         6.67         0.13        75.19        22.06 
TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7875 
        0.23        16.24        44.68         6.90        14.53         0.33 
TCGA-HT-7877 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HW-7487 
        0.13         9.40         6.25        10.49         0.07        13.45 
TCGA-HW-7491 TCGA-IK-8125 TCGA-P5-A5F0 TCGA-QH-A65V TCGA-QH-A65Z 
       40.18        42.77         4.11         4.83         4.11 

$`CIC 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-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5273 
       17.95        12.43         8.48         7.56         7.40        81.96 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        46.65        44.52        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-A64O TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5140 
       72.95        12.59        18.84        15.42        10.92        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       30.31        14.40        42.05        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         8.45         6.81        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 
      138.28        14.99         6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 
       50.14        67.46        41.13        79.99        57.93       130.78 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       17.98        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       13.58        17.88        40.08        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.13         0.10         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-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-7609 
       23.18       107.93         4.57        17.29         3.16        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 
       56.09        57.60        14.27         0.16         0.76         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-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        2.96        17.52        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7879 TCGA-HT-7880 
       50.63         0.49        23.61        37.15         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-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        21.50        33.01        12.23         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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 
        3.88         1.71        16.04        15.72         0.23         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7489 
        1.81        16.14         5.33         6.38        29.92         8.32 
TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       19.23         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV 
       20.35         7.89        20.81        20.71        19.00         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         2.30         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        0.76         1.28         2.53 

  CIC MUTATED CIC WILD-TYPE 
         0.07          0.03 
  CIC MUTATED CIC WILD-TYPE 
       182.33        156.23 
  CIC MUTATED CIC WILD-TYPE 
        15.35         15.72 
[1] "0.1 - 182.3 (15.3)" "0.0 - 156.2 (15.7)"
[1] "hr=" "2.2"
D4V2, continuous
D4V3, binary
               cls
clus              0   1
  CIC MUTATED    27  26
  CIC WILD-TYPE 100 133
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     27   26
  CIC WILD-TYPE  100  133
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE          27           100
  MALE            26           133
[1] 2 2
[1] FALSE
D4V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CIC MUTATED             1                9                43
  CIC WILD-TYPE          96               67                70
D4V5, multiclass
                   clus
vv                  CIC MUTATED CIC WILD-TYPE
  ASTROCYTOMA                 1            96
  OLIGOASTROCYTOMA            9            67
  OLIGODENDROGLIOMA          43            70
[1] 3 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
  CIC MUTATED    11  42
  CIC WILD-TYPE  74 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     11   42
  CIC WILD-TYPE   74  159
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           11            74
  YES          42           159
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  CIC MUTATED                                  0                         1
  CIC WILD-TYPE                                1                        11
               vv
clus            WHITE
  CIC MUTATED      50
  CIC WILD-TYPE   219
D4V7, multiclass
                                  clus
vv                                 CIC MUTATED CIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  BLACK OR AFRICAN AMERICAN                  1            11
  WHITE                                     50           219
[1] 3 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
  CIC MUTATED     2  48
  CIC WILD-TYPE  12 207
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      2   48
  CIC WILD-TYPE   12  207
                        clus
vv                       CIC MUTATED CIC WILD-TYPE
  HISPANIC OR LATINO               2            12
  NOT HISPANIC OR LATINO          48           207
[1] 2 2
[1] FALSE

Clustering(5) Variable = NOTCH1 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    22   6
  NOTCH1 WILD-TYPE 203  53
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              28              256 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               6               53 
$`NOTCH1 MUTATED`
TCGA-CS-5390 TCGA-DB-A4XG TCGA-DB-A64L TCGA-DH-5144 TCGA-DH-A66B TCGA-DU-6394 
       64.64        72.95        11.01         8.02        42.05        22.42 
TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-8168 
        1.22        30.67        62.01        25.91        60.30        14.17 
TCGA-DU-A5TR TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-7638 TCGA-FG-8186 TCGA-HT-7470 
       12.59       134.27        47.77        22.55        16.01         8.81 
TCGA-HT-7481 TCGA-HT-7875 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A616 TCGA-HW-8322 
       59.18         0.33         9.40         6.25         1.81        17.82 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5F0 TCGA-P5-A5F2 
       20.35        42.77         4.11         7.63 

$`NOTCH1 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-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-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-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-A4XH TCGA-DB-A64O 
       27.62        27.02        18.84        18.38        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-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       17.19        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-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       52.11        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 
       14.99         6.54         8.84        90.77        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-7306 
        7.96        94.32        18.94        44.02        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-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       19.13        16.96        15.48        14.24        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        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-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-7637 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        40.08        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        14.24        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       23.70        14.76        17.82         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        7.82         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7482 
        6.54        24.26         6.38         7.10        75.19        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-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       23.61        37.15         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-8013 
        1.71        11.28        31.43         1.64        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        21.50        33.01        12.23         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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
       13.02        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV 
       19.59         7.89        20.81        20.71        19.00         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F4 
        6.71         1.64         2.37         2.30         5.88         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.33             0.03 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          134.27           182.33 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          19.085           15.450 
[1] "0.3 - 134.3 (19.1)" "0.0 - 182.3 (15.4)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    13  16
  NOTCH1 WILD-TYPE 114 143
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     13   16
  NOTCH1 WILD-TYPE  114  143
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             13              114
  MALE               16              143
[1] 2 2
[1] FALSE
D5V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NOTCH1 MUTATED             3                3                23
  NOTCH1 WILD-TYPE          94               73                90
D5V5, multiclass
                   clus
vv                  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASTROCYTOMA                    3               94
  OLIGOASTROCYTOMA               3               73
  OLIGODENDROGLIOMA             23               90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     6  23
  NOTCH1 WILD-TYPE  79 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      6   23
  NOTCH1 WILD-TYPE   79  178
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO               6               79
  YES             23              178
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  NOTCH1 MUTATED                                  0                         0
  NOTCH1 WILD-TYPE                                1                        12
                  vv
clus               WHITE
  NOTCH1 MUTATED      29
  NOTCH1 WILD-TYPE   240
D5V7, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                        29              240
[1] 3 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
  NOTCH1 MUTATED     1  26
  NOTCH1 WILD-TYPE  13 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      1   26
  NOTCH1 WILD-TYPE   13  229
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO             26              229
[1] 2 2
[1] FALSE

Clustering(6) Variable = IDH2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED    11   1
  IDH2 WILD-TYPE 214  58
  IDH2 MUTATED IDH2 WILD-TYPE 
            12            272 
  IDH2 MUTATED IDH2 WILD-TYPE 
             1             58 
$`IDH2 MUTATED`
TCGA-DB-A4XG TCGA-DH-5141 TCGA-DU-5849 TCGA-DU-7309 TCGA-E1-5318 TCGA-FG-8189 
       72.95        31.82        14.56         2.76        78.21        22.52 
TCGA-HT-7476 TCGA-HT-7681 TCGA-HT-7856 TCGA-HT-8113 TCGA-HT-A5R9 TCGA-HW-7491 
        6.54        44.68        39.09        29.59         0.07        40.18 

$`IDH2 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A4XH 
       12.72        27.62        27.02        18.84        18.38        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-5142 
       27.81        14.73        13.64        10.92        19.96        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5851 
       14.40         8.02        42.05        17.19        18.02        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        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-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-7009 TCGA-DU-7010 TCGA-DU-7012 
       11.47        62.96       156.23       138.28        14.99         6.54 
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-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-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-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-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-E1-5319 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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        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-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-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-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23         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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8114 
        0.46         2.50         3.95         4.70         0.23         3.88 
TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        19.23         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         1.28         2.53 
TCGA-QH-A65V TCGA-QH-A65Z 
        4.83         4.11 

  IDH2 MUTATED IDH2 WILD-TYPE 
          0.07           0.03 
  IDH2 MUTATED IDH2 WILD-TYPE 
         78.21         182.33 
  IDH2 MUTATED IDH2 WILD-TYPE 
        30.705         15.450 
[1] "0.1 - 78.2 (30.7)"  "0.0 - 182.3 (15.4)"
[1] "hr=" "3.1"
D6V2, continuous
D6V3, binary
                cls
clus               0   1
  IDH2 MUTATED     6   6
  IDH2 WILD-TYPE 121 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      6    6
  IDH2 WILD-TYPE  121  153
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE            6            121
  MALE              6            153
[1] 2 2
[1] FALSE
D6V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IDH2 MUTATED             1                1                10
  IDH2 WILD-TYPE          96               75               103
D6V5, multiclass
                   clus
vv                  IDH2 MUTATED IDH2 WILD-TYPE
  ASTROCYTOMA                  1             96
  OLIGOASTROCYTOMA             1             75
  OLIGODENDROGLIOMA           10            103
[1] 3 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
  IDH2 MUTATED     4   8
  IDH2 WILD-TYPE  81 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      4    8
  IDH2 WILD-TYPE   81  193
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO             4             81
  YES            8            193
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  IDH2 MUTATED                                  0                         1
  IDH2 WILD-TYPE                                1                        11
                vv
clus             WHITE
  IDH2 MUTATED      11
  IDH2 WILD-TYPE   258
D6V7, multiclass
                                  clus
vv                                 IDH2 MUTATED IDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   1             11
  WHITE                                      11            258
[1] 3 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
  IDH2 MUTATED     2   9
  IDH2 WILD-TYPE  12 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      2    9
  IDH2 WILD-TYPE   12  246
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                2             12
  NOT HISPANIC OR LATINO            9            246
[1] 2 2
[1] FALSE

Clustering(7) Variable = FUBP1 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  FUBP1 MUTATED    21   5
  FUBP1 WILD-TYPE 204  54
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             26             258 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
              5              54 
$`FUBP1 MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-DB-5274 TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V 
       64.64         0.10        75.25        11.01         5.98        14.73 
TCGA-DH-5144 TCGA-DU-5849 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-7300 TCGA-DU-8164 
        8.02        14.56        22.42        46.06        62.01        21.40 
TCGA-DU-8168 TCGA-E1-5319 TCGA-EZ-7264 TCGA-HT-7467 TCGA-HT-7471 TCGA-HT-7481 
       14.17        95.57        14.33         0.10         0.13        59.18 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7694 TCGA-HT-8105 
       22.06         0.23        14.27        16.24         6.90         6.25 
TCGA-HT-A615 TCGA-HW-7487 
       13.02        13.45 

$`FUBP1 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-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-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       12.43         8.48         7.56         8.02         7.40        81.96 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       47.93        72.92        46.65        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-A64O TCGA-DB-A64P 
       18.84        18.38        72.95        12.59        18.84        16.80 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5140 
       16.08        15.42        27.81        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 
       31.82        30.31        14.40        42.05        17.19        18.02 
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-6393 TCGA-DU-6395 TCGA-DU-6396 
       18.94        17.49        15.16        52.11        49.02        75.16 
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-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28        14.99         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-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       18.94        44.02        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-8165 
        2.76         5.10        23.74         3.98        20.68        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        15.48        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 TCGA-FG-5962 
       79.99        57.93       134.27        78.21       130.78        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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         0.13 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67         7.82         8.81         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-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-7609 TCGA-HT-7610 
      107.93         4.57        17.29         3.16        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
       57.60         0.16         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-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
       17.52        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-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 TCGA-HT-8563 
        4.70         0.23        29.59         3.88         1.71        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         5.33         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33         6.38        29.92         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV 
        7.89        20.81        20.71        19.00        42.77         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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        7.63         0.76         1.28         2.53         4.83         4.11 

  FUBP1 MUTATED FUBP1 WILD-TYPE 
           0.10            0.03 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
          95.57          182.33 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
          14.30           16.06 
[1] "0.1 - 95.6 (14.3)"  "0.0 - 182.3 (16.1)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                 cls
clus                0   1
  FUBP1 MUTATED    11  15
  FUBP1 WILD-TYPE 116 144
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED     11   15
  FUBP1 WILD-TYPE  116  144
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  FEMALE            11             116
  MALE              15             144
[1] 2 2
[1] FALSE
D7V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FUBP1 MUTATED             1                3                22
  FUBP1 WILD-TYPE          96               73                91
D7V5, multiclass
                   clus
vv                  FUBP1 MUTATED FUBP1 WILD-TYPE
  ASTROCYTOMA                   1              96
  OLIGOASTROCYTOMA              3              73
  OLIGODENDROGLIOMA            22              91
[1] 3 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
  FUBP1 MUTATED     8  18
  FUBP1 WILD-TYPE  77 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED      8   18
  FUBP1 WILD-TYPE   77  183
     clus
vv    FUBP1 MUTATED FUBP1 WILD-TYPE
  NO              8              77
  YES            18             183
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  FUBP1 MUTATED                                  0                         1
  FUBP1 WILD-TYPE                                1                        11
                 vv
clus              WHITE
  FUBP1 MUTATED      24
  FUBP1 WILD-TYPE   245
D7V7, multiclass
                                  clus
vv                                 FUBP1 MUTATED FUBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    1              11
  WHITE                                       24             245
[1] 3 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
  FUBP1 MUTATED     0  23
  FUBP1 WILD-TYPE  14 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP1 MUTATED      0   23
  FUBP1 WILD-TYPE   14  232
                        clus
vv                       FUBP1 MUTATED FUBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO            23             232
[1] 2 2
[1] FALSE

Clustering(8) Variable = NF1 MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    11   8
  NF1 WILD-TYPE 214  51
  NF1 MUTATED NF1 WILD-TYPE 
           19           265 
  NF1 MUTATED NF1 WILD-TYPE 
            8            51 
$`NF1 MUTATED`
TCGA-CS-5397 TCGA-DB-A4XG TCGA-DB-A64O TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-6394 
        6.38        72.95        18.84        19.96        18.02        22.42 
TCGA-DU-6397 TCGA-DU-6402 TCGA-DU-7006 TCGA-DU-7299 TCGA-FG-5963 TCGA-FG-6688 
       46.06         7.04        11.47        44.02        17.98        18.77 
TCGA-HT-7608 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7880 TCGA-HT-8010 TCGA-HT-8564 
       22.06         0.23         0.49         5.33         1.64        15.72 
TCGA-HT-A4DS 
        0.23 

