[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"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/10005995/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/10668119/LGG-TP.mergedcluster.txt"

nPatients in clinical file=403, in cluster file=516, common to both=403
[1]  12 403
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
 9 10  8 
 1  2  3 
 9 10  8 
[1] "MRNA_CHIERARCHICAL"
[1] 3
1 2 3 4 
7 7 7 6 
1 2 3 4 
7 7 7 6 
[1] "CN_CNMF"
[1] 3
  1   2   3 
126  91 183 
  1   2   3 
126  91 183 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
168  54  52 124 
  1   2   3   4 
168  54  52 124 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
51 62 69 72 
 1  2  3  4 
51 62 69 72 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 67 131  56 
  1   2   3 
 67 131  56 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
102  91  83 105  19 
  1   2   3   4   5 
102  91  83 105  19 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
103  90  96 111 
  1   2   3   4 
103  90  96 111 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
108  83 153  53 
  1   2   3   4 
108  83 153  53 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
127  79 111  80 
  1   2   3   4 
127  79 111  80 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5   6   7 
 88  74  50 117  34  14  20 
  1   2   3   4   5   6   7 
 88  74  50 117  34  14  20 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
122 108  89  78 
  1   2   3   4 
122 108  89  78 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 403 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
         143           NA           NA          552          323         1966 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        1222            3           NA          303           NA           NA 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
         725          546          378          258          230          244 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
         225          201         3733         2493         2289         1458 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
        2218         1419         1526         1354         1112         2381 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
         915          313          387          840          822          573 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
         559         2219          383          335          573          511 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
         182          489          469          846          448          415 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
         332           NA          968          922          438          244 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
          NA          901          479          237          117          548 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
         443          531           NA          407          257          207 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        5546          576          532          461         6423         1585 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
         682         1491         2286         1401           NA           37 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        2660          214           NA           NA          605           NA 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
          NA         3470          242          235           NA           NA 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        4752         4206           NA           NA           NA           NA 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
          NA         2761           NA          800           NA           NA 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        2869           NA           NA           NA           NA         1834 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
          NA         1277           84           NA           NA          121 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
         629          651          582          516          471          431 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
         433          383          460          151          111          172 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
         371          263           82         2372          220          182 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
          NA           NA          217           NA         3787         1525 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        2052         1251         2433         1762         4084         2379 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
        2907         3978          436         1453          547         1045 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
         979          571          454          760          729          413 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
         467          544         1219          686          627          611 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
         394          416          433          487          611          455 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
         361          472          744           18          160          113 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
         294          214          202          214          128          124 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
         322          328          698          159            4            3 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
         203          238          268            4            1          503 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
         114          530          199          738          194          216 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        2287         1800         1826         4690          122          153 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
         908          705         3283          139          526           NA 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
         671         1399         1706         1752           NA          434 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
           5          494           23         1359          184         1300 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
           3          964          455            3            3           90 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
         533          210          442         1201          585         1189 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
           7         1540           15          718         1130           10 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
           4          112          162           89           52          343 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
         956           50          494          286           NA          654 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
        1004          372          190            3           14           76 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 
         120          143            7          900          118           52 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
         488          478            7          319            4            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-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
         585         1222         1092          131          262          272 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
         596          542          321          240          294          201 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5ET TCGA-P5-A5EU 
          NA         1301          159          144           NA           NA 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
           7          204           50           72           70          125 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
         179           39          175           77          147          237 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
         125          127           NA           90           NA           NA 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
          67           96           18          192          119          144 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
          58            7          153         2702         2860          993 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
        1806           NA         2101          571          860          856 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
         684          658          498          344          475          610 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
         300         2878         2546           NA         3156         1897 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
        2208         2146          697         2149          331          283 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
         275          231          187          103          434           NA 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
         597          383          128          285          249           62 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
         247          109          123          554          396           NA 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
        2649          530         2549           NA          152         1504 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
        1093          770          687         1472          365          459 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
        1544         1045          738          589          532           NA 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
         502          910          575          287          139          365 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
        1006          915          411            3           NA          815 
TCGA-VM-A8CH 
         333 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=301,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 403 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 5 4
  subtype2 7 3
  subtype3 5 3
subtype1 subtype2 subtype3 
       9       10        8 
subtype1 subtype2 subtype3 
       4        3        3 
$subtype1
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-DB-5273 TCGA-DB-5280 TCGA-DH-5142 
       43.89        18.15        10.62        81.96        36.56        30.31 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 
       50.14        67.46       130.78 

$subtype2
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DB-5275 TCGA-DH-5140 
       64.64         0.10         9.96        75.25        47.93        19.96 
TCGA-DH-5141 TCGA-DH-5144 TCGA-E1-5304 TCGA-E1-5318 
       31.82         8.02        41.13        78.21 

$subtype3
TCGA-CS-5395 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 
       21.01       122.73        72.92        46.65        50.17        78.28 
TCGA-DH-5143 TCGA-E1-5311 
       14.40       134.27 

subtype1 subtype2 subtype3 
   10.62     0.10    14.40 
subtype1 subtype2 subtype3 
  130.78    78.21   134.27 
subtype1 subtype2 subtype3 
  43.890   36.475   61.545 
[1] "10.6 - 130.8 (43.9)" "0.1 - 78.2 (36.5)"   "14.4 - 134.3 (61.5)"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 2 7
  subtype2 6 4
  subtype3 1 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    6    4
  subtype3    1    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        6        1
  MALE          7        4        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1           7                2                 0
  subtype2           2                3                 5
  subtype3           1                4                 3
D1V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA              7        2        1
  OLIGOASTROCYTOMA         2        3        4
  OLIGODENDROGLIOMA        0        5        3
[1] 3 3
[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
  subtype1 7 2
  subtype2 8 2
  subtype3 5 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2    8    2
  subtype3    5    3
     clus
vv    subtype1 subtype2 subtype3
  NO         7        8        5
  YES        2        2        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         1     8
  subtype2                         0    10
  subtype3                         1     7
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        1        0        1
  WHITE                            8       10        7
[1] 2 3
[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
  subtype1 0 6
  subtype2 1 7
  subtype3 0 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    1    7
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        0
  NOT HISPANIC OR LATINO        6        7        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 4
  subtype2 3 4
  subtype3 6 1
  subtype4 5 1
subtype1 subtype2 subtype3 subtype4 
       7        7        7        6 
subtype1 subtype2 subtype3 subtype4 
       4        4        1        1 
$subtype1
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5395 TCGA-DB-5273 TCGA-DB-5280 TCGA-E1-5302 
       43.89        10.62        21.01        81.96        36.56        50.14 
TCGA-E1-5303 
       67.46 