$`NF1 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-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-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-A4XH TCGA-DB-A64L 
       27.62        27.02        18.84        18.38        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-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-A66F TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       42.05        17.19        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-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       52.11        49.02        75.16        65.75         1.22        87.45 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 
        7.73        62.96       156.23       138.28        14.99         6.54 
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-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        62.01        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-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-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-5962 TCGA-FG-5964 
       78.21        95.57       130.78        14.33        47.77        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        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        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-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-7609 TCGA-HT-7610 
      107.93         4.57        17.29         3.16        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-7858 TCGA-HT-7873 TCGA-HT-7874 
       39.48        19.23        39.09        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         3.68         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       16.04        10.49         0.13        14.01         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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         6.38        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  NF1 MUTATED NF1 WILD-TYPE 
         0.23          0.03 
  NF1 MUTATED NF1 WILD-TYPE 
        72.95        182.33 
  NF1 MUTATED NF1 WILD-TYPE 
        17.98         15.48 
[1] "0.2 - 73.0 (18.0)"  "0.0 - 182.3 (15.5)"
[1] "hr=" "3.5"
D8V2, continuous
D8V3, binary
               cls
clus              0   1
  NF1 MUTATED     9  10
  NF1 WILD-TYPE 118 149
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      9   10
  NF1 WILD-TYPE  118  149
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           9           118
  MALE            10           149
[1] 2 2
[1] FALSE
D8V4, continuous
               vv
clus            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NF1 MUTATED            11                4                 4
  NF1 WILD-TYPE          86               72               109
D8V5, multiclass
                   clus
vv                  NF1 MUTATED NF1 WILD-TYPE
  ASTROCYTOMA                11            86
  OLIGOASTROCYTOMA            4            72
  OLIGODENDROGLIOMA           4           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
  NF1 MUTATED     9  10
  NF1 WILD-TYPE  76 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      9   10
  NF1 WILD-TYPE   76  191
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            9            76
  YES          10           191
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  NF1 MUTATED                                  0                         2
  NF1 WILD-TYPE                                1                        10
               vv
clus            WHITE
  NF1 MUTATED      17
  NF1 WILD-TYPE   252
D8V7, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  BLACK OR AFRICAN AMERICAN                  2            10
  WHITE                                     17           252
[1] 3 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
  NF1 MUTATED     2  17
  NF1 WILD-TYPE  12 238
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      2   17
  NF1 WILD-TYPE   12  238
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               2            12
  NOT HISPANIC OR LATINO          17           238
[1] 2 2
[1] FALSE

Clustering(9) Variable = PIK3R1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     9   3
  PIK3R1 WILD-TYPE 216  56
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              12              272 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               3               56 
$`PIK3R1 MUTATED`
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6188 TCGA-DB-5279 TCGA-DU-5870 
       43.89        10.62         0.10        23.84        44.52       182.33 
TCGA-DU-6394 TCGA-DU-7300 TCGA-FG-5962 TCGA-FG-8188 TCGA-HT-7481 TCGA-HT-7694 
       22.42        62.01        47.77        14.96        59.18         6.90 

$`PIK3R1 WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5395 
        4.70         7.69        18.15        64.64        40.18        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        9.96         6.38        17.69        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.56         8.02         7.40        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        46.65        50.17        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-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       17.19        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        8.45         6.81        18.94        17.49        15.16        52.11 
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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        44.02        25.91 
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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 
       18.71        23.70        14.76        17.82         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-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        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-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        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-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        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-8558 TCGA-HT-8563 
        4.70         0.23        29.59         3.88         1.71        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         6.38        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         1.28         2.53 
TCGA-QH-A65V TCGA-QH-A65Z 
        4.83         4.11 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.10             0.03 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          182.33           156.23 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          33.865           15.450 
[1] "0.1 - 182.3 (33.9)" "0.0 - 156.2 (15.4)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     3  10
  PIK3R1 WILD-TYPE 124 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      3   10
  PIK3R1 WILD-TYPE  124  149
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              3              124
  MALE               10              149
[1] 2 2
[1] FALSE
D9V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PIK3R1 MUTATED             5                1                 7
  PIK3R1 WILD-TYPE          92               75               106
D9V5, multiclass
                   clus
vv                  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASTROCYTOMA                    5               92
  OLIGOASTROCYTOMA               1               75
  OLIGODENDROGLIOMA              7              106
[1] 3 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
  PIK3R1 MUTATED     6   7
  PIK3R1 WILD-TYPE  79 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      6    7
  PIK3R1 WILD-TYPE   79  194
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               6               79
  YES              7              194
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  PIK3R1 MUTATED                                  0                         1
  PIK3R1 WILD-TYPE                                1                        11
                  vv
clus               WHITE
  PIK3R1 MUTATED      11
  PIK3R1 WILD-TYPE   258
D9V7, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     1               11
  WHITE                                        11              258
[1] 3 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
  PIK3R1 MUTATED     0   9
  PIK3R1 WILD-TYPE  14 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0    9
  PIK3R1 WILD-TYPE   14  246
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              9              246
[1] 2 2
[1] FALSE

Clustering(10) Variable = STK19 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     7   1
  STK19 WILD-TYPE 218  58
  STK19 MUTATED STK19 WILD-TYPE 
              8             276 
  STK19 MUTATED STK19 WILD-TYPE 
              1              58 
$`STK19 MUTATED`
TCGA-FG-A60J TCGA-HT-8015 TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       14.76         0.10         0.13        14.70         0.10         5.33 
TCGA-P5-A5F1 TCGA-P5-A5F2 
        5.88         7.63 

$`STK19 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        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        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       17.82         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-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-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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59         3.88         1.71        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       10.49        14.01         0.07         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         6.38        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        4.11         0.76         1.28         2.53         4.83         4.11 

  STK19 MUTATED STK19 WILD-TYPE 
           0.10            0.03 
  STK19 MUTATED STK19 WILD-TYPE 
          14.76          182.33 
  STK19 MUTATED STK19 WILD-TYPE 
          5.605          16.110 
[1] "0.1 - 14.8 (5.6)"   "0.0 - 182.3 (16.1)"
[1] "hr=" "3.3"
D10V2, continuous
D10V3, binary
                 cls
clus                0   1
  STK19 MUTATED     5   3
  STK19 WILD-TYPE 122 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      5    3
  STK19 WILD-TYPE  122  156
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             5             122
  MALE               3             156
[1] 2 2
[1] FALSE
D10V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  STK19 MUTATED             6                1                 1
  STK19 WILD-TYPE          91               75               112
D10V5, multiclass
                   clus
vv                  STK19 MUTATED STK19 WILD-TYPE
  ASTROCYTOMA                   6              91
  OLIGOASTROCYTOMA              1              75
  OLIGODENDROGLIOMA             1             112
[1] 3 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
  STK19 MUTATED     0   8
  STK19 WILD-TYPE  85 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    8
  STK19 WILD-TYPE   85  193
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              0              85
  YES             8             193
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  STK19 MUTATED                                  0                         0
  STK19 WILD-TYPE                                1                        12
                 vv
clus              WHITE
  STK19 MUTATED       8
  STK19 WILD-TYPE   261
D10V7, multiclass
                                  clus
vv                                 STK19 MUTATED STK19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        8             261
[1] 3 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
  STK19 MUTATED     2   6
  STK19 WILD-TYPE  12 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    6
  STK19 WILD-TYPE   12  249
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 2              12
  NOT HISPANIC OR LATINO             6             249
[1] 2 2
[1] FALSE

Clustering(11) Variable = PTEN MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     6   7
  PTEN WILD-TYPE 219  52
  PTEN MUTATED PTEN WILD-TYPE 
            13            271 
  PTEN MUTATED PTEN WILD-TYPE 
             7             52 
$`PTEN MUTATED`
TCGA-CS-5395 TCGA-DU-5847 TCGA-DU-6402 TCGA-DU-7012 TCGA-DU-7290 TCGA-DU-8158 
       21.01        18.02         7.04         6.54        10.36         5.10 
TCGA-FG-6692 TCGA-FG-A4MW TCGA-HT-7860 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 
       13.58         5.26         0.49        16.24        12.23         4.70 
TCGA-HT-A5RA 
       14.70 

$`PTEN 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-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10         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-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-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-A66B TCGA-DH-A66F TCGA-DU-5849 
       30.31        14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 
       75.16        46.06        65.75         1.22        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-7009 TCGA-DU-7010 TCGA-DU-7013 
       11.47        62.96       156.23       138.28        14.99         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        26.30         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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-7634 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.71        23.70        14.76        17.82 
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-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        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-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-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-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-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-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 
        3.95         0.23        29.59         3.88         1.71        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         6.38        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  PTEN MUTATED PTEN WILD-TYPE 
          0.49           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         21.01         182.33 
  PTEN MUTATED PTEN WILD-TYPE 
         10.36          16.08 
[1] "0.5 - 21.0 (10.4)"  "0.0 - 182.3 (16.1)"
[1] "hr=" "9.9"
D11V2, continuous
D11V3, binary
                cls
clus               0   1
  PTEN MUTATED     7   6
  PTEN WILD-TYPE 120 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      7    6
  PTEN WILD-TYPE  120  153
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            7            120
  MALE              6            153
[1] 2 2
[1] FALSE
D11V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PTEN MUTATED            10                1                 2
  PTEN WILD-TYPE          87               75               111
D11V5, multiclass
                   clus
vv                  PTEN MUTATED PTEN WILD-TYPE
  ASTROCYTOMA                 10             87
  OLIGOASTROCYTOMA             1             75
  OLIGODENDROGLIOMA            2            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"
D11V6, binary
                cls
clus               0   1
  PTEN MUTATED     5   8
  PTEN WILD-TYPE  80 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    8
  PTEN WILD-TYPE   80  193
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             5             80
  YES            8            193
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  PTEN MUTATED                                  0                         2
  PTEN WILD-TYPE                                1                        10
                vv
clus             WHITE
  PTEN MUTATED      11
  PTEN WILD-TYPE   258
D11V7, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   2             10
  WHITE                                      11            258
[1] 3 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
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  14 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   14  243
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO           12            243
[1] 2 2
[1] FALSE

Clustering(12) Variable = PIK3CA MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    19   6
  PIK3CA WILD-TYPE 206  53
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              259 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               6               53 
$`PIK3CA MUTATED`
TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A64W TCGA-DU-6405 TCGA-DU-7006 TCGA-DU-7018 
        5.98        14.73        13.64        19.89        11.47        30.67 
TCGA-DU-7298 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-FG-5962 
       18.94        21.40        19.13        14.17         4.96        47.77 
TCGA-FG-7634 TCGA-FG-8187 TCGA-HT-7468 TCGA-HT-7478 TCGA-HT-7481 TCGA-HT-7605 
       15.35        20.09         6.67         6.38        59.18         4.57 
TCGA-HT-7607 TCGA-HT-7620 TCGA-HT-7692 TCGA-HT-7874 TCGA-HT-7882 TCGA-HW-7491 
        3.16        14.27         2.96        37.15         1.71        40.18 
TCGA-P5-A5F0 
        4.11 

$`PIK3CA 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A64R TCGA-DB-A64S 
       12.59        11.01        18.84        16.80        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       27.81        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 
      133.74        94.52       114.08         7.96         7.73        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99         6.54         8.84        90.77 
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-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       23.74         3.98        20.68        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 
       12.59        15.12         3.65         5.65        12.20        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-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        14.33        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        13.58        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.13         0.10         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-7479 
       16.54         3.75        17.42         6.54        24.26         7.10 
TCGA-HT-7480 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
       23.18       107.93        17.29        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        23.61         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.13         3.68         5.33         2.93        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        19.23         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            1.71             0.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           59.18           182.33 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           14.27            16.04 
[1] "1.7 - 59.2 (14.3)"  "0.0 - 182.3 (16.0)"
[1] "hr=" "2.1"
D12V2, continuous
D12V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10  15
  PIK3CA WILD-TYPE 117 144
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10   15
  PIK3CA WILD-TYPE  117  144
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             10              117
  MALE               15              144
[1] 2 2
[1] FALSE
D12V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PIK3CA MUTATED             5                4                16
  PIK3CA WILD-TYPE          92               72                97
D12V5, multiclass
                   clus
vv                  PIK3CA MUTATED PIK3CA WILD-TYPE
  ASTROCYTOMA                    5               92
  OLIGOASTROCYTOMA               4               72
  OLIGODENDROGLIOMA             16               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     6  19
  PIK3CA WILD-TYPE  79 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      6   19
  PIK3CA WILD-TYPE   79  182
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               6               79
  YES             19              182
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  PIK3CA MUTATED                                  0                         1
  PIK3CA WILD-TYPE                                1                        11
                  vv
clus               WHITE
  PIK3CA MUTATED      23
  PIK3CA WILD-TYPE   246
D12V7, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     1               11
  WHITE                                        23              246
[1] 3 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
  PIK3CA MUTATED     1  22
  PIK3CA WILD-TYPE  13 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   22
  PIK3CA WILD-TYPE   13  233
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO             22              233
[1] 2 2
[1] FALSE

Clustering(13) Variable = ARID1A MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    11   1
  ARID1A WILD-TYPE 214  58
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              272 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               58 
$`ARID1A MUTATED`
TCGA-DB-5275 TCGA-DB-A4XA TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7304 TCGA-FG-5962 
       47.93        10.29         7.96       138.28        23.31        47.77 
TCGA-FG-7637 TCGA-HT-7468 TCGA-HT-7611 TCGA-HT-7688 TCGA-HT-8564 TCGA-HW-7490 
       40.08         6.67        57.60        31.69        15.72        19.23 

$`ARID1A 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-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
        7.40        81.96        75.25        72.92        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        78.28        30.08        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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6542 
       11.64       133.74        19.89        94.52       114.08         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       11.47        62.96       156.23        14.99         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-7306 
       18.94        44.02        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-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 
       15.12         4.96         3.65         5.65        12.20        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-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        14.33        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       17.82         0.13         0.10         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        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-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-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-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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
        1.71        16.04         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         1.28         2.53 
TCGA-QH-A65V TCGA-QH-A65Z 
        4.83         4.11 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.67             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
          138.28           182.33 
  ARID1A MUTATED ARID1A WILD-TYPE 
          27.500           15.385 
[1] "6.7 - 138.3 (27.5)" "0.0 - 182.3 (15.4)"
[1] "hr=" "4.2"
D13V2, continuous
D13V3, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  11
  ARID1A WILD-TYPE 126 148
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   11
  ARID1A WILD-TYPE  126  148
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              1              126
  MALE               11              148
[1] 2 2
[1] FALSE
D13V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ARID1A MUTATED             2                5                 5
  ARID1A WILD-TYPE          95               71               108
D13V5, multiclass
                   clus
vv                  ARID1A MUTATED ARID1A WILD-TYPE
  ASTROCYTOMA                    2               95
  OLIGOASTROCYTOMA               5               71
  OLIGODENDROGLIOMA              5              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"
D13V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED     3   9
  ARID1A WILD-TYPE  82 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    9
  ARID1A WILD-TYPE   82  192
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               3               82
  YES              9              192
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  ARID1A MUTATED                                  0                         0
  ARID1A WILD-TYPE                                1                        12
                  vv
clus               WHITE
  ARID1A MUTATED      12
  ARID1A WILD-TYPE   257
D13V7, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                        12              257
[1] 3 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
  ARID1A MUTATED     1  11
  ARID1A WILD-TYPE  13 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   11
  ARID1A WILD-TYPE   13  244
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO             11              244
[1] 2 2
[1] FALSE

Clustering(14) Variable = EGFR MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     7   9
  EGFR WILD-TYPE 218  50
  EGFR MUTATED EGFR WILD-TYPE 
            16            268 
  EGFR MUTATED EGFR WILD-TYPE 
             9             50 
$`EGFR MUTATED`
TCGA-DU-5852 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7292 TCGA-DU-8158 
        6.74         7.96        11.47         6.54         7.96         5.10 
TCGA-DU-8162 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW 
        3.98         4.96        12.20        13.58        10.72         5.26 
TCGA-HT-8104 TCGA-HT-8107 TCGA-HT-8110 TCGA-HT-A5RC 
       12.23         0.46         4.70         5.33 

$`EGFR 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        14.56        17.46        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7013 
        7.73        62.96       156.23       138.28        14.99         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        26.30        10.36        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-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
        2.76        23.74        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-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
        5.65        50.14        67.46        41.13        79.99        57.93 
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-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-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
       23.97        15.35        17.88        40.08        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-A4MX TCGA-FG-A4MY 
       14.96        22.52        15.52        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-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-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-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        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-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.10         2.50         3.95         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 
        0.13        14.01         0.07        14.70         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  EGFR MUTATED EGFR WILD-TYPE 
          0.46           0.03 
  EGFR MUTATED EGFR WILD-TYPE 
         13.58         182.33 
  EGFR MUTATED EGFR WILD-TYPE 
          6.64          16.67 
[1] "0.5 - 13.6 (6.6)"   "0.0 - 182.3 (16.7)"
[1] "hr=" "19" 
D14V2, continuous
D14V3, binary
                cls
clus               0   1
  EGFR MUTATED     8   8
  EGFR WILD-TYPE 119 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      8    8
  EGFR WILD-TYPE  119  151
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            8            119
  MALE              8            151
[1] 2 2
[1] FALSE
D14V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EGFR MUTATED             8                4                 4
  EGFR WILD-TYPE          89               72               109
D14V5, multiclass
                   clus
vv                  EGFR MUTATED EGFR WILD-TYPE
  ASTROCYTOMA                  8             89
  OLIGOASTROCYTOMA             4             72
  OLIGODENDROGLIOMA            4            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"
D14V6, binary
                cls
clus               0   1
  EGFR MUTATED     2  14
  EGFR WILD-TYPE  83 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      2   14
  EGFR WILD-TYPE   83  187
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO             2             83
  YES           14            187
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  EGFR MUTATED                                  0                         1
  EGFR WILD-TYPE                                1                        11
                vv
clus             WHITE
  EGFR MUTATED      15
  EGFR WILD-TYPE   254
D14V7, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   1             11
  WHITE                                      15            254
[1] 3 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
  EGFR MUTATED     0  16
  EGFR WILD-TYPE  14 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   16
  EGFR WILD-TYPE   14  239
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO           16            239
[1] 2 2
[1] FALSE

Clustering(15) Variable = GAGE2B MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  GAGE2B MUTATED     3   1
  GAGE2B WILD-TYPE 222  58
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               4              280 
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               1               58 
$`GAGE2B MUTATED`
TCGA-DU-5849 TCGA-E1-5303 TCGA-FG-A4MY TCGA-HT-7481 
       14.56        67.46        23.70        59.18 

$`GAGE2B 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-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-E1-5302 TCGA-E1-5304 TCGA-E1-5305 
        3.65         5.65        12.20        50.14        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-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-7637 
       24.99        23.97        13.58        15.35        17.88        40.08 
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        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
       10.72         5.26        18.71        14.76        17.82         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-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        7.10        75.19        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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  GAGE2B MUTATED GAGE2B WILD-TYPE 
           14.56             0.03 
  GAGE2B MUTATED GAGE2B WILD-TYPE 
           67.46           182.33 
  GAGE2B MUTATED GAGE2B WILD-TYPE 
           41.44            15.50 
[1] "14.6 - 67.5 (41.4)" "0.0 - 182.3 (15.5)"
[1] "hr=" "1.4"
D15V2, continuous
D15V3, binary
                  cls
clus                 0   1
  GAGE2B MUTATED     1   3
  GAGE2B WILD-TYPE 126 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2B MUTATED      1    3
  GAGE2B WILD-TYPE  126  156
        clus
vv       GAGE2B MUTATED GAGE2B WILD-TYPE
  FEMALE              1              126
  MALE                3              156
[1] 2 2
[1] FALSE
D15V4, continuous
[1] "Remove cluster labels:" "GAGE2B MUTATED"        
clus
  GAGE2B MUTATED GAGE2B WILD-TYPE 
               1              136 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DH-5140       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DH-A66B       TCGA-DH-A66F       TCGA-DU-5851       TCGA-DU-5852 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-5853       TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-5871       TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-6404       TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-6410       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-E1-5302       TCGA-E1-5304 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-E1-5319       TCGA-E1-5322       TCGA-FG-5963       TCGA-FG-5965 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-7468       TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-7485       TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-7689       TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-7854       TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-A4DV       TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-HT-A615       TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-IK-7675       TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-P5-A5EX       TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
      TCGA-P5-A5F6       TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65Z 
"GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" "GAGE2B WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  GAGE2B MUTATED             1                1                 2
  GAGE2B WILD-TYPE          96               75               111
D15V5, multiclass
                   clus
vv                  GAGE2B MUTATED GAGE2B WILD-TYPE
  ASTROCYTOMA                    1               96
  OLIGOASTROCYTOMA               1               75
  OLIGODENDROGLIOMA              2              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"
D15V6, binary
                  cls
clus                 0   1
  GAGE2B MUTATED     1   3
  GAGE2B WILD-TYPE  84 198
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2B MUTATED      1    3
  GAGE2B WILD-TYPE   84  198
     clus
vv    GAGE2B MUTATED GAGE2B WILD-TYPE
  NO               1               84
  YES              3              198
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  GAGE2B MUTATED                                  0                         0
  GAGE2B WILD-TYPE                                1                        12
                  vv
clus               WHITE
  GAGE2B MUTATED       4
  GAGE2B WILD-TYPE   265
D15V7, multiclass
                                  clus
vv                                 GAGE2B MUTATED GAGE2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         4              265
[1] 3 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
  GAGE2B MUTATED     1   3
  GAGE2B WILD-TYPE  13 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2B MUTATED      1    3
  GAGE2B WILD-TYPE   13  252
                        clus
vv                       GAGE2B MUTATED GAGE2B WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO              3              252
[1] 2 2
[1] FALSE

Clustering(16) Variable = CREBZF MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2                0   1
  CREBZF MUTATED     4   1
  CREBZF WILD-TYPE 221  58
  CREBZF MUTATED CREBZF WILD-TYPE 
               5              279 
  CREBZF MUTATED CREBZF WILD-TYPE 
               1               58 
$`CREBZF MUTATED`
TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-8168 TCGA-HT-7694 TCGA-P5-A5EX 
       18.94        60.30        14.17         6.90         1.64 

$`CREBZF 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       12.20        50.14        67.46        41.13        79.99        57.93 
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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-7692 TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
        2.96        17.52        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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       20.71        19.00        42.77         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  CREBZF MUTATED CREBZF WILD-TYPE 
            1.64             0.03 
  CREBZF MUTATED CREBZF WILD-TYPE 
           60.30           182.33 
  CREBZF MUTATED CREBZF WILD-TYPE 
           14.17            15.72 
[1] "1.6 - 60.3 (14.2)"  "0.0 - 182.3 (15.7)"
[1] "hr=" "1.3"
D16V2, continuous
D16V3, binary
                  cls
clus                 0   1
  CREBZF MUTATED     4   1
  CREBZF WILD-TYPE 123 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      4    1
  CREBZF WILD-TYPE  123  158
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  FEMALE              4              123
  MALE                1              158
[1] 2 2
[1] FALSE
D16V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  CREBZF MUTATED             1                0                 4
  CREBZF WILD-TYPE          96               76               109
D16V5, multiclass
                   clus
vv                  CREBZF MUTATED CREBZF WILD-TYPE
  ASTROCYTOMA                    1               96
  OLIGOASTROCYTOMA               0               76
  OLIGODENDROGLIOMA              4              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"
D16V6, binary
                  cls
clus                 0   1
  CREBZF MUTATED     1   4
  CREBZF WILD-TYPE  84 197
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      1    4
  CREBZF WILD-TYPE   84  197
     clus
vv    CREBZF MUTATED CREBZF WILD-TYPE
  NO               1               84
  YES              4              197
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  CREBZF MUTATED                                  0                         1
  CREBZF WILD-TYPE                                1                        11
                  vv
clus               WHITE
  CREBZF MUTATED       4
  CREBZF WILD-TYPE   265
D16V7, multiclass
                                  clus
vv                                 CREBZF MUTATED CREBZF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     1               11
  WHITE                                         4              265
[1] 3 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
  CREBZF MUTATED     0   5
  CREBZF WILD-TYPE  14 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBZF MUTATED      0    5
  CREBZF WILD-TYPE   14  250
                        clus
vv                       CREBZF MUTATED CREBZF WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              5              250
[1] 2 2
[1] FALSE

Clustering(17) Variable = TCF12 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  TCF12 MUTATED     6   2
  TCF12 WILD-TYPE 219  57
  TCF12 MUTATED TCF12 WILD-TYPE 
              8             276 
  TCF12 MUTATED TCF12 WILD-TYPE 
              2              57 
$`TCF12 MUTATED`
TCGA-CS-6668 TCGA-DU-7018 TCGA-E1-5307 TCGA-FG-8182 TCGA-HT-7601 TCGA-HT-7875 
        8.02        30.67        57.93        13.68         5.03         0.33 
TCGA-HT-8011 TCGA-HT-8105 
       16.24         6.25 

$`TCF12 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-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 
       14.99         6.54         8.84        90.77        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        67.46        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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        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        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 
       18.71        23.70        14.76        17.82         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-7602 
       75.19        59.18        60.03       154.19         4.01        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-7877 TCGA-HT-7879 
       50.63         0.49        23.61        37.15         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-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59         3.88         1.71        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        6.38        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV 
        7.89        20.81        20.71        19.00        42.77         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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        7.63         0.76         1.28         2.53         4.83         4.11 

  TCF12 MUTATED TCF12 WILD-TYPE 
           0.33            0.03 
  TCF12 MUTATED TCF12 WILD-TYPE 
          57.93          182.33 
  TCF12 MUTATED TCF12 WILD-TYPE 
         10.850          15.865 
[1] "0.3 - 57.9 (10.8)"  "0.0 - 182.3 (15.9)"
[1] "hr=" "2"  
D17V2, continuous
D17V3, binary
                 cls
clus                0   1
  TCF12 MUTATED     4   4
  TCF12 WILD-TYPE 123 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      4    4
  TCF12 WILD-TYPE  123  155
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  FEMALE             4             123
  MALE               4             155
[1] 2 2
[1] FALSE
D17V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TCF12 MUTATED             3                0                 5
  TCF12 WILD-TYPE          94               76               108
D17V5, multiclass
                   clus
vv                  TCF12 MUTATED TCF12 WILD-TYPE
  ASTROCYTOMA                   3              94
  OLIGOASTROCYTOMA              0              76
  OLIGODENDROGLIOMA             5             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"
D17V6, binary
                 cls
clus                0   1
  TCF12 MUTATED     1   7
  TCF12 WILD-TYPE  84 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      1    7
  TCF12 WILD-TYPE   84  194
     clus
vv    TCF12 MUTATED TCF12 WILD-TYPE
  NO              1              84
  YES             7             194
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  TCF12 MUTATED                                  0                         0
  TCF12 WILD-TYPE                                1                        12
                 vv
clus              WHITE
  TCF12 MUTATED       8
  TCF12 WILD-TYPE   261
D17V7, multiclass
                                  clus
vv                                 TCF12 MUTATED TCF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        8             261
[1] 3 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
  TCF12 MUTATED     0   8
  TCF12 WILD-TYPE  14 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      0    8
  TCF12 WILD-TYPE   14  247
                        clus
vv                       TCF12 MUTATED TCF12 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             8             247
[1] 2 2
[1] FALSE