$subtype2
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-E1-5304 
       18.15        47.93        46.65        19.96        30.31        41.13 
TCGA-E1-5322 
      130.78 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DH-5141 TCGA-DH-5144 
       64.64         0.10         9.96        75.25        31.82         8.02 
TCGA-E1-5318 
       78.21 

$subtype4
TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5281 TCGA-DH-5143 TCGA-E1-5311 
      122.73        72.92        50.17        78.28        14.40       134.27 

subtype1 subtype2 subtype3 subtype4 
   10.62    18.15     0.10    14.40 
subtype1 subtype2 subtype3 subtype4 
   81.96   130.78    78.21   134.27 
subtype1 subtype2 subtype3 subtype4 
   43.89    41.13    31.82    75.60 
[1] "10.6 - 82.0 (43.9)"  "18.1 - 130.8 (41.1)" "0.1 - 78.2 (31.8)"  
[4] "14.4 - 134.3 (75.6)"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 2 5
  subtype3 5 2
  subtype4 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    2    5
  subtype3    5    2
  subtype4    1    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        5        1
  MALE          6        5        2        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        5        5        2 
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype2"
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1           5                1                 1
  subtype2           4                3                 0
  subtype3           1                1                 5
  subtype4           0                4                 2
D2V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA              5        4        1        0
  OLIGOASTROCYTOMA         1        3        1        4
  OLIGODENDROGLIOMA        1        0        5        2
[1] 3 4
[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
  subtype1 6 1
  subtype2 6 1
  subtype3 5 2
  subtype4 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    6    1
  subtype3    5    2
  subtype4    3    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        6        5        3
  YES        1        1        2        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         2     5
  subtype2                         0     7
  subtype3                         0     7
  subtype4                         0     6
D2V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        2        0        0        0
  WHITE                            5        7        7        6
[1] 2 4
[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
  subtype1 0 4
  subtype2 0 6
  subtype3 1 4
  subtype4 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype2    0    6
  subtype3    1    4
  subtype4    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        0        1        0
  NOT HISPANIC OR LATINO        4        6        4        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 101  24
  subtype2  56  33
  subtype3 167  14
subtype1 subtype2 subtype3 
     125       89      181 
subtype1 subtype2 subtype3 
      24       33       14 
$subtype1
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        4.70        18.15        40.18        17.95        12.43         8.48 
TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       47.93        46.65        78.28        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64X TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       18.84        18.38        10.92        29.62        15.75         3.85 
TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 
       13.38        18.94        75.16        65.75        87.45       114.08 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7299 
        7.73        62.96       156.23        14.99       117.40        44.02 
TCGA-DU-7304 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S7 
       23.31        15.48        14.24        15.12         3.65         7.23 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.13       124.50        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       57.93       130.78        17.98        14.93        24.99        23.97 
TCGA-FG-7636 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MY 
       17.88        13.68        14.24        14.96        15.52         9.67 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7474 
        7.04         7.04        10.59         7.82         8.81         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 
       17.42         6.54        24.26         6.38         7.10        60.03 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7688 
      107.93        17.29        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-7873 
       14.96         0.10        17.52        19.23         0.23        23.61 
TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8106 
        3.68        11.28        31.43        63.55        21.50         0.10 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 
        0.23         3.88        16.04         0.10         2.70         1.81 
TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KM 
        5.33         8.32        35.90         8.61        19.59         6.61 
TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A6X3 
       19.00         2.30         5.88         1.28         2.53         0.59 
TCGA-QH-A6XA TCGA-S9-A6TS TCGA-S9-A6U6 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WO 
        0.23        62.17         9.86         5.85        70.55         7.59 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R7 
        3.39         7.92         9.37         4.04        87.09        83.80 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84H 
        5.00        35.93        22.59        48.39        50.76        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-VM-A8C8 
       19.36        17.49        40.83        18.90        33.07 

$subtype2
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        7.69        43.89        21.01         6.38        17.69        23.84 
TCGA-DB-5270 TCGA-DB-A4X9 TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-A669 TCGA-DU-5847 
      122.73        30.08        18.84        19.96        30.21        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
        6.74         8.45         6.81        17.49       211.17        49.02 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7290 
        7.96        11.47         6.54         8.84        90.77        10.36 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
        7.96        18.94        25.91        41.98         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
        3.98        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-FG-5965 TCGA-FG-6688 
        5.65        12.20        11.41        26.76        32.19        18.77 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z 
       13.58        15.35        20.09         0.59         5.26        10.78 
TCGA-HT-7473 TCGA-HT-7692 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 
       16.54         2.96         0.49         1.71        16.24        12.23 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 
        2.50         4.70        15.72         0.23         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-8322 TCGA-HW-A5KK TCGA-KT-A7W1 
       14.70         5.33        16.14        17.82         7.89         4.73 
TCGA-P5-A5EV TCGA-P5-A5F0 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-QH-A6XC 
        0.23         4.11         4.18         2.96         1.91         5.03 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       22.49        16.37         9.30        14.27        19.63         4.21 
TCGA-S9-A7QW TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-VM-A8CD 
        3.58        10.39        49.45        12.00         7.89 