Clustering(18) Variable = SMARCA4 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    12   1
  SMARCA4 WILD-TYPE 213  58
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               271 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                1                58 
$`SMARCA4 MUTATED`
TCGA-CS-5393 TCGA-CS-6667 TCGA-DU-7008 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
       40.18         7.56       156.23        30.67        26.30        94.32 
TCGA-FG-6690 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7855 TCGA-HT-8109 TCGA-HT-A614 
       24.99        17.29        31.69        19.23         3.95         2.70 
TCGA-HW-8322 
       17.82 

$`SMARCA4 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-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95        12.43         8.48         8.02         7.40        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-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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 
        7.73        11.47        62.96       138.28        14.99         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 
        8.84        90.77        10.36         7.96        18.94        44.02 
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-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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        14.93        23.97        13.58        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       17.82         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-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-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-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-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-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        2.96        17.52         6.90        14.53        39.48        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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 
        2.50         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        14.70         0.10         5.33        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         6.38        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             2.70              0.03 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           156.23            182.33 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
            24.99             15.35 
[1] "2.7 - 156.2 (25.0)" "0.0 - 182.3 (15.3)"
[1] "hr=" "4.5"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     5   8
  SMARCA4 WILD-TYPE 122 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      5    8
  SMARCA4 WILD-TYPE  122  151
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE               5               122
  MALE                 8               151
[1] 2 2
[1] FALSE
D18V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SMARCA4 MUTATED             4                2                 7
  SMARCA4 WILD-TYPE          93               74               106
D18V5, multiclass
                   clus
vv                  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  ASTROCYTOMA                     4                93
  OLIGOASTROCYTOMA                2                74
  OLIGODENDROGLIOMA               7               106
[1] 3 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
  SMARCA4 MUTATED     7   6
  SMARCA4 WILD-TYPE  78 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      7    6
  SMARCA4 WILD-TYPE   78  195
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO                7                78
  YES               6               195
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  SMARCA4 MUTATED                                  0                         0
  SMARCA4 WILD-TYPE                                1                        12
                   vv
clus                WHITE
  SMARCA4 MUTATED      13
  SMARCA4 WILD-TYPE   256
D18V7, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  BLACK OR AFRICAN AMERICAN                      0                12
  WHITE                                         13               256
[1] 3 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
  SMARCA4 MUTATED     1  11
  SMARCA4 WILD-TYPE  13 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      1   11
  SMARCA4 WILD-TYPE   13  244
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              11               244
[1] 2 2
[1] FALSE

Clustering(19) Variable = VAV3 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  VAV3 MUTATED     6   1
  VAV3 WILD-TYPE 219  58
  VAV3 MUTATED VAV3 WILD-TYPE 
             7            277 
  VAV3 MUTATED VAV3 WILD-TYPE 
             1             58 
$`VAV3 MUTATED`
TCGA-CS-5397 TCGA-FG-6689 TCGA-HT-7689 TCGA-HT-7875 TCGA-HT-7902 TCGA-HT-A5R5 
        6.38        14.93        14.96         0.33        31.43         0.13 
TCGA-P5-A5EX 
        1.64 

$`VAV3 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-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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        50.14        67.46        41.13 
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-5965 TCGA-FG-6688 
       14.33        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       24.99        23.97        13.58        15.35        17.88        40.08 
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        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
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-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        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-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-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-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        31.69         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-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49        14.01         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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         6.38        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
       42.77         0.23         6.71         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  VAV3 MUTATED VAV3 WILD-TYPE 
          0.13           0.03 
  VAV3 MUTATED VAV3 WILD-TYPE 
         31.43         182.33 
  VAV3 MUTATED VAV3 WILD-TYPE 
          6.38          16.04 
[1] "0.1 - 31.4 (6.4)"   "0.0 - 182.3 (16.0)"
[1] "hr=" "2.1"
D19V2, continuous
D19V3, binary
                cls
clus               0   1
  VAV3 MUTATED     5   3
  VAV3 WILD-TYPE 122 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED      5    3
  VAV3 WILD-TYPE  122  156
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  FEMALE            5            122
  MALE              3            156
[1] 2 2
[1] FALSE
D19V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  VAV3 MUTATED             3                1                 4
  VAV3 WILD-TYPE          94               75               109
D19V5, multiclass
                   clus
vv                  VAV3 MUTATED VAV3 WILD-TYPE
  ASTROCYTOMA                  3             94
  OLIGOASTROCYTOMA             1             75
  OLIGODENDROGLIOMA            4            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"
D19V6, binary
                cls
clus               0   1
  VAV3 MUTATED     3   5
  VAV3 WILD-TYPE  82 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED      3    5
  VAV3 WILD-TYPE   82  196
     clus
vv    VAV3 MUTATED VAV3 WILD-TYPE
  NO             3             82
  YES            5            196
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  VAV3 MUTATED                                  0                         0
  VAV3 WILD-TYPE                                1                        12
                vv
clus             WHITE
  VAV3 MUTATED       8
  VAV3 WILD-TYPE   261
D19V7, multiclass
                                  clus
vv                                 VAV3 MUTATED VAV3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   0             12
  WHITE                                       8            261
[1] 3 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
  VAV3 MUTATED     1   7
  VAV3 WILD-TYPE  13 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED      1    7
  VAV3 WILD-TYPE   13  248
                        clus
vv                       VAV3 MUTATED VAV3 WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            7            248
[1] 2 2
[1] FALSE

Clustering(20) Variable = TMEM216 MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     3   0
  TMEM216 WILD-TYPE 222  59
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                3               281 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                0                59 
$`TMEM216 MUTATED`
TCGA-FG-A60J TCGA-HT-A5R9 TCGA-P5-A5F4 
       14.76         0.07         0.76 

$`TMEM216 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        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        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       17.82         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-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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 
        0.23        29.59         3.88         1.71        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13        14.01        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        6.38        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV 
        7.89        20.81        20.71        19.00        42.77         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-A5F2 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        7.63         1.28         2.53         4.83         4.11 

  TMEM216 MUTATED TMEM216 WILD-TYPE 
             0.07              0.03 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
            14.76            182.33 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
             0.76             16.01 
[1] "0.1 - 14.8 (0.8)"   "0.0 - 182.3 (16.0)"
[1] "hr="     "1200000"
D20V2, continuous
D20V3, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     3   0
  TMEM216 WILD-TYPE 124 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      3    0
  TMEM216 WILD-TYPE  124  159
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  FEMALE               3               124
  MALE                 0               159
[1] 2 2
[1] FALSE
D20V4, continuous
[1] "Remove cluster labels:" "TMEM216 MUTATED"       
clus
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                2               135 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DH-A66B        TCGA-DH-A66F        TCGA-DU-5851        TCGA-DU-5852 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-6410        TCGA-DU-7013        TCGA-DU-7015        TCGA-DU-7018 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-E1-5302        TCGA-E1-5303 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-FG-5963 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7468        TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7485        TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7689        TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-A4DV        TCGA-HT-A5R7        TCGA-HT-A5RA        TCGA-HT-A5RC 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-HT-A615        TCGA-HT-A617        TCGA-HT-A618        TCGA-HT-A61A 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-IK-7675        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F6 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
       TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65Z 
"TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" "TMEM216 WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TMEM216 MUTATED             0                1                 2
  TMEM216 WILD-TYPE          97               75               111
D20V5, multiclass
                   clus
vv                  TMEM216 MUTATED TMEM216 WILD-TYPE
  ASTROCYTOMA                     0                97
  OLIGOASTROCYTOMA                1                75
  OLIGODENDROGLIOMA               2               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"
D20V6, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   3
  TMEM216 WILD-TYPE  85 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    3
  TMEM216 WILD-TYPE   85  198
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                0                85
  YES               3               198
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  TMEM216 MUTATED                                  0                         0
  TMEM216 WILD-TYPE                                1                        12
                   vv
clus                WHITE
  TMEM216 MUTATED       3
  TMEM216 WILD-TYPE   266
D20V7, multiclass
                                  clus
vv                                 TMEM216 MUTATED TMEM216 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  BLACK OR AFRICAN AMERICAN                      0                12
  WHITE                                          3               266
[1] 3 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
  TMEM216 MUTATED     0   3
  TMEM216 WILD-TYPE  14 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    3
  TMEM216 WILD-TYPE   14  252
                        clus
vv                       TMEM216 MUTATED TMEM216 WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO               3               252
[1] 2 2
[1] FALSE

Clustering(21) Variable = ROBO3 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ROBO3 MUTATED     4   0
  ROBO3 WILD-TYPE 221  59
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4             280 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              0              59 
$`ROBO3 MUTATED`
TCGA-CS-6667 TCGA-DB-A64L TCGA-HT-7676 TCGA-P5-A5F2 
        7.56        11.01         0.16         7.63 

$`ROBO3 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-6668 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         8.02         7.40 
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-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-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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        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-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-7637 
       24.99        23.97        13.58        15.35        17.88        40.08 
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        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
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-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        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-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-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-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23        14.27        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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A 
        2.70        13.02         1.81        16.14         5.33         6.38 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        13.45         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 
        1.64         2.37         2.30         4.11         5.88         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  ROBO3 MUTATED ROBO3 WILD-TYPE 
           0.16            0.03 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
          11.01          182.33 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
          7.595          16.025 
[1] "0.2 - 11.0 (7.6)"   "0.0 - 182.3 (16.0)"
[1] "hr="     "3300000"
D21V2, continuous
D21V3, binary
                 cls
clus                0   1
  ROBO3 MUTATED     3   1
  ROBO3 WILD-TYPE 124 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      3    1
  ROBO3 WILD-TYPE  124  158
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  FEMALE             3             124
  MALE               1             158
[1] 2 2
[1] FALSE
D21V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ROBO3 MUTATED             2                0                 2
  ROBO3 WILD-TYPE          95               76               111
D21V5, multiclass
                   clus
vv                  ROBO3 MUTATED ROBO3 WILD-TYPE
  ASTROCYTOMA                   2              95
  OLIGOASTROCYTOMA              0              76
  OLIGODENDROGLIOMA             2             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"
D21V6, binary
                 cls
clus                0   1
  ROBO3 MUTATED     1   3
  ROBO3 WILD-TYPE  84 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      1    3
  ROBO3 WILD-TYPE   84  198
     clus
vv    ROBO3 MUTATED ROBO3 WILD-TYPE
  NO              1              84
  YES             3             198
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  ROBO3 MUTATED                                  0                         0
  ROBO3 WILD-TYPE                                1                        12
                 vv
clus              WHITE
  ROBO3 MUTATED       4
  ROBO3 WILD-TYPE   265
D21V7, multiclass
                                  clus
vv                                 ROBO3 MUTATED ROBO3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        4             265
[1] 3 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
  ROBO3 MUTATED     0   4
  ROBO3 WILD-TYPE  14 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      0    4
  ROBO3 WILD-TYPE   14  251
                        clus
vv                       ROBO3 MUTATED ROBO3 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             4             251
[1] 2 2
[1] FALSE

Clustering(22) Variable = IRS4 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED     4   1
  IRS4 WILD-TYPE 221  58
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            279 
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             58 
$`IRS4 MUTATED`
TCGA-DB-A4XD TCGA-DB-A64L TCGA-E1-5304 TCGA-HT-8108 TCGA-HT-8564 
       27.02        11.01        41.13         2.50        15.72 

$`IRS4 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       12.72        27.62        18.84        18.38        72.95        12.59 
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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
        5.65        12.20        50.14        67.46        79.99        57.93 
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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
        1.71        16.04         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        42.77         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  IRS4 MUTATED IRS4 WILD-TYPE 
          2.50           0.03 
  IRS4 MUTATED IRS4 WILD-TYPE 
         41.13         182.33 
  IRS4 MUTATED IRS4 WILD-TYPE 
         15.72          15.52 
[1] "2.5 - 41.1 (15.7)"  "0.0 - 182.3 (15.5)"
[1] "hr=" "1.5"
D22V2, continuous
D22V3, binary
                cls
clus               0   1
  IRS4 MUTATED     2   3
  IRS4 WILD-TYPE 125 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2    3
  IRS4 WILD-TYPE  125  156
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            2            125
  MALE              3            156
[1] 2 2
[1] FALSE
D22V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  IRS4 MUTATED             3                0                 2
  IRS4 WILD-TYPE          94               76               111
D22V5, multiclass
                   clus
vv                  IRS4 MUTATED IRS4 WILD-TYPE
  ASTROCYTOMA                  3             94
  OLIGOASTROCYTOMA             0             76
  OLIGODENDROGLIOMA            2            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"
D22V6, binary
                cls
clus               0   1
  IRS4 MUTATED     1   4
  IRS4 WILD-TYPE  84 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1    4
  IRS4 WILD-TYPE   84  197
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             1             84
  YES            4            197
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  IRS4 MUTATED                                  0                         0
  IRS4 WILD-TYPE                                1                        12
                vv
clus             WHITE
  IRS4 MUTATED       5
  IRS4 WILD-TYPE   264
D22V7, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   0             12
  WHITE                                       5            264
[1] 3 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
  IRS4 MUTATED     1   4
  IRS4 WILD-TYPE  13 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1    4
  IRS4 WILD-TYPE   13  251
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            4            251
[1] 2 2
[1] FALSE

Clustering(23) Variable = HTRA2 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  HTRA2 MUTATED     4   0
  HTRA2 WILD-TYPE 221  59
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              4             280 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              0              59 
$`HTRA2 MUTATED`
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-P5-A5F1 TCGA-P5-A5F6 
        0.07         0.10         5.88         1.28 

$`HTRA2 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        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        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-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-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-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        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-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        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-8558 TCGA-HT-8563 
        4.70         0.23        29.59         3.88         1.71        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13        14.01        14.70 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        6.38        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV 
        7.89        20.81        20.71        19.00        42.77         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F2 
        6.71         1.64         2.37         2.30         4.11         7.63 
TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        0.76         2.53         4.83         4.11 

  HTRA2 MUTATED HTRA2 WILD-TYPE 
           0.07            0.03 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
           5.88          182.33 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
          0.690          16.025 
[1] "0.1 - 5.9 (0.7)"    "0.0 - 182.3 (16.0)"
[1] "hr="    "450000"
D23V2, continuous
D23V3, binary
                 cls
clus                0   1
  HTRA2 MUTATED     1   3
  HTRA2 WILD-TYPE 126 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      1    3
  HTRA2 WILD-TYPE  126  156
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  FEMALE             1             126
  MALE               3             156
[1] 2 2
[1] FALSE
D23V4, continuous
[1] "Remove cluster labels:" "HTRA2 MUTATED"         
clus
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              1             136 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DH-A66B      TCGA-DH-A66F      TCGA-DU-5851      TCGA-DU-5852 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-5853      TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-5871      TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-6404      TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-6410      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-E1-5302      TCGA-E1-5303 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-FG-5963 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-FG-A60J      TCGA-HT-7468      TCGA-HT-7470      TCGA-HT-7475 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7477      TCGA-HT-7485      TCGA-HT-7607      TCGA-HT-7609 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7611      TCGA-HT-7689      TCGA-HT-7692      TCGA-HT-7693 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-7694      TCGA-HT-7854      TCGA-HT-7875      TCGA-HT-7884 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-8564      TCGA-HT-A4DV      TCGA-HT-A5R7      TCGA-HT-A5RA 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-A5RC      TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-HT-A61A      TCGA-IK-7675      TCGA-P5-A5EU      TCGA-P5-A5EV 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-P5-A5EW      TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
     TCGA-P5-A5F4      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65Z 
"HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" "HTRA2 WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  HTRA2 MUTATED             2                0                 2
  HTRA2 WILD-TYPE          95               76               111
D23V5, multiclass
                   clus
vv                  HTRA2 MUTATED HTRA2 WILD-TYPE
  ASTROCYTOMA                   2              95
  OLIGOASTROCYTOMA              0              76
  OLIGODENDROGLIOMA             2             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"
D23V6, binary
                 cls
clus                0   1
  HTRA2 MUTATED     0   4
  HTRA2 WILD-TYPE  85 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      0    4
  HTRA2 WILD-TYPE   85  197
     clus
vv    HTRA2 MUTATED HTRA2 WILD-TYPE
  NO              0              85
  YES             4             197
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  HTRA2 MUTATED                                  0                         0
  HTRA2 WILD-TYPE                                1                        12
                 vv
clus              WHITE
  HTRA2 MUTATED       4
  HTRA2 WILD-TYPE   265
D23V7, multiclass
                                  clus
vv                                 HTRA2 MUTATED HTRA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        4             265
[1] 3 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
  HTRA2 MUTATED     1   3
  HTRA2 WILD-TYPE  13 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      1    3
  HTRA2 WILD-TYPE   13  252
                        clus
vv                       HTRA2 MUTATED HTRA2 WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             3             252
[1] 2 2
[1] FALSE

Clustering(24) Variable = EIF1AX MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  EIF1AX MUTATED     4   0
  EIF1AX WILD-TYPE 221  59
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               4              280 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               0               59 
$`EIF1AX MUTATED`
TCGA-DB-A4XB TCGA-DU-7306 TCGA-DU-A5TP TCGA-HT-7609 
       12.72        41.98        14.24        45.99 

$`EIF1AX 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       12.20        50.14        67.46        41.13        79.99        57.93 
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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-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-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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
           12.72             0.03 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           45.99           182.33 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           28.11            15.62 
[1] "12.7 - 46.0 (28.1)" "0.0 - 182.3 (15.6)"
[1] "hr="     "9200000"
D24V2, continuous
D24V3, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   4
  EIF1AX WILD-TYPE 127 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    4
  EIF1AX WILD-TYPE  127  155
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              0              127
  MALE                4              155
[1] 2 2
[1] FALSE
D24V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  EIF1AX MUTATED             2                2                 0
  EIF1AX WILD-TYPE          95               74               113
D24V5, multiclass
                   clus
vv                  EIF1AX MUTATED EIF1AX WILD-TYPE
  ASTROCYTOMA                    2               95
  OLIGOASTROCYTOMA               2               74
  OLIGODENDROGLIOMA              0              113
[1] 3 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
  EIF1AX MUTATED     2   2
  EIF1AX WILD-TYPE  83 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      2    2
  EIF1AX WILD-TYPE   83  199
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               2               83
  YES              2              199
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  EIF1AX MUTATED                                  0                         0
  EIF1AX WILD-TYPE                                1                        12
                  vv
clus               WHITE
  EIF1AX MUTATED       4
  EIF1AX WILD-TYPE   265
D24V7, multiclass
                                  clus
vv                                 EIF1AX MUTATED EIF1AX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         4              265
[1] 3 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
  EIF1AX MUTATED     0   4
  EIF1AX WILD-TYPE  14 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    4
  EIF1AX WILD-TYPE   14  251
                        clus
vv                       EIF1AX MUTATED EIF1AX WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              4              251
[1] 2 2
[1] FALSE

Clustering(25) Variable = FAM47C MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  FAM47C MUTATED     7   0
  FAM47C WILD-TYPE 218  59
  FAM47C MUTATED FAM47C WILD-TYPE 
               7              277 
  FAM47C MUTATED FAM47C WILD-TYPE 
               0               59 
$`FAM47C MUTATED`
TCGA-DH-A66F TCGA-FG-7643 TCGA-FG-8186 TCGA-HT-7470 TCGA-HT-7480 TCGA-HT-7610 
       17.19        20.09        16.01         8.81        75.19        56.09 
TCGA-IK-8125 
       42.77 

$`FAM47C 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-DU-5847 
       31.82        30.31        14.40         8.02        42.05        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        50.14        67.46        41.13 
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-5965 TCGA-FG-6688 
       14.33        47.77        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-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       40.08        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-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-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-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-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        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-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        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-8558 TCGA-HT-8563 
        4.70         0.23        29.59         3.88         1.71        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         6.38        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
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-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         2.53         4.83 
TCGA-QH-A65Z 
        4.11 

  FAM47C MUTATED FAM47C WILD-TYPE 
            8.81             0.03 
  FAM47C MUTATED FAM47C WILD-TYPE 
           75.19           182.33 
  FAM47C MUTATED FAM47C WILD-TYPE 
           20.09            15.42 
[1] "8.8 - 75.2 (20.1)"  "0.0 - 182.3 (15.4)"
[1] "hr="     "2.6e+07"
D25V2, continuous
D25V3, binary
                  cls
clus                 0   1
  FAM47C MUTATED     3   4
  FAM47C WILD-TYPE 124 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      3    4
  FAM47C WILD-TYPE  124  155
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE              3              124
  MALE                4              155
[1] 2 2
[1] FALSE
D25V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  FAM47C MUTATED             0                4                 3
  FAM47C WILD-TYPE          97               72               110
D25V5, multiclass
                   clus
vv                  FAM47C MUTATED FAM47C WILD-TYPE
  ASTROCYTOMA                    0               97
  OLIGOASTROCYTOMA               4               72
  OLIGODENDROGLIOMA              3              110
[1] 3 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
  FAM47C MUTATED     2   5
  FAM47C WILD-TYPE  83 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      2    5
  FAM47C WILD-TYPE   83  196
     clus
vv    FAM47C MUTATED FAM47C WILD-TYPE
  NO               2               83
  YES              5              196
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  FAM47C MUTATED                                  0                         0
  FAM47C WILD-TYPE                                1                        12
                  vv
clus               WHITE
  FAM47C MUTATED       7
  FAM47C WILD-TYPE   262
D25V7, multiclass
                                  clus
vv                                 FAM47C MUTATED FAM47C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         7              262
[1] 3 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
  FAM47C MUTATED     1   6
  FAM47C WILD-TYPE  13 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1    6
  FAM47C WILD-TYPE   13  249
                        clus
vv                       FAM47C MUTATED FAM47C WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO              6              249
[1] 2 2
[1] FALSE

Clustering(26) Variable = PLCG1 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  PLCG1 MUTATED     1   3
  PLCG1 WILD-TYPE 224  56
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              4             280 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              3              56 
$`PLCG1 MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-DU-5852 TCGA-DU-5855 
        7.69        21.01         6.74         6.81 

$`PLCG1 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-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       12.43         8.48         7.56         8.02         7.40        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-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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46        13.38         8.45       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28        14.99         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-7304 
       18.94        44.02        62.01        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-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-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-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-7637 TCGA-FG-7638 TCGA-FG-7641 
       13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 
       18.71        23.70        14.76        17.82         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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  PLCG1 MUTATED PLCG1 WILD-TYPE 
           6.74            0.03 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
          21.01          182.33 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
          7.250          15.865 
[1] "6.7 - 21.0 (7.2)"   "0.0 - 182.3 (15.9)"
[1] "hr=" "11" 
D26V2, continuous
D26V3, binary
                 cls
clus                0   1
  PLCG1 MUTATED     2   2
  PLCG1 WILD-TYPE 125 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      2    2
  PLCG1 WILD-TYPE  125  157
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  FEMALE             2             125
  MALE               2             157
[1] 2 2
[1] FALSE
D26V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  PLCG1 MUTATED             1                2                 1
  PLCG1 WILD-TYPE          96               74               112
D26V5, multiclass
                   clus
vv                  PLCG1 MUTATED PLCG1 WILD-TYPE
  ASTROCYTOMA                   1              96
  OLIGOASTROCYTOMA              2              74
  OLIGODENDROGLIOMA             1             112
[1] 3 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
  PLCG1 MUTATED     2   2
  PLCG1 WILD-TYPE  83 199
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      2    2
  PLCG1 WILD-TYPE   83  199
     clus
vv    PLCG1 MUTATED PLCG1 WILD-TYPE
  NO              2              83
  YES             2             199
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  PLCG1 MUTATED                                  0                         1
  PLCG1 WILD-TYPE                                1                        11
                 vv
clus              WHITE
  PLCG1 MUTATED       3
  PLCG1 WILD-TYPE   266
D26V7, multiclass
                                  clus
vv                                 PLCG1 MUTATED PLCG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    1              11
  WHITE                                        3             266
[1] 3 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
  PLCG1 MUTATED     0   3
  PLCG1 WILD-TYPE  14 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      0    3
  PLCG1 WILD-TYPE   14  252
                        clus
vv                       PLCG1 MUTATED PLCG1 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             3             252
[1] 2 2
[1] FALSE

Clustering(27) Variable = DDX5 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     4   0
  DDX5 WILD-TYPE 221  59
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            280 
  DDX5 MUTATED DDX5 WILD-TYPE 
             0             59 
$`DDX5 MUTATED`
TCGA-CS-4943 TCGA-DU-5853 TCGA-FG-8186 TCGA-HT-7687 
       18.15        13.38        16.01         0.10 

$`DDX5 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-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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46         6.74         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        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-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-7637 
       24.99        23.97        13.58        15.35        17.88        40.08 
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-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74        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-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        1.71        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  DDX5 MUTATED DDX5 WILD-TYPE 
          0.10           0.03 
  DDX5 MUTATED DDX5 WILD-TYPE 
         18.15         182.33 
  DDX5 MUTATED DDX5 WILD-TYPE 
        14.695         15.620 
[1] "0.1 - 18.1 (14.7)"  "0.0 - 182.3 (15.6)"
[1] "hr="     "3300000"
D27V2, continuous
D27V3, binary
                cls
clus               0   1
  DDX5 MUTATED     1   3
  DDX5 WILD-TYPE 126 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      1    3
  DDX5 WILD-TYPE  126  156
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            1            126
  MALE              3            156
[1] 2 2
[1] FALSE
D27V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DDX5 MUTATED             1                2                 1
  DDX5 WILD-TYPE          96               74               112
D27V5, multiclass
                   clus
vv                  DDX5 MUTATED DDX5 WILD-TYPE
  ASTROCYTOMA                  1             96
  OLIGOASTROCYTOMA             2             74
  OLIGODENDROGLIOMA            1            112
[1] 3 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
  DDX5 MUTATED     1   3
  DDX5 WILD-TYPE  84 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      1    3
  DDX5 WILD-TYPE   84  198
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             1             84
  YES            3            198
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  DDX5 MUTATED                                  0                         0
  DDX5 WILD-TYPE                                1                        12
                vv
clus             WHITE
  DDX5 MUTATED       4
  DDX5 WILD-TYPE   265
D27V7, multiclass
                                  clus
vv                                 DDX5 MUTATED DDX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   0             12
  WHITE                                       4            265
[1] 3 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
  DDX5 MUTATED     1   2
  DDX5 WILD-TYPE  13 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      1    2
  DDX5 WILD-TYPE   13  253
                        clus
vv                       DDX5 MUTATED DDX5 WILD-TYPE
  HISPANIC OR LATINO                1             13
  NOT HISPANIC OR LATINO            2            253
[1] 2 2
[1] FALSE

Clustering(28) Variable = ZNF709 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  ZNF709 MUTATED     3   0
  ZNF709 WILD-TYPE 222  59
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3              281 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               0               59 
$`ZNF709 MUTATED`
TCGA-HT-7470 TCGA-HT-7608 TCGA-HT-7620 
        8.81        22.06        14.27 