$subtype3
TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6667 TCGA-CS-6668 
       10.62        64.64         0.10         9.96         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
        7.40         6.61        81.96        75.25        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       44.52        36.56        10.29        72.95        12.59        11.01 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66F 
       13.64        31.82        30.31        14.40         8.02         7.79 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       14.56        17.46       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7018 TCGA-DU-7019 
       46.06         1.22       138.28       105.21        30.67        26.30 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8168 
       94.32        62.01        60.30         2.76        21.40        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5311 
        8.65         2.70        77.98         5.98        21.30       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7638 
       78.21        95.57        14.33        47.77        34.36        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A4MT 
       20.61        12.95        16.01        20.09        11.87        24.46 
TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 
        3.72         6.64         4.21         4.08        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7480 
        0.13         0.10         6.67         0.13         0.03        75.19 
TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       59.18       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
        4.57         3.16        22.06        45.99        56.09         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-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 
        0.10         6.90        14.53        39.48        39.09        50.63 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 
       37.15         0.33         0.13         5.33         2.93         1.64 
TCGA-HT-8012 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 
        9.40        33.01         6.25         0.46         3.95        29.59 
TCGA-HT-A4DV TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 
       10.49        13.02        29.92        13.45        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X 
        4.31         8.94        10.55         9.67        42.77         5.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        6.71         1.64         2.37         5.75         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        4.11         2.20         3.16         6.31         3.91         4.73 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.27        28.14        21.63        11.31        15.62        20.05 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       94.62        83.70       103.76        62.37        72.59        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 
       70.65        10.88         9.04         6.15        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R4 TCGA-S9-A7R8 
        2.04         8.12        18.21        13.02        17.42        31.59 
TCGA-TM-A7C5 TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R 
       25.32        15.09        34.36        16.50        29.92         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
        4.57        12.00        30.08        13.51         0.10        26.79 
TCGA-VM-A8CH 
       10.95 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  156.23   211.17   182.33 
subtype1 subtype2 subtype3 
   17.29    12.20    14.56 
[1] "0.1 - 156.2 (17.3)" "0.1 - 211.2 (12.2)" "0.0 - 182.3 (14.6)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  50  76
  subtype2  47  44
  subtype3  79 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   76
  subtype2   47   44
  subtype3   79  104
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       47       79
  MALE         76       44      104
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          69               36                21
  subtype2          43               26                22
  subtype3          31               42               110
D3V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             69       43       31
  OLIGOASTROCYTOMA        36       26       42
  OLIGODENDROGLIOMA       21       22      110
[1] 3 3
[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
  subtype1  33  93
  subtype2  21  70
  subtype3  35 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   93
  subtype2   21   70
  subtype3   35  148
     clus
vv    subtype1 subtype2 subtype3
  NO        33       21       35
  YES       93       70      148
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                1     1                         8
  subtype3                                0     1                         4
          vv
clus       WHITE
  subtype1   123
  subtype2    81
  subtype3   172
D3V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        1        1
  BLACK OR AFRICAN AMERICAN               2        8        4
  WHITE                                 123       81      172
[1] 4 3
[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
  subtype1   4 117
  subtype2   4  82
  subtype3   7 160
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  117
  subtype2    4   82
  subtype3    7  160
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        7
  NOT HISPANIC OR LATINO      117       82      160
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 139  27
  subtype2  28  26
  subtype3  47   4
  subtype4 112  10
subtype1 subtype2 subtype3 subtype4 
     166       54       51      122 
subtype1 subtype2 subtype3 subtype4 
      27       26        4       10 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 
        4.70        43.89        18.15        40.18        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5280 
        8.48         7.56        81.96        47.93        46.65        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        30.08        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B 
       18.38        15.42        10.92        30.31        14.40        29.62 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
       15.75         3.85        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-7014 
      114.08         7.73        62.96       156.23        14.99       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
       90.77        26.30        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
        2.76        20.68        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 
       15.12         3.65         5.65         7.23         7.13       124.50 
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-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-8188 
       32.19        14.93        24.99        17.88        14.24        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       15.52        24.46         3.72         9.67         7.04         7.04 
TCGA-FG-A6J3 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 
       10.59         0.13         8.81         0.03        16.54        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        6.54        24.26         6.38        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 
        5.03        23.18       107.93        17.29        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 
       57.60         0.16         6.05        42.74        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 
        0.10        17.52        19.23        50.63        23.61         3.68 
TCGA-HT-7884 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
       11.28        63.55         2.50         0.23         3.88        16.04 
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-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM 
       35.90         8.61         8.94        19.59         9.67         6.61 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A65S 
       19.00         0.23         6.71         2.30         5.88         2.53 
TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        0.59         1.91         0.23        62.17        69.07        18.77 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO 
       21.63        11.31         9.86        94.62        83.70         7.59 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
        3.39         7.92         4.21         9.37         3.58         4.04 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 
       87.09        17.42        83.80        31.59         5.00        35.93 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L 
       22.59        48.39        50.76        24.26        19.36        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH 
       18.90        12.00        33.07        10.95 

$subtype2
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DH-5140 
        7.69        21.01         6.38        17.69        23.84        19.96 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6403 TCGA-DU-6404 
       18.02         6.74         8.45       211.17        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 
       19.89        16.83        11.47         6.54         8.84        10.36 
TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY 
        7.96         5.10        23.74        19.13         4.96        12.20 
TCGA-DU-A76K TCGA-DU-A76L TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z 
       11.41        26.76        13.58         0.59         5.26        10.78 
TCGA-HT-7469 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 
        7.82         0.49         1.71        16.24        12.23         4.70 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-KT-A7W1 TCGA-QH-A6CV 
       15.72         0.23        14.70         5.33         4.73         2.96 
TCGA-QH-A6XC TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IX 
        5.03        16.37         5.85         9.30         9.04        19.63 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84J TCGA-VM-A8CD 
       10.39        49.45        12.00        15.09        17.49         7.89 

$subtype3
TCGA-CS-4944 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-A64O 
       10.62         7.40       122.73        72.92        50.17        18.84 
TCGA-DU-7298 TCGA-DU-8162 TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7643 
       18.94         3.98        17.98        18.77        23.97        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8189 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7474 
       12.95        13.68        11.87         5.23         0.10         3.75 
TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7607 TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7854 
        7.10        29.85         3.16         0.76         0.10        39.48 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
       39.09         0.23        37.15         5.33         2.93        31.43 
TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8113 
        1.64        21.50        33.01         0.10         0.46        29.59 
TCGA-HT-8558 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A617 TCGA-HT-A61A TCGA-HW-A5KK 
        1.71        10.49         0.13        16.14         6.38         7.89 
TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A7IQ 
        2.37         1.28         4.18        70.55        70.65        14.27 
TCGA-TM-A84R TCGA-VM-A8C9 TCGA-VM-A8CE 
        9.44        30.08        26.79 