$`ZNF709 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
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-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-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-6407 
       87.45         7.04        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-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       17.88        40.08        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        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29         3.16        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23         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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A 
        2.70        13.02         1.81        16.14         5.33         6.38 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        13.45         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        0.76         1.28         2.53         4.83         4.11 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
            8.81             0.03 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           22.06           182.33 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           14.27            15.72 
[1] "8.8 - 22.1 (14.3)"  "0.0 - 182.3 (15.7)"
[1] "hr="     "3300000"
D28V2, continuous
D28V3, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     0   3
  ZNF709 WILD-TYPE 127 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    3
  ZNF709 WILD-TYPE  127  156
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  FEMALE              0              127
  MALE                3              156
[1] 2 2
[1] FALSE
D28V4, continuous
[1] "Remove cluster labels:" "ZNF709 MUTATED"        
clus
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               1              136 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DH-5140       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DH-A66B       TCGA-DH-A66F       TCGA-DU-5851       TCGA-DU-5852 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-5853       TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-5871       TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-6404       TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-6410       TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7019       TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7300       TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-7306       TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-8162       TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-8168       TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-DU-A5TU       TCGA-DU-A5TW       TCGA-E1-5302       TCGA-E1-5303 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5319       TCGA-E1-5322       TCGA-FG-5963 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-5965       TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-6691       TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-8185       TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-8189       TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FG-A60J       TCGA-HT-7468       TCGA-HT-7475       TCGA-HT-7477 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7485       TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7689       TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-7854       TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-A4DV       TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HT-A615       TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-IK-7675       TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-P5-A5EX       TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-P5-A5F6       TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65Z 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZNF709 MUTATED             0                1                 2
  ZNF709 WILD-TYPE          97               75               111
D28V5, multiclass
                   clus
vv                  ZNF709 MUTATED ZNF709 WILD-TYPE
  ASTROCYTOMA                    0               97
  OLIGOASTROCYTOMA               1               75
  OLIGODENDROGLIOMA              2              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"
D28V6, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     2   1
  ZNF709 WILD-TYPE  83 200
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      2    1
  ZNF709 WILD-TYPE   83  200
     clus
vv    ZNF709 MUTATED ZNF709 WILD-TYPE
  NO               2               83
  YES              1              200
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  ZNF709 MUTATED                                  0                         1
  ZNF709 WILD-TYPE                                1                        11
                  vv
clus               WHITE
  ZNF709 MUTATED       2
  ZNF709 WILD-TYPE   267
D28V7, multiclass
                                  clus
vv                                 ZNF709 MUTATED ZNF709 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     1               11
  WHITE                                         2              267
[1] 3 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
  ZNF709 MUTATED     0   3
  ZNF709 WILD-TYPE  14 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    3
  ZNF709 WILD-TYPE   14  252
                        clus
vv                       ZNF709 MUTATED ZNF709 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              3              252
[1] 2 2
[1] FALSE

Clustering(29) Variable = TRERF1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED     2   1
  TRERF1 WILD-TYPE 223  58
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               3              281 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               1               58 
$`TRERF1 MUTATED`
TCGA-CS-4938 TCGA-E1-5307 TCGA-HT-7902 
        4.70        57.93        31.43 

$`TRERF1 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-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-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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        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-7637 
       24.99        23.97        13.58        15.35        17.88        40.08 
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        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
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-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        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-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-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-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-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-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        11.28         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A 
        2.70        13.02         1.81        16.14         5.33         6.38 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        13.45         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        0.76         1.28         2.53         4.83         4.11 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
            4.70             0.03 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           57.93           182.33 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           31.43            15.52 
[1] "4.7 - 57.9 (31.4)"  "0.0 - 182.3 (15.5)"
[1] "hr=" "1.4"
D29V2, continuous
D29V3, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     3   0
  TRERF1 WILD-TYPE 124 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      3    0
  TRERF1 WILD-TYPE  124  159
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE              3              124
  MALE                0              159
[1] 2 2
[1] FALSE
D29V4, continuous
[1] "Remove cluster labels:" "TRERF1 MUTATED"        
clus
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               2              135 
      TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395       TCGA-CS-5396 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188       TCGA-CS-6290 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667       TCGA-CS-6668 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE       TCGA-DB-A64L 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S       TCGA-DB-A64U 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X       TCGA-DH-5140 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299       TCGA-DU-7300 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304       TCGA-DU-7306 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161       TCGA-DU-8162 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167       TCGA-DU-8168 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TU 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-DU-A5TW       TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-E1-5305       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5319 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-E1-5322       TCGA-FG-5963       TCGA-FG-5965       TCGA-FG-6688 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691       TCGA-FG-7636 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185       TCGA-FG-8186 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189       TCGA-FG-A4MT 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J       TCGA-HT-7468 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-IK-7675 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
      TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65Z 
"TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" "TRERF1 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TRERF1 MUTATED             2                1                 0
  TRERF1 WILD-TYPE          95               75               113
D29V5, multiclass
                   clus
vv                  TRERF1 MUTATED TRERF1 WILD-TYPE
  ASTROCYTOMA                    2               95
  OLIGOASTROCYTOMA               1               75
  OLIGODENDROGLIOMA              0              113
[1] 3 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
  TRERF1 MUTATED     0   3
  TRERF1 WILD-TYPE  85 198
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      0    3
  TRERF1 WILD-TYPE   85  198
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO               0               85
  YES              3              198
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  TRERF1 MUTATED                                  0                         0
  TRERF1 WILD-TYPE                                1                        12
                  vv
clus               WHITE
  TRERF1 MUTATED       3
  TRERF1 WILD-TYPE   266
D29V7, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         3              266
[1] 3 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
  TRERF1 MUTATED     0   3
  TRERF1 WILD-TYPE  14 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      0    3
  TRERF1 WILD-TYPE   14  252
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              3              252
[1] 2 2
[1] FALSE

Clustering(30) Variable = BCOR MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  BCOR MUTATED     6   3
  BCOR WILD-TYPE 219  56
  BCOR MUTATED BCOR WILD-TYPE 
             9            275 
  BCOR MUTATED BCOR WILD-TYPE 
             3             56 
$`BCOR MUTATED`
TCGA-CS-4942 TCGA-DB-5276 TCGA-DB-A64W TCGA-DB-A64X TCGA-DU-6403 TCGA-DU-7302 
       43.89        72.92        13.64        10.92        11.64        60.30 
TCGA-E1-5318 TCGA-HT-7610 TCGA-HW-A5KJ 
       78.21        56.09        20.35 

$`BCOR 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-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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        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-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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       14.73        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22        87.45         7.04       133.74        19.89 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99         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-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        62.01        25.91        23.31        41.98         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-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-E1-5302 TCGA-E1-5303 
        4.96         3.65         5.65        12.20        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93       134.27        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        47.77        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-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       17.82         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-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-7611 
        4.57        17.29         3.16        22.06        45.99        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-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       29.59         3.88         1.71        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        6.38        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KK 
        4.31        21.70        21.60        19.59        17.82         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        0.76         1.28         2.53         4.83         4.11 

  BCOR MUTATED BCOR WILD-TYPE 
         10.92           0.03 
  BCOR MUTATED BCOR WILD-TYPE 
         78.21         182.33 
  BCOR MUTATED BCOR WILD-TYPE 
         43.89          15.48 
[1] "10.9 - 78.2 (43.9)" "0.0 - 182.3 (15.5)"
[1] "hr=" "1"  
D30V2, continuous
D30V3, binary
                cls
clus               0   1
  BCOR MUTATED     7   2
  BCOR WILD-TYPE 120 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      7    2
  BCOR WILD-TYPE  120  157
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE            7            120
  MALE              2            157
[1] 2 2
[1] FALSE
D30V4, continuous
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  BCOR MUTATED             2                4                 3
  BCOR WILD-TYPE          95               72               110
D30V5, multiclass
                   clus
vv                  BCOR MUTATED BCOR WILD-TYPE
  ASTROCYTOMA                  2             95
  OLIGOASTROCYTOMA             4             72
  OLIGODENDROGLIOMA            3            110
[1] 3 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
  BCOR MUTATED     3   6
  BCOR WILD-TYPE  82 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      3    6
  BCOR WILD-TYPE   82  195
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO             3             82
  YES            6            195
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  BCOR MUTATED                                  0                         1
  BCOR WILD-TYPE                                1                        11
                vv
clus             WHITE
  BCOR MUTATED       8
  BCOR WILD-TYPE   261
D30V7, multiclass
                                  clus
vv                                 BCOR MUTATED BCOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   1             11
  WHITE                                       8            261
[1] 3 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
  BCOR MUTATED     0   7
  BCOR WILD-TYPE  14 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      0    7
  BCOR WILD-TYPE   14  248
                        clus
vv                       BCOR MUTATED BCOR WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            7            248
[1] 2 2
[1] FALSE

Clustering(31) Variable = SRPX MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  SRPX MUTATED     1   2
  SRPX WILD-TYPE 224  57
  SRPX MUTATED SRPX WILD-TYPE 
             3            281 
  SRPX MUTATED SRPX WILD-TYPE 
             2             57 
$`SRPX MUTATED`
TCGA-DH-5144 TCGA-DU-7006 TCGA-E1-5319 
        8.02        11.47        95.57 

$`SRPX 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66B TCGA-DH-A66F TCGA-DU-5847 
       31.82        30.31        14.40        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        62.96       156.23       138.28        14.99 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
       57.93       134.27        78.21       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-7636 TCGA-FG-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A 
        2.70        13.02         1.81        16.14         5.33         6.38 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        13.45         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00        42.77         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        0.76         1.28         2.53         4.83         4.11 

  SRPX MUTATED SRPX WILD-TYPE 
          8.02           0.03 
  SRPX MUTATED SRPX WILD-TYPE 
         95.57         182.33 
  SRPX MUTATED SRPX WILD-TYPE 
         11.47          15.72 
[1] "8.0 - 95.6 (11.5)"  "0.0 - 182.3 (15.7)"
[1] "hr=" "1.7"
D31V2, continuous
D31V3, binary
                cls
clus               0   1
  SRPX MUTATED     3   0
  SRPX WILD-TYPE 124 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      3    0
  SRPX WILD-TYPE  124  159
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE            3            124
  MALE              0            159
[1] 2 2
[1] FALSE
D31V4, continuous
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             2            135 
    TCGA-CS-4938     TCGA-CS-4941     TCGA-CS-4942     TCGA-CS-4943 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5393     TCGA-CS-5395 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-5396     TCGA-CS-5397     TCGA-CS-6186     TCGA-CS-6188 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-6290     TCGA-CS-6665     TCGA-CS-6666     TCGA-CS-6667 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-CS-6668     TCGA-CS-6669     TCGA-DB-5274     TCGA-DB-A4XE 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-A64L     TCGA-DB-A64Q     TCGA-DB-A64R     TCGA-DB-A64S 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DB-A64U     TCGA-DB-A64V     TCGA-DB-A64W     TCGA-DB-A64X 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-5140     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-A66B 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DH-A66F     TCGA-DU-5851     TCGA-DU-5852     TCGA-DU-5853 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-5854     TCGA-DU-5855     TCGA-DU-5870     TCGA-DU-5871 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-5874     TCGA-DU-6396     TCGA-DU-6403     TCGA-DU-6404 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-6405     TCGA-DU-6407     TCGA-DU-6408     TCGA-DU-6410 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7013     TCGA-DU-7015     TCGA-DU-7018     TCGA-DU-7019 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7294     TCGA-DU-7298     TCGA-DU-7299     TCGA-DU-7300 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7301     TCGA-DU-7302     TCGA-DU-7304     TCGA-DU-7306 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-7309     TCGA-DU-8158     TCGA-DU-8161     TCGA-DU-8162 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-8163     TCGA-DU-8165     TCGA-DU-8167     TCGA-DU-8168 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A5TP     TCGA-DU-A5TR     TCGA-DU-A5TS     TCGA-DU-A5TU 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-DU-A5TW     TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5305     TCGA-E1-5307     TCGA-E1-5311     TCGA-E1-5318 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-E1-5322     TCGA-FG-5963     TCGA-FG-5965     TCGA-FG-6688 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-6689     TCGA-FG-6690     TCGA-FG-6691     TCGA-FG-7636 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-7638     TCGA-FG-8181     TCGA-FG-8185     TCGA-FG-8186 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-8187     TCGA-FG-8188     TCGA-FG-8189     TCGA-FG-A4MT 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-FG-A4MW     TCGA-FG-A4MX     TCGA-FG-A60J     TCGA-HT-7468 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7470     TCGA-HT-7475     TCGA-HT-7477     TCGA-HT-7485 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7607     TCGA-HT-7609     TCGA-HT-7611     TCGA-HT-7689 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7692     TCGA-HT-7693     TCGA-HT-7694     TCGA-HT-7854 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-7875     TCGA-HT-7884     TCGA-HT-8564     TCGA-HT-A4DV 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-A5R7     TCGA-HT-A5RA     TCGA-HT-A5RC     TCGA-HT-A615 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-HT-A617     TCGA-HT-A618     TCGA-HT-A61A     TCGA-IK-7675 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-P5-A5EU     TCGA-P5-A5EV     TCGA-P5-A5EW     TCGA-P5-A5EX 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-P5-A5F0     TCGA-P5-A5F2     TCGA-P5-A5F4     TCGA-P5-A5F6 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-QH-A65S     TCGA-QH-A65V     TCGA-QH-A65Z 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
                vv
clus             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  SRPX MUTATED             1                0                 2
  SRPX WILD-TYPE          96               76               111
D31V5, multiclass
                   clus
vv                  SRPX MUTATED SRPX WILD-TYPE
  ASTROCYTOMA                  1             96
  OLIGOASTROCYTOMA             0             76
  OLIGODENDROGLIOMA            2            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"
D31V6, binary
                cls
clus               0   1
  SRPX MUTATED     1   2
  SRPX WILD-TYPE  84 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    2
  SRPX WILD-TYPE   84  199
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO             1             84
  YES            2            199
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  SRPX MUTATED                                  0                         0
  SRPX WILD-TYPE                                1                        12
                vv
clus             WHITE
  SRPX MUTATED       3
  SRPX WILD-TYPE   266
D31V7, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  BLACK OR AFRICAN AMERICAN                   0             12
  WHITE                                       3            266
[1] 3 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
  SRPX MUTATED     0   3
  SRPX WILD-TYPE  14 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0    3
  SRPX WILD-TYPE   14  252
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0             14
  NOT HISPANIC OR LATINO            3            252
[1] 2 2
[1] FALSE