$subtype4
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       44.52        10.29        72.95        12.59        11.01        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DH-5141 
        5.98        16.08        27.81        14.73        13.64        31.82 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 
        8.02        30.21         7.79        14.56       182.33        15.16 
TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7294 
       52.11         1.22         7.96       138.28        30.67        94.32 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 
       62.01        60.30        21.40        14.17         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       77.98         5.98        21.30       134.27        78.21        95.57 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 
       14.33        47.77        34.36        15.35        40.08        22.55 
TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       20.61        16.01        20.09         6.64         4.21         4.08 
TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 
       22.95         6.67         0.13        75.19        59.18         4.57 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 
        0.23        14.27        16.24        44.68         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-8012 TCGA-HT-8105 
        6.90        14.53         0.33         0.13         9.40         6.25 
TCGA-HT-8109 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
        3.95         0.07        13.02        29.92        13.45        40.18 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX 
        4.31        17.82        10.55        42.77         5.23         1.64 
TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY 
        4.11         5.75         4.83         7.79         4.11         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML 
        3.16         6.31         3.91         4.73        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 
       32.65        59.38        28.27        28.14        22.49        15.62 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL 
       20.05       103.76        62.37        72.59        22.92        10.88 
TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
        6.15        12.59         8.19         2.04         8.12        18.21 
TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S 
       13.02        25.32        34.36        16.50        29.92         4.57 
TCGA-VM-A8CA TCGA-VM-A8CB 
       13.51         0.10 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.23     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
  156.23   211.17   122.73   182.33 
subtype1 subtype2 subtype3 subtype4 
  17.440   11.095   11.870   14.430 
[1] "0.0 - 156.2 (17.4)" "0.2 - 211.2 (11.1)" "0.1 - 122.7 (11.9)"
[4] "0.1 - 182.3 (14.4)"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 71 97
  subtype2 27 27
  subtype3 26 26
  subtype4 54 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71   97
  subtype2   27   27
  subtype3   26   26
  subtype4   54   70
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       71       27       26       54
  MALE         97       27       26       70
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          87               55                26
  subtype2          34               10                10
  subtype3          18               13                21
  subtype4           3               25                96
D4V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             87       34       18        3
  OLIGOASTROCYTOMA        55       10       13       25
  OLIGODENDROGLIOMA       26       10       21       96
[1] 3 4
[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
  subtype1  48 120
  subtype2  12  42
  subtype3   9  43
  subtype4  16 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48  120
  subtype2   12   42
  subtype3    9   43
  subtype4   16  108
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        48       12        9       16
  YES      120       42       43      108
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                0     1                         3
  subtype3                                1     0                         4
  subtype4                                0     1                         1
          vv
clus       WHITE
  subtype1   162
  subtype2    50
  subtype3    46
  subtype4   117
D4V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   0        1        0        1
  BLACK OR AFRICAN AMERICAN               5        3        4        1
  WHITE                                 162       50       46      117
[1] 4 4
[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
  subtype1   5 155
  subtype2   2  50
  subtype3   3  43
  subtype4   5 109
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  155
  subtype2    2   50
  subtype3    3   43
  subtype4    5  109
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        3        5
  NOT HISPANIC OR LATINO      155       50       43      109
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 45  5
  subtype2 32 29
  subtype3 59 10
  subtype4 61 11
subtype1 subtype2 subtype3 subtype4 
      50       61       69       72 
subtype1 subtype2 subtype3 subtype4 
       5       29       10       11 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-5273 
        4.70        43.89        17.69        23.84        12.43        81.96 
TCGA-DB-5276 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DH-5143 TCGA-DU-5874 TCGA-DU-6395 
       72.92        18.38        12.59        14.40        15.16        49.02 
TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5302 TCGA-FG-6688 
       23.31        20.68        12.59        15.12        50.14        18.77 
TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 
       23.97        13.68        16.01        20.09        14.96        15.52 
TCGA-FG-A4MW TCGA-FG-A60J TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 
        5.26         7.04         7.10        60.03         4.01        29.85 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7691 
       57.60        14.27         0.16         0.76        44.68         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8111 
        2.96        17.52        39.48        23.61         3.68         0.23 
TCGA-HT-8114 TCGA-HT-A5R5 TCGA-HW-8319 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
        3.88         0.13         8.61         6.71         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F6 
        5.88         1.28 

$subtype2
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XG TCGA-DH-5140 
       18.15         6.38         8.48        46.65        72.95        19.96 
TCGA-DH-5142 TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6393 
       30.31        18.02         6.74         8.45         6.81        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       22.42        75.16         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7301 
      156.23        14.99         6.54         8.84        10.36        25.91 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU 
        5.10        23.74        19.13        14.17         4.96         3.65 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-5322 TCGA-FG-7636 TCGA-FG-8185 
       12.20        41.13        78.21       130.78        17.88        14.24 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7606 
       24.46         0.59         7.82        24.26       107.93        17.29 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        0.23         0.49         1.71        16.24         9.40        63.55 
TCGA-HT-8104 TCGA-HT-A5R9 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KM 
       12.23         0.07        40.18        17.82         7.89         6.61 
TCGA-IK-7675 
       19.00 

$subtype3
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       10.62        40.18         0.10         9.96         8.02         6.61 
TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC 
       47.93        44.52        36.56        78.28        10.29        27.62 
TCGA-DB-A4XD TCGA-DH-5141 TCGA-DH-5144 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 
       27.02        31.82         8.02        13.38       182.33        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       17.49       211.17        46.06        65.75        87.45        94.52 
TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7306 
      105.21       117.40        90.77        30.67        26.30        41.98 
TCGA-DU-8167 TCGA-DU-A5TW TCGA-E1-5303 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5964 
       15.48         5.65        67.46        95.57        14.33        34.36 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-A4MX TCGA-FG-A4MY 
       15.35        40.08        22.55        20.61         3.72         9.67 
TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7483 
        6.67         0.03        16.54         6.54         6.38       154.19 
TCGA-HT-7601 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7684 
        5.03        22.06        45.99         0.23        16.24         6.05 
TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7875 TCGA-HT-8105 
       42.74        14.96        19.23        50.63         0.33         6.25 
TCGA-HT-8106 TCGA-HT-8110 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 
        0.10         4.70         8.32        19.23         8.94        19.59 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5EV 
       10.55        42.77         0.23 

$subtype4
TCGA-CS-5390 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-A4X9 
       64.64         7.40       122.73        75.25        50.17        30.08 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6400 TCGA-DU-7009 
       12.72        18.84        14.56        17.46         1.22       138.28 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 
        7.96        94.32        18.94        62.01        60.30         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-E1-5305 TCGA-E1-5307 
        3.98        21.40        16.96        14.24        79.99        57.93 
TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
      134.27        47.77        17.98        32.19        14.93        24.99 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 
       20.09        12.95        11.87         0.10         8.81         0.13 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 
        3.75        17.42        75.19        59.18        23.18         4.57 
TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 
        3.16        56.09         0.10        31.69         0.10         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       14.53        39.09        37.15         0.13         5.33         2.93 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 
       11.28        31.43         1.64        21.50        33.01         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5RB 
        3.95        29.59         1.71        15.72        10.49         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 TCGA-P5-A5EX TCGA-P5-A5F0 
       29.92        13.45        35.90         4.31         1.64         4.11 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.03     0.10 
subtype1 subtype2 subtype3 subtype4 
   81.96   156.23   211.17   138.28 
subtype1 subtype2 subtype3 subtype4 
   14.68    16.24    19.23    16.34 
[1] "0.1 - 82.0 (14.7)"  "0.1 - 156.2 (16.2)" "0.0 - 211.2 (19.2)"
[4] "0.1 - 138.3 (16.3)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 18 33
  subtype2 33 29
  subtype3 20 49
  subtype4 37 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   33
  subtype2   33   29
  subtype3   20   49
  subtype4   37   35
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18       33       20       37
  MALE         33       29       49       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          19               21                11
  subtype2          31               11                20
  subtype3          20               21                28
  subtype4          13               17                42
D5V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             19       31       20       13
  OLIGOASTROCYTOMA        21       11       21       17
  OLIGODENDROGLIOMA       11       20       28       42
[1] 3 4
[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
  subtype1 15 36
  subtype2 20 42
  subtype3 30 39
  subtype4 19 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   36
  subtype2   20   42
  subtype3   30   39
  subtype4   19   53
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        15       20       30       19
  YES       36       42       39       53
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         3    48
  subtype2                         2    60
  subtype3                         3    65
  subtype4                         3    69
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        3        2        3        3
  WHITE                           48       60       65       69
[1] 2 4
[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
  subtype1  3 47
  subtype2  2 56
  subtype3  4 60
  subtype4  4 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   47
  subtype2    2   56
  subtype3    4   60
  subtype4    4   66
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        4        4
  NOT HISPANIC OR LATINO       47       56       60       66
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 57  9
  subtype2 93 37
  subtype3 47  9
subtype1 subtype2 subtype3 
      66      130       56 
subtype1 subtype2 subtype3 
       9       37        9 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-5390 TCGA-CS-6186 TCGA-CS-6665 TCGA-CS-6670 
        4.70        43.89        64.64        17.69        12.43         6.61 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DH-5143 
       75.25        72.92        18.84        18.38        12.59        14.40 
TCGA-DU-5853 TCGA-DU-6395 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7294 TCGA-DU-7298 
       13.38        49.02       138.28        14.99        94.32        18.94 
TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5319 TCGA-FG-5963 
       20.68        16.96        15.12        50.14        95.57        17.98 
TCGA-FG-6688 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       18.77        15.35        20.61        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A60J TCGA-HT-7467 TCGA-HT-7472 TCGA-HT-7479 
       14.96        15.52         7.04         0.10         0.03         7.10 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7611 TCGA-HT-7620 
       59.18        60.03         4.01        29.85        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7854 
        0.16         0.76        44.68        14.96         2.96        39.48 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       50.63        23.61         3.68         5.33         2.93        11.28 
TCGA-HT-8010 TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-A5R5 TCGA-HW-7486 TCGA-HW-7487 
        1.64        63.55         0.23         0.13        29.92        13.45 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 TCGA-P5-A5EW TCGA-P5-A5F0 TCGA-P5-A5F1 
        4.31         8.61        17.82         6.71         4.11         5.88 

$subtype2
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 
       18.15        10.62        40.18         0.10         9.96         6.38 
TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 
       23.84         8.48         8.02        81.96        47.93        46.65 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD 
       44.52        36.56        78.28        10.29        27.62        27.02 
TCGA-DB-A4XG TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DU-5847 
       72.95        19.96        31.82        30.31         8.02        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47        62.96       156.23       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7301 
      117.40        90.77        30.67        26.30        10.36        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TR 
       23.31        41.98         5.10        23.74        19.13        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5303 TCGA-E1-5318 
        4.96         3.65         5.65        12.20        67.46        78.21 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5964 TCGA-FG-6691 TCGA-FG-7637 TCGA-FG-8185 
      130.78        14.33        34.36        23.97        40.08        14.24 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-HT-7468 
       24.46         0.59         5.26         3.72         9.67         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        7.82         0.13        16.54         6.54        24.26         6.38 
TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 
       75.19       154.19         5.03       107.93        17.29        22.06 
TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7691 
       45.99         0.23        16.24         6.05        42.74         0.10 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       17.52        19.23         0.23         0.49        37.15         0.33 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        1.71        16.24         9.40        12.23         6.25         0.10 
TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-A5R9 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        4.70         3.88         0.07         8.32        19.23        40.18 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 
        8.94        19.59        10.55         7.89         6.61        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F6 
       42.77         0.23         2.30         1.28 