Clustering(32) Variable = DOCK5 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED     3   2
  DOCK5 WILD-TYPE 222  57
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              5             279 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              2              57 
$`DOCK5 MUTATED`
TCGA-CS-6186 TCGA-CS-6665 TCGA-DU-6405 TCGA-DU-A5TT TCGA-HT-7467 
       17.69        12.43        19.89         4.96         0.10 

$`DOCK5 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-6188 
       40.18         0.10        21.01         9.96         6.38        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95         8.48         7.56         8.02         7.40        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-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-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       11.64       133.74        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-7012 
       11.47        62.96       156.23       138.28        14.99         6.54 
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-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-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-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         3.65         5.65        12.20 
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-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-7637 TCGA-FG-7638 TCGA-FG-7641 
       13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7468 
       18.71        23.70        14.76        17.82         0.13         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-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        42.77         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.10            0.03 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          19.89          182.33 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          12.43           15.72 
[1] "0.1 - 19.9 (12.4)"  "0.0 - 182.3 (15.7)"
[1] "hr=" "5.6"
D32V2, continuous
D32V3, binary
                 cls
clus                0   1
  DOCK5 MUTATED     2   3
  DOCK5 WILD-TYPE 125 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      2    3
  DOCK5 WILD-TYPE  125  156
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  FEMALE             2             125
  MALE               3             156
[1] 2 2
[1] FALSE
D32V4, continuous
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DOCK5 MUTATED             2                1                 2
  DOCK5 WILD-TYPE          95               75               111
D32V5, multiclass
                   clus
vv                  DOCK5 MUTATED DOCK5 WILD-TYPE
  ASTROCYTOMA                   2              95
  OLIGOASTROCYTOMA              1              75
  OLIGODENDROGLIOMA             2             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"
D32V6, binary
                 cls
clus                0   1
  DOCK5 MUTATED     2   3
  DOCK5 WILD-TYPE  83 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      2    3
  DOCK5 WILD-TYPE   83  198
     clus
vv    DOCK5 MUTATED DOCK5 WILD-TYPE
  NO              2              83
  YES             3             198
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  DOCK5 MUTATED                                  0                         0
  DOCK5 WILD-TYPE                                1                        12
                 vv
clus              WHITE
  DOCK5 MUTATED       5
  DOCK5 WILD-TYPE   264
D32V7, multiclass
                                  clus
vv                                 DOCK5 MUTATED DOCK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        5             264
[1] 3 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
  DOCK5 MUTATED     0   5
  DOCK5 WILD-TYPE  14 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      0    5
  DOCK5 WILD-TYPE   14  250
                        clus
vv                       DOCK5 MUTATED DOCK5 WILD-TYPE
  HISPANIC OR LATINO                 0              14
  NOT HISPANIC OR LATINO             5             250
[1] 2 2
[1] FALSE

Clustering(33) Variable = GIGYF2 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  GIGYF2 MUTATED     2   2
  GIGYF2 WILD-TYPE 223  57
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              280 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               2               57 
$`GIGYF2 MUTATED`
TCGA-DU-5853 TCGA-DU-6402 TCGA-DU-6405 TCGA-HT-A5R9 
       13.38         7.04        19.89         0.07 

$`GIGYF2 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A66F 
       31.82        30.31        14.40         8.02        42.05        17.19 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
       18.02        14.56        17.46         6.74         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-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       11.64       133.74        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-7012 
       11.47        62.96       156.23       138.28        14.99         6.54 
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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       12.20        50.14        67.46        41.13        79.99        57.93 
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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        3.88         1.71        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        14.01        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
       13.02         1.81        16.14         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        1.28         2.53         4.83         4.11 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
            0.07             0.03 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           19.89           182.33 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          10.210           15.865 
[1] "0.1 - 19.9 (10.2)"  "0.0 - 182.3 (15.9)"
[1] "hr=" "7.2"
D33V2, continuous
D33V3, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED     2   2
  GIGYF2 WILD-TYPE 125 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      2    2
  GIGYF2 WILD-TYPE  125  157
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  FEMALE              2              125
  MALE                2              157
[1] 2 2
[1] FALSE
D33V4, continuous
[1] "Remove cluster labels:" "GIGYF2 MUTATED"        
clus
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               2              135 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-5274       TCGA-DB-A4XE 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DB-A64L       TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DB-A64U       TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DH-5140       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DH-A66B       TCGA-DH-A66F       TCGA-DU-5851       TCGA-DU-5852 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410       TCGA-DU-7013 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019       TCGA-DU-7294 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-7298       TCGA-DU-7299       TCGA-DU-7300       TCGA-DU-7301 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-7302       TCGA-DU-7304       TCGA-DU-7306       TCGA-DU-7309 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-8158       TCGA-DU-8161       TCGA-DU-8162       TCGA-DU-8163 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-8165       TCGA-DU-8167       TCGA-DU-8168       TCGA-DU-A5TP 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TU       TCGA-DU-A5TW 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5305 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5319 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-E1-5322       TCGA-FG-5963       TCGA-FG-5965       TCGA-FG-6688 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691       TCGA-FG-7636 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185       TCGA-FG-8186 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189       TCGA-FG-A4MT 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J       TCGA-HT-7468 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477       TCGA-HT-7485 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611       TCGA-HT-7689 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7694       TCGA-HT-7854 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-IK-7675 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65Z 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  GIGYF2 MUTATED             2                1                 1
  GIGYF2 WILD-TYPE          95               75               112
D33V5, multiclass
                   clus
vv                  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  ASTROCYTOMA                    2               95
  OLIGOASTROCYTOMA               1               75
  OLIGODENDROGLIOMA              1              112
[1] 3 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
  GIGYF2 MUTATED     3   1
  GIGYF2 WILD-TYPE  82 200
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      3    1
  GIGYF2 WILD-TYPE   82  200
     clus
vv    GIGYF2 MUTATED GIGYF2 WILD-TYPE
  NO               3               82
  YES              1              200
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  GIGYF2 MUTATED                                  0                         0
  GIGYF2 WILD-TYPE                                1                        12
                  vv
clus               WHITE
  GIGYF2 MUTATED       4
  GIGYF2 WILD-TYPE   265
D33V7, multiclass
                                  clus
vv                                 GIGYF2 MUTATED GIGYF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         4              265
[1] 3 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
  GIGYF2 MUTATED     0   4
  GIGYF2 WILD-TYPE  14 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      0    4
  GIGYF2 WILD-TYPE   14  251
                        clus
vv                       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              4              251
[1] 2 2
[1] FALSE

Clustering(34) Variable = NIPBL MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED     5   0
  NIPBL WILD-TYPE 220  59
  NIPBL MUTATED NIPBL WILD-TYPE 
              5             279 
  NIPBL MUTATED NIPBL WILD-TYPE 
              0              59 
$`NIPBL MUTATED`
TCGA-DB-A4XG TCGA-DH-5141 TCGA-DU-7009 TCGA-FN-7833 TCGA-HT-7468 
       72.95        31.82       138.28         0.13         6.67 

$`NIPBL 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-A4XH 
       12.72        27.62        27.02        18.84        18.38        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-5142 
       27.81        14.73        13.64        10.92        19.96        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
       14.40         8.02        42.05        17.19        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-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        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-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 
        7.73        11.47        62.96       156.23        14.99         6.54 
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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       12.20        50.14        67.46        41.13        79.99        57.93 
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-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-7637 TCGA-FG-7638 
       23.97        13.58        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-HT-7467 
        5.26        18.71        23.70        14.76        17.82         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-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-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        42.77         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  NIPBL MUTATED NIPBL WILD-TYPE 
           0.13            0.03 
  NIPBL MUTATED NIPBL WILD-TYPE 
         138.28          182.33 
  NIPBL MUTATED NIPBL WILD-TYPE 
          31.82           15.52 
[1] "0.1 - 138.3 (31.8)" "0.0 - 182.3 (15.5)"
[1] "hr="     "2.8e+07"
D34V2, continuous
D34V3, binary
                 cls
clus                0   1
  NIPBL MUTATED     1   4
  NIPBL WILD-TYPE 126 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      1    4
  NIPBL WILD-TYPE  126  155
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE             1             126
  MALE               4             155
[1] 2 2
[1] FALSE
D34V4, continuous
[1] "Remove cluster labels:" "NIPBL MUTATED"         
clus
  NIPBL MUTATED NIPBL WILD-TYPE 
              1             136 
     TCGA-CS-4938      TCGA-CS-4941      TCGA-CS-4942      TCGA-CS-4943 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-4944      TCGA-CS-5390      TCGA-CS-5393      TCGA-CS-5395 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-5396      TCGA-CS-5397      TCGA-CS-6186      TCGA-CS-6188 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-6290      TCGA-CS-6665      TCGA-CS-6666      TCGA-CS-6667 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-CS-6668      TCGA-CS-6669      TCGA-DB-5274      TCGA-DB-A4XE 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-A64L      TCGA-DB-A64Q      TCGA-DB-A64R      TCGA-DB-A64S 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DB-A64U      TCGA-DB-A64V      TCGA-DB-A64W      TCGA-DB-A64X 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DH-5140      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DH-A66B      TCGA-DH-A66F      TCGA-DU-5851      TCGA-DU-5852 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-5853      TCGA-DU-5854      TCGA-DU-5855      TCGA-DU-5870 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-5871      TCGA-DU-5874      TCGA-DU-6396      TCGA-DU-6403 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-6404      TCGA-DU-6405      TCGA-DU-6407      TCGA-DU-6408 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-6410      TCGA-DU-7013      TCGA-DU-7015      TCGA-DU-7018 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-7019      TCGA-DU-7294      TCGA-DU-7298      TCGA-DU-7299 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-7300      TCGA-DU-7301      TCGA-DU-7302      TCGA-DU-7304 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-7306      TCGA-DU-7309      TCGA-DU-8158      TCGA-DU-8161 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-8162      TCGA-DU-8163      TCGA-DU-8165      TCGA-DU-8167 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-8168      TCGA-DU-A5TP      TCGA-DU-A5TR      TCGA-DU-A5TS 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-DU-A5TU      TCGA-DU-A5TW      TCGA-E1-5302      TCGA-E1-5303 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5304      TCGA-E1-5305      TCGA-E1-5307      TCGA-E1-5311 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5319      TCGA-E1-5322      TCGA-FG-5963 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-FG-5965      TCGA-FG-6688      TCGA-FG-6689      TCGA-FG-6690 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-FG-6691      TCGA-FG-7636      TCGA-FG-7638      TCGA-FG-8181 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-FG-8185      TCGA-FG-8186      TCGA-FG-8187      TCGA-FG-8188 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-FG-8189      TCGA-FG-A4MT      TCGA-FG-A4MW      TCGA-FG-A4MX 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-FG-A60J      TCGA-HT-7470      TCGA-HT-7475      TCGA-HT-7477 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-HT-7485      TCGA-HT-7607      TCGA-HT-7609      TCGA-HT-7611 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-HT-7689      TCGA-HT-7692      TCGA-HT-7693      TCGA-HT-7694 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-HT-7854      TCGA-HT-7875      TCGA-HT-7884      TCGA-HT-8564 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-HT-A4DV      TCGA-HT-A5R7      TCGA-HT-A5RA      TCGA-HT-A5RC 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-HT-A615      TCGA-HT-A617      TCGA-HT-A618      TCGA-HT-A61A 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-IK-7675      TCGA-P5-A5EU      TCGA-P5-A5EV      TCGA-P5-A5EW 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-P5-A5EX      TCGA-P5-A5F0      TCGA-P5-A5F2      TCGA-P5-A5F4 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
     TCGA-P5-A5F6      TCGA-QH-A65S      TCGA-QH-A65V      TCGA-QH-A65Z 
"NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" "NIPBL WILD-TYPE" 
                 vv
clus              ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  NIPBL MUTATED             0                1                 4
  NIPBL WILD-TYPE          97               75               109
D34V5, multiclass
                   clus
vv                  NIPBL MUTATED NIPBL WILD-TYPE
  ASTROCYTOMA                   0              97
  OLIGOASTROCYTOMA              1              75
  OLIGODENDROGLIOMA             4             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"
D34V6, binary
                 cls
clus                0   1
  NIPBL MUTATED     1   4
  NIPBL WILD-TYPE  84 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      1    4
  NIPBL WILD-TYPE   84  197
     clus
vv    NIPBL MUTATED NIPBL WILD-TYPE
  NO              1              84
  YES             4             197
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  NIPBL MUTATED                                  0                         0
  NIPBL WILD-TYPE                                1                        12
                 vv
clus              WHITE
  NIPBL MUTATED       5
  NIPBL WILD-TYPE   264
D34V7, multiclass
                                  clus
vv                                 NIPBL MUTATED NIPBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  BLACK OR AFRICAN AMERICAN                    0              12
  WHITE                                        5             264
[1] 3 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
  NIPBL MUTATED     1   4
  NIPBL WILD-TYPE  13 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      1    4
  NIPBL WILD-TYPE   13  251
                        clus
vv                       NIPBL MUTATED NIPBL WILD-TYPE
  HISPANIC OR LATINO                 1              13
  NOT HISPANIC OR LATINO             4             251
[1] 2 2
[1] FALSE

Clustering(35) Variable = ZBTB20 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    11   1
  ZBTB20 WILD-TYPE 214  58
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              12              272 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               1               58 
$`ZBTB20 MUTATED`
TCGA-DB-A4XH TCGA-DB-A64V TCGA-DB-A64W TCGA-DU-5849 TCGA-DU-6408 TCGA-FG-8187 
       12.59        14.73        13.64        14.56       114.08        20.09 
TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7881 TCGA-HT-8563 TCGA-HT-8564 TCGA-HW-A5KJ 
        4.57        22.06         2.93        16.04        15.72        20.35 