$subtype3
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DU-5849 
        7.40       122.73        50.17        30.08        12.72        14.56 
TCGA-DU-5851 TCGA-DU-7292 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8162 
       17.46         7.96        62.01        60.30         2.76         3.98 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-E1-5304 TCGA-E1-5305 
       21.40        15.48        14.17        14.24        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       57.93       134.27        47.77        32.19        14.93        24.99 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-HT-7470 
       17.88        22.55        20.09        12.95        11.87         8.81 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
        3.75        17.42        23.18         4.57         3.16        56.09 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
        0.10        31.69         0.10         6.90        14.53        39.09 
TCGA-HT-7877 TCGA-HT-7902 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 
        0.13        31.43        21.50        33.01         0.46         3.95 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HW-7493 
       29.59         1.71        15.72        10.49         0.10        35.90 
TCGA-P5-A5EX TCGA-P5-A5EY 
        1.64         2.37 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  138.28   211.17   134.27 
subtype1 subtype2 subtype3 
  15.235   17.060   15.600 
[1] "0.0 - 138.3 (15.2)" "0.1 - 211.2 (17.1)" "0.1 - 134.3 (15.6)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 28 39
  subtype2 53 78
  subtype3 27 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   39
  subtype2   53   78
  subtype3   27   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       53       27
  MALE         39       78       29
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          18               23                26
  subtype2          52               33                46
  subtype3          13               14                29
D6V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             18       52       13
  OLIGOASTROCYTOMA        23       33       14
  OLIGODENDROGLIOMA       26       46       29
[1] 3 3
[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
  subtype1 20 47
  subtype2 48 83
  subtype3 16 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   47
  subtype2   48   83
  subtype3   16   40
     clus
vv    subtype1 subtype2 subtype3
  NO        20       48       16
  YES       47       83       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         5    62
  subtype2                         5   125
  subtype3                         1    55
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        5        5        1
  WHITE                           62      125       55
[1] 2 3
[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
  subtype1   4  61
  subtype2   6 116
  subtype3   3  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   61
  subtype2    6  116
  subtype3    3   52
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        6        3
  NOT HISPANIC OR LATINO       61      116       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 84 17
  subtype2 56 33
  subtype3 75  7
  subtype4 91 14
  subtype5 18  0
subtype1 subtype2 subtype3 subtype4 subtype5 
     101       89       82      105       18 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       33        7       14        0 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        4.70        43.89        18.15        17.95         8.48         7.56 
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XD TCGA-DB-A64S 
       81.96        47.93        36.56        30.08        27.02        15.42 
TCGA-DB-A64X TCGA-DH-5142 TCGA-DH-A66D TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
       10.92        30.31        15.75        13.38         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 
       17.49        49.02        65.75        87.45        94.52       114.08 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 
      117.40        90.77        44.02        25.91        41.98        20.68 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O 
       16.96        15.48        15.12         5.65         7.23         7.13 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-FG-5965 TCGA-FG-6690 
      124.50        50.14        67.46       130.78        32.19        24.99 
TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 
       23.97        17.88        13.68        14.24        14.96        15.52 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FN-7833 
       24.46         3.72         9.67         7.04         7.04         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 
        0.03        16.54         6.38        60.03         4.01       107.93 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 
       45.99        57.60         0.16        17.52        19.23        50.63 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 
       23.61         3.68        63.55         2.50         0.23         3.88 
TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.23         8.94        19.59         9.67         6.61        19.00 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5F1 TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-S9-A6TU 
        0.23         6.71         5.88         0.59         0.23        69.07 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WG TCGA-S9-A6WO 
       21.63        11.31        94.62        83.70        70.55         7.59 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84H 
        3.58         4.04        87.09        17.42        31.59        24.26 
TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH 
       40.83        18.90        12.00        33.07        10.95 

$subtype2
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        7.69        10.62        21.01         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-DH-5140 TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5852 
       12.43        19.96        30.21        29.62        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6396 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
        8.45       211.17        75.16         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 
       19.89        16.83        11.47        62.96        14.99         6.54 
TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP 
        8.84        10.36         5.10        23.74        19.13        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76L TCGA-E1-5304 
       12.59         4.96         3.65        12.20        26.76        41.13 
TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 
       17.98        18.77        13.58         0.59         5.26        10.59 
TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7601 TCGA-HT-7616 TCGA-HT-7680 
       10.78         7.82        24.26         5.03         0.23         0.76 
TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
       42.74         0.10        39.48         0.23         0.49         1.71 
TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-A4DS 
       16.24        12.23         0.10         4.70        16.04         0.23 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK TCGA-KT-A7W1 
       14.70         5.33        16.14         5.33         7.89         4.73 
TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6TV TCGA-S9-A6U0 
        1.64         2.30         1.28         2.96        18.77        16.37 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 
        5.85         9.30         9.04         7.92        19.63         9.37 
TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C 
       10.39        83.80         5.00        49.45        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8C9 TCGA-VM-A8CD 
       50.76        19.36        17.49        30.08         7.89 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-A4XA 
       64.64         0.10         9.96         8.02        75.25        10.29 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       72.95        12.59        16.80         5.98        16.08        27.81 
TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A66F TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       31.82         8.02         7.79       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7018 TCGA-DU-7294 
       22.42        46.06         1.22         7.96        30.67        94.32 
TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S8 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 
       21.40        14.17         5.98        78.21        95.57        14.33 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       15.35        40.08        16.01         6.64         4.21         4.08 
TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7481 TCGA-HT-7606 TCGA-HT-7677 
       22.95         6.67         0.13        59.18        17.29        16.24 
TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7875 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A5R9 
        0.10         2.96         0.33         9.40         6.25         0.07 
TCGA-HT-A615 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-QH-A65R 
       13.02        40.18        17.82        10.55         5.23         5.75 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML 
        7.79         4.11         6.31         4.73        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 
       32.65        59.38        28.27        28.14        15.62        20.05 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7J1 
      103.76        62.37        72.59        22.92         6.15         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M 
        2.04         8.12        13.02        25.32        34.36        16.50 
TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CB TCGA-VM-A8CE 
       29.92         4.57         0.10        26.79 

$subtype4
TCGA-CS-5393 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 
       40.18         7.40         6.61       122.73        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE 
       50.17        44.52        78.28        12.72        27.62        18.84 
TCGA-DB-A4XF TCGA-DB-A64L TCGA-DB-A64W TCGA-DH-5143 TCGA-DU-5849 TCGA-DU-5851 
       18.38        11.01        13.64        14.40        14.56        17.46 
TCGA-DU-6542 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7019 TCGA-DU-7292 
        7.73       156.23       138.28       105.21        26.30         7.96 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 
       18.94        62.01        60.30        23.31         2.76         3.98 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76R TCGA-E1-5305 
        8.65         2.70        77.98        11.41        21.30        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7638 
       57.93       134.27        47.77        34.36        14.93        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A713 TCGA-HT-7467 
       20.61        20.09        12.95        11.87         5.23         0.10 
TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7483 
        8.81         3.75        17.42         6.54        75.19       154.19 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7681 
       23.18         4.57         3.16        22.06        56.09        44.68 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
       31.69         0.10         6.90        14.53        39.09        37.15 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 
        0.13         5.33         2.93         1.64        21.50        33.01 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV 
        0.46         3.95        29.59         1.71        15.72        10.49 
TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 
        0.13         0.10         1.81        13.45         8.32        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-QH-A6CY 
        4.31         8.61        42.77         2.37         4.11         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
        3.16         1.91         5.03        62.17        22.49         9.86 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IZ TCGA-TM-A7C4 TCGA-TM-A7CA 
       70.65        10.88        14.27         4.21        35.93        22.59 
TCGA-TM-A7CF TCGA-TM-A84R TCGA-VM-A8CA 
       48.39         9.44        13.51 

$subtype5
TCGA-DB-A64O TCGA-DB-A64V TCGA-FG-8187 TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7620 
       18.84        14.73        20.09         7.10        29.85        14.27 
TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-A614 TCGA-HW-7486 
        6.05        14.96        11.28        31.43         2.70        29.92 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6X5 TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7QY 
        2.53         4.83         3.91         3.39        12.59        18.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.07     0.10     2.53 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.78   211.17   182.33   156.23    31.43 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.950   11.640   15.485   14.560   13.430 
[1] "0.0 - 130.8 (17.9)" "0.1 - 211.2 (11.6)" "0.1 - 182.3 (15.5)"
[4] "0.1 - 156.2 (14.6)" "2.5 - 31.4 (13.4)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 40 62
  subtype2 44 47
  subtype3 38 45
  subtype4 45 60
  subtype5  9 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   62
  subtype2   44   47
  subtype3   38   45
  subtype4   45   60
  subtype5    9   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       40       44       38       45        9
  MALE         62       47       45       60       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          49               35                18
  subtype2          63               13                15
  subtype3           3               15                65
  subtype4          25               32                48
  subtype5           2               10                 7
D7V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5
  ASTROCYTOMA             49       63        3       25        2
  OLIGOASTROCYTOMA        35       13       15       32       10
  OLIGODENDROGLIOMA       18       15       65       48        7
[1] 3 5
[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
  subtype1 29 73
  subtype2 22 69
  subtype3 11 72
  subtype4 25 80
  subtype5  2 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   73
  subtype2   22   69
  subtype3   11   72
  subtype4   25   80
  subtype5    2   17
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        29       22       11       25        2
  YES       73       69       72       80       17
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     1                         4
  subtype3                                0     1                         0
  subtype4                                0     0                         5
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    96
  subtype2    84
  subtype3    79
  subtype4    98
  subtype5    19
D7V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        1        1        0        0
  BLACK OR AFRICAN AMERICAN               5        4        0        5        0
  WHITE                                  96       84       79       98       19
[1] 4 5
[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
  subtype1  3 92
  subtype2  2 83
  subtype3  4 70
  subtype4  6 95
  subtype5  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   92
  subtype2    2   83
  subtype3    4   70
  subtype4    6   95
  subtype5    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        4        6        0
  NOT HISPANIC OR LATINO       92       83       70       95       19
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 85 17
  subtype2 58 30
  subtype3 85 10
  subtype4 96 14
subtype1 subtype2 subtype3 subtype4 
     102       88       95      110 
subtype1 subtype2 subtype3 subtype4 
      17       30       10       14 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-6290 TCGA-CS-6666 
        4.70        43.89        18.15        10.62        17.95         8.48 
TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 TCGA-DB-A4XD TCGA-DB-A64S 
        7.56        81.96        47.93        36.56        27.02        15.42 
TCGA-DH-A66D TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 
       15.75        13.38         6.81        18.94        17.49        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 
       75.16        65.75        87.45        94.52       114.08       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 
       90.77        26.30        44.02        25.91        41.98        20.68 
TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 
       15.48        15.12         5.65         7.23         7.13       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 
       50.14        67.46       130.78        32.19        24.99        23.97 
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        24.46         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 
        9.67         7.04         7.04         0.13         0.03        16.54 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 
        7.10        60.03         4.01       107.93        45.99        57.60 
TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 
        0.16         6.05        14.96        17.52        19.23        50.63 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 
       23.61         3.68        31.43        63.55         2.50         0.23 
TCGA-HT-8114 TCGA-HT-A614 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
        3.88         2.70        19.23         8.94        19.59         9.67 
TCGA-HW-A5KM TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A65S 
        6.61         0.23         6.71         2.30         5.88         2.53 
TCGA-QH-A6X3 TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 
        0.59        69.07        21.63        11.31        94.62        83.70 
TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
       70.55         7.59         3.39         4.04        87.09        17.42 
TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH 
       31.59        24.26        40.83        12.00        33.07        10.95 

$subtype2
TCGA-CS-4941 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A64O TCGA-DH-5140 
        7.69        17.69        23.84        12.43        18.84        19.96 
TCGA-DH-5142 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 
       30.31        29.62        18.02         6.74         8.45       211.17 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 
        7.04        11.64       133.74        19.89        16.83        11.47 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 
       62.96        14.99         6.54         8.84        10.36         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       23.74        19.13        14.24        12.59         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 
       12.20        26.76        41.13        17.98        18.77        13.58 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7477 
        0.59         5.26        10.59        10.78         7.82        24.26 
TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7680 TCGA-HT-7686 
        6.38         5.03        17.29         0.23         0.76        42.74 
TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
        0.10        39.48         0.23         0.49         1.71        16.24 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA 
       12.23         0.10         4.70        16.04         0.23        14.70 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 
        5.33        16.14         5.33         7.89        19.00         4.73 
TCGA-P5-A5EX TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA 
        1.64         1.28         2.96        18.77        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 
        9.30         9.04         7.92         9.37        10.39        83.80 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84I 
        5.00        49.45        12.00        15.09        50.76        19.36 
TCGA-TM-A84J TCGA-TM-A84Q TCGA-VM-A8C9 TCGA-VM-A8CD 
       17.49        18.90        30.08         7.89 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-5279 
       64.64         0.10         9.96         8.02        75.25        44.52 
TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       10.29        72.95        12.59        11.01        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 
       16.08        27.81        14.73        31.82         8.02        30.21 
TCGA-DH-A66F TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
        7.79       182.33        15.16        52.11        22.42        46.06 
TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8168 TCGA-DU-A6S8 
        1.22         7.96        30.67        94.32        14.17         5.98 
TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5964 
       21.30       134.27        78.21        95.57        14.33        34.36 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A6IZ 
       15.35        40.08        16.01        20.09         6.64         4.21 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7602 TCGA-HT-7608 
        4.08        22.95         6.67         0.13        29.85        22.06 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-8012 TCGA-HT-8105 
       14.27        16.24         0.10         2.96         9.40         6.25 
TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7491 TCGA-HW-8322 
       10.49         0.07        13.02        29.92        40.18        17.82 
TCGA-HW-A5KJ TCGA-KT-A74X TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       10.55         5.23         5.75         4.83         7.79         4.11 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        6.31         3.91         4.73        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB 
       59.38        28.27        28.14        15.62        20.05       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IY 
       62.37        72.59        22.92        10.88         6.15        12.59 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-TM-A7C5 TCGA-TM-A84G 
        8.19         2.04         8.12        18.21        25.32        34.36 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CB TCGA-VM-A8CE 
       16.50        29.92         4.57         0.10        26.79 