$`ZBTB20 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-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        7.40        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-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-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       27.81        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
        8.02        42.05        17.19        18.02        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        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-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       19.89        94.52         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99         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-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5302 
       15.12         4.96         3.65         5.65        12.20        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-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       15.35        17.88        40.08        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       14.76        17.82         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-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-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
      107.93        17.29         3.16        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-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        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-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-7882 
       37.15         0.33         0.13         3.68         5.33         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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        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-8558 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
        3.88         1.71         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       42.77         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         1.28         2.53 
TCGA-QH-A65V TCGA-QH-A65Z 
        4.83         4.11 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
            2.93             0.03 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          114.08           182.33 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          15.225           15.765 
[1] "2.9 - 114.1 (15.2)" "0.0 - 182.3 (15.8)"
[1] "hr=" "2.4"
D35V2, continuous
D35V3, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     4   9
  ZBTB20 WILD-TYPE 123 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      4    9
  ZBTB20 WILD-TYPE  123  150
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE              4              123
  MALE                9              150
[1] 2 2
[1] FALSE
D35V4, continuous
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  ZBTB20 MUTATED             2                4                 7
  ZBTB20 WILD-TYPE          95               72               106
D35V5, multiclass
                   clus
vv                  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASTROCYTOMA                    2               95
  OLIGOASTROCYTOMA               4               72
  OLIGODENDROGLIOMA              7              106
[1] 3 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
  ZBTB20 MUTATED     1  12
  ZBTB20 WILD-TYPE  84 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      1   12
  ZBTB20 WILD-TYPE   84  189
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO               1               84
  YES             12              189
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  ZBTB20 MUTATED                                  0                         2
  ZBTB20 WILD-TYPE                                1                        10
                  vv
clus               WHITE
  ZBTB20 MUTATED      11
  ZBTB20 WILD-TYPE   258
D35V7, multiclass
                                  clus
vv                                 ZBTB20 MUTATED ZBTB20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     2               10
  WHITE                                        11              258
[1] 3 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
  ZBTB20 MUTATED     1  11
  ZBTB20 WILD-TYPE  13 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      1   11
  ZBTB20 WILD-TYPE   13  244
                        clus
vv                       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  HISPANIC OR LATINO                  1               13
  NOT HISPANIC OR LATINO             11              244
[1] 2 2
[1] FALSE

Clustering(36) Variable = TRIP12 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  TRIP12 MUTATED     5   0
  TRIP12 WILD-TYPE 220  59
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5              279 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               0               59 
$`TRIP12 MUTATED`
TCGA-DB-5274 TCGA-HT-7610 TCGA-HT-7677 TCGA-HT-7694 TCGA-HT-7873 
       75.25        56.09        16.24         6.90        23.61 

$`TRIP12 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-DB-5273 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
        7.40        81.96        47.93        72.92        46.65        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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        3.65         5.65        12.20        50.14        67.46        41.13 
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-5965 TCGA-FG-6688 
       14.33        47.77        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-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       40.08        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        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       17.82         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-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-7611 
        4.57        17.29         3.16        22.06        45.99        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23        14.27         0.16         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-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
        2.96        17.52        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-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        42.77         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  TRIP12 MUTATED TRIP12 WILD-TYPE 
            6.90             0.03 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
           75.25           182.33 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
           23.61            15.48 
[1] "6.9 - 75.2 (23.6)"  "0.0 - 182.3 (15.5)"
[1] "hr="     "2.5e+07"
D36V2, continuous
D36V3, binary
                  cls
clus                 0   1
  TRIP12 MUTATED     2   3
  TRIP12 WILD-TYPE 125 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED      2    3
  TRIP12 WILD-TYPE  125  156
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  FEMALE              2              125
  MALE                3              156
[1] 2 2
[1] FALSE
D36V4, continuous
[1] "Remove cluster labels:" "TRIP12 MUTATED"        
clus
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               2              135 
      TCGA-CS-4938       TCGA-CS-4941       TCGA-CS-4942       TCGA-CS-4943 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-4944       TCGA-CS-5390       TCGA-CS-5393       TCGA-CS-5395 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-5396       TCGA-CS-5397       TCGA-CS-6186       TCGA-CS-6188 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-6290       TCGA-CS-6665       TCGA-CS-6666       TCGA-CS-6667 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-CS-6668       TCGA-CS-6669       TCGA-DB-A4XE       TCGA-DB-A64L 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-A64Q       TCGA-DB-A64R       TCGA-DB-A64S       TCGA-DB-A64U 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DB-A64V       TCGA-DB-A64W       TCGA-DB-A64X       TCGA-DH-5140 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-DH-A66B 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DH-A66F       TCGA-DU-5851       TCGA-DU-5852       TCGA-DU-5853 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-5854       TCGA-DU-5855       TCGA-DU-5870       TCGA-DU-5871 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-5874       TCGA-DU-6396       TCGA-DU-6403       TCGA-DU-6404 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-6405       TCGA-DU-6407       TCGA-DU-6408       TCGA-DU-6410 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-7013       TCGA-DU-7015       TCGA-DU-7018       TCGA-DU-7019 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-7294       TCGA-DU-7298       TCGA-DU-7299       TCGA-DU-7300 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-7301       TCGA-DU-7302       TCGA-DU-7304       TCGA-DU-7306 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-7309       TCGA-DU-8158       TCGA-DU-8161       TCGA-DU-8162 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-8163       TCGA-DU-8165       TCGA-DU-8167       TCGA-DU-8168 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-A5TP       TCGA-DU-A5TR       TCGA-DU-A5TS       TCGA-DU-A5TU 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-DU-A5TW       TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5305       TCGA-E1-5307       TCGA-E1-5311       TCGA-E1-5318 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-E1-5319       TCGA-E1-5322       TCGA-FG-5963       TCGA-FG-5965 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-FG-6688       TCGA-FG-6689       TCGA-FG-6690       TCGA-FG-6691 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-FG-7636       TCGA-FG-7638       TCGA-FG-8181       TCGA-FG-8185 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-FG-8186       TCGA-FG-8187       TCGA-FG-8188       TCGA-FG-8189 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-FG-A4MT       TCGA-FG-A4MW       TCGA-FG-A4MX       TCGA-FG-A60J 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-7468       TCGA-HT-7470       TCGA-HT-7475       TCGA-HT-7477 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-7485       TCGA-HT-7607       TCGA-HT-7609       TCGA-HT-7611 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-7689       TCGA-HT-7692       TCGA-HT-7693       TCGA-HT-7854 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-7875       TCGA-HT-7884       TCGA-HT-8564       TCGA-HT-A4DV 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-A5R7       TCGA-HT-A5RA       TCGA-HT-A5RC       TCGA-HT-A615 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-HT-A617       TCGA-HT-A618       TCGA-HT-A61A       TCGA-IK-7675 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-P5-A5EU       TCGA-P5-A5EV       TCGA-P5-A5EW       TCGA-P5-A5EX 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-P5-A5F0       TCGA-P5-A5F2       TCGA-P5-A5F4       TCGA-P5-A5F6 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
      TCGA-QH-A65S       TCGA-QH-A65V       TCGA-QH-A65Z 
"TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" "TRIP12 WILD-TYPE" 
                  vv
clus               ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  TRIP12 MUTATED             0                3                 2
  TRIP12 WILD-TYPE          97               73               111
D36V5, multiclass
                   clus
vv                  TRIP12 MUTATED TRIP12 WILD-TYPE
  ASTROCYTOMA                    0               97
  OLIGOASTROCYTOMA               3               73
  OLIGODENDROGLIOMA              2              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"
D36V6, binary
                  cls
clus                 0   1
  TRIP12 MUTATED     3   2
  TRIP12 WILD-TYPE  82 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED      3    2
  TRIP12 WILD-TYPE   82  199
     clus
vv    TRIP12 MUTATED TRIP12 WILD-TYPE
  NO               3               82
  YES              2              199
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  TRIP12 MUTATED                                  0                         0
  TRIP12 WILD-TYPE                                1                        12
                  vv
clus               WHITE
  TRIP12 MUTATED       5
  TRIP12 WILD-TYPE   264
D36V7, multiclass
                                  clus
vv                                 TRIP12 MUTATED TRIP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  BLACK OR AFRICAN AMERICAN                     0               12
  WHITE                                         5              264
[1] 3 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
  TRIP12 MUTATED     0   5
  TRIP12 WILD-TYPE  14 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED      0    5
  TRIP12 WILD-TYPE   14  250
                        clus
vv                       TRIP12 MUTATED TRIP12 WILD-TYPE
  HISPANIC OR LATINO                  0               14
  NOT HISPANIC OR LATINO              5              250
[1] 2 2
[1] FALSE

Clustering(37) Variable = KIAA0664 MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  KIAA0664 MUTATED     4   1
  KIAA0664 WILD-TYPE 221  58
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                279 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 1                 58 
$`KIAA0664 MUTATED`
TCGA-CS-6188 TCGA-DU-7302 TCGA-FG-6692 TCGA-HT-7603 TCGA-HT-8012 
       23.84        60.30        13.58        23.18         9.40 

$`KIAA0664 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-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-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-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-A66B TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        42.05        17.19        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-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-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        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-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99         6.54         8.84        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-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        23.31        41.98         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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        5.65        12.20        50.14        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-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-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 
       24.99        23.97        15.35        17.88        40.08        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        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FN-7833 
        5.26        18.71        23.70        14.76        17.82         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-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
        5.03        29.85       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-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43         1.64        16.24        63.55         0.10        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-8558 
        3.95         4.70         0.23        29.59         3.88         1.71 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
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-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         6.38        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        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       19.00        42.77         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        2.53         4.83         4.11 

  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
              9.40               0.03 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
             60.30             182.33 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
             23.18              15.52 
[1] "9.4 - 60.3 (23.2)"  "0.0 - 182.3 (15.5)"
[1] "hr=" "1"  
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     2   3
  KIAA0664 WILD-TYPE 125 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      2    3
  KIAA0664 WILD-TYPE  125  156
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  FEMALE                2                125
  MALE                  3                156
[1] 2 2
[1] FALSE
D37V4, continuous
[1] "Remove cluster labels:" "KIAA0664 MUTATED"      
clus
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 2                135 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6290 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-CS-6665         TCGA-CS-6666         TCGA-CS-6667 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-CS-6668         TCGA-CS-6669         TCGA-DB-5274 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DB-A4XE         TCGA-DB-A64L         TCGA-DB-A64Q 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DB-A64R         TCGA-DB-A64S         TCGA-DB-A64U 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DB-A64V         TCGA-DB-A64W         TCGA-DB-A64X 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5142         TCGA-DH-5143 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66F 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-5851         TCGA-DU-5852         TCGA-DU-5853 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-5854         TCGA-DU-5855         TCGA-DU-5870 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-5871         TCGA-DU-5874         TCGA-DU-6396 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-6407         TCGA-DU-6408         TCGA-DU-6410 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7015         TCGA-DU-7018 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-7019         TCGA-DU-7294         TCGA-DU-7298 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-7299         TCGA-DU-7300         TCGA-DU-7301 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8165         TCGA-DU-8167 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-8168         TCGA-DU-A5TP         TCGA-DU-A5TR 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-DU-A5TS         TCGA-DU-A5TU         TCGA-DU-A5TW 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-5963         TCGA-FG-5965         TCGA-FG-6688 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-7636         TCGA-FG-7638         TCGA-FG-8181 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-8185         TCGA-FG-8186         TCGA-FG-8187 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-8188         TCGA-FG-8189         TCGA-FG-A4MT 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A60J 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-7468         TCGA-HT-7470         TCGA-HT-7475 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-7477         TCGA-HT-7485         TCGA-HT-7607 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7611         TCGA-HT-7689 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-7692         TCGA-HT-7693         TCGA-HT-7694 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-7854         TCGA-HT-7875         TCGA-HT-7884 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-8564         TCGA-HT-A4DV         TCGA-HT-A5R7 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-A5RA         TCGA-HT-A5RC         TCGA-HT-A615 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-HT-A617         TCGA-HT-A618         TCGA-HT-A61A 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-IK-7675         TCGA-P5-A5EU         TCGA-P5-A5EV 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-P5-A5EW         TCGA-P5-A5EX         TCGA-P5-A5F0 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-P5-A5F2         TCGA-P5-A5F4         TCGA-P5-A5F6 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
        TCGA-QH-A65S         TCGA-QH-A65V         TCGA-QH-A65Z 
"KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" "KIAA0664 WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  KIAA0664 MUTATED             1                0                 4
  KIAA0664 WILD-TYPE          96               76               109
D37V5, multiclass
                   clus
vv                  KIAA0664 MUTATED KIAA0664 WILD-TYPE
  ASTROCYTOMA                      1                 96
  OLIGOASTROCYTOMA                 0                 76
  OLIGODENDROGLIOMA                4                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"
D37V6, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     3   2
  KIAA0664 WILD-TYPE  82 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      3    2
  KIAA0664 WILD-TYPE   82  199
     clus
vv    KIAA0664 MUTATED KIAA0664 WILD-TYPE
  NO                 3                 82
  YES                2                199
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE BLACK OR AFRICAN AMERICAN
  KIAA0664 MUTATED                                  0                         0
  KIAA0664 WILD-TYPE                                1                        12
                    vv
clus                 WHITE
  KIAA0664 MUTATED       5
  KIAA0664 WILD-TYPE   264
D37V7, multiclass
                                  clus
vv                                 KIAA0664 MUTATED KIAA0664 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  BLACK OR AFRICAN AMERICAN                       0                 12
  WHITE                                           5                264
[1] 3 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
  KIAA0664 MUTATED     0   5
  KIAA0664 WILD-TYPE  14 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      0    5
  KIAA0664 WILD-TYPE   14  250
                        clus
vv                       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO                5                250
[1] 2 2
[1] FALSE