$subtype4
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       40.18        21.01         6.38         7.40         6.61       122.73 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        46.65        50.17        78.28        30.08        12.72 
TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-5143 
       27.62        18.84        18.38        13.64        10.92        14.40 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6542 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
       14.56        17.46         7.73       156.23       138.28       105.21 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
        7.96        18.94        62.01        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.98        21.40        16.96         8.65         2.70        77.98 
TCGA-DU-A76K TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5962 TCGA-FG-6689 TCGA-FG-7636 
       11.41        79.99        57.93        47.77        14.93        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A713 
       22.55        20.61        20.09        12.95        11.87         5.23 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 
        0.10         8.81         3.75        17.42         6.54        75.19 
TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
       59.18       154.19        23.18         4.57         3.16        56.09 
TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       44.68        31.69         0.10         6.90        14.53        39.09 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.33         0.13         5.33         2.93        11.28 
TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 
        1.64        21.50        33.01         0.46         3.95        29.59 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HW-7487 
        1.71        15.72         0.13         0.10         1.81        13.45 
TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 TCGA-P5-A5EY 
        8.32        35.90         4.31         8.61        42.77         2.37 
TCGA-P5-A5F0 TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        4.11         2.20         3.16         1.91         0.23         5.03 
TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A7IQ TCGA-S9-A7IX 
       62.17        22.49         9.86        70.65        14.27        19.63 
TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
        4.21         3.58        13.02        35.93        22.59        48.39 
TCGA-TM-A84R TCGA-VM-A8CA 
        9.44        13.51 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  130.78   211.17   182.33   156.23 
subtype1 subtype2 subtype3 subtype4 
  17.505   12.100   15.620   14.465 
[1] "0.0 - 130.8 (17.5)" "0.1 - 211.2 (12.1)" "0.1 - 182.3 (15.6)"
[4] "0.1 - 156.2 (14.5)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 40 63
  subtype2 43 47
  subtype3 43 53
  subtype4 50 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   63
  subtype2   43   47
  subtype3   43   53
  subtype4   50   61
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       43       43       50
  MALE         63       47       53       61
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          46               39                18
  subtype2          63               13                14
  subtype3           3               20                73
  subtype4          30               33                48
D8V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             46       63        3       30
  OLIGOASTROCYTOMA        39       13       20       33
  OLIGODENDROGLIOMA       18       14       73       48
[1] 3 4
[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
  subtype1 29 74
  subtype2 22 68
  subtype3 12 84
  subtype4 26 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   74
  subtype2   22   68
  subtype3   12   84
  subtype4   26   85
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        29       22       12       26
  YES       74       68       84       85
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     1                         3
  subtype3                                0     1                         1
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1    97
  subtype2    84
  subtype3    90
  subtype4   105
D8V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   0        1        1        0
  BLACK OR AFRICAN AMERICAN               5        3        1        5
  WHITE                                  97       84       90      105
[1] 4 4
[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
  subtype1   2  93
  subtype2   3  83
  subtype3   4  82
  subtype4   6 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   93
  subtype2    3   83
  subtype3    4   82
  subtype4    6  101
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        4        6
  NOT HISPANIC OR LATINO       93       83       82      101
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1  86  20
  subtype2  59  23
  subtype3 133  19
  subtype4  45   8
subtype1 subtype2 subtype3 subtype4 
     106       82      152       53 
subtype1 subtype2 subtype3 subtype4 
      20       23       19        8 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 
        4.70         7.69        43.89        10.62        21.01        17.69 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5280 
       17.95         8.48         7.56        75.25        72.92        36.56 
TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A64O TCGA-DB-A64V TCGA-DH-5140 TCGA-DH-5141 
       10.29        27.02        18.84        14.73        19.96        31.82 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 
        7.79        18.02         6.74         8.45         6.81        17.49 
TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7290 
       75.16        94.52         7.73         6.54       117.40        10.36 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       25.91        41.98         5.10        23.74        19.13         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76L TCGA-E1-5318 TCGA-E1-5319 
        5.65        12.20         7.23        26.76        78.21        95.57 
TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 
       18.77        23.97        15.35        13.68        14.96        15.52 
TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A60L TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 
       24.46         9.67         7.04         0.13         0.03        16.54 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
        7.10        60.03         4.01         5.03        29.85       107.93 
TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7689 
       17.29        22.06        45.99        57.60         0.76        14.96 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-8011 TCGA-HT-8013 
       39.48        19.23        50.63         0.49        16.24        63.55 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-A617 TCGA-HW-7490 TCGA-HW-8320 
        4.70         0.23        16.04        16.14        19.23         8.94 
TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 
        7.89         0.23         6.71         2.30         5.88         1.28 
TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-R8-A6MK TCGA-R8-A6ML 
        2.53         4.18         2.96         0.59        88.83        94.03 
TCGA-S9-A6TU TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 
       69.07        28.14        15.62        20.05        94.62        83.70 
TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IY TCGA-S9-A7QX TCGA-S9-A7R2 
       62.37         9.30         7.59        12.59         4.04        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84S 
       87.09        31.59        12.00         4.57 

$subtype2
TCGA-CS-4943 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-5273 TCGA-DB-A4XE TCGA-DB-A4XF 
       18.15        23.84        12.43        81.96        18.84        18.38 
TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5142 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       15.42        10.92        30.31        29.62        15.75         3.85 
TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
      211.17        65.75        87.45         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7013 TCGA-DU-A5TP 
       16.83       114.08        11.47        62.96         8.84        14.24 
TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       12.59         3.65       124.50        50.14        67.46        41.13 
TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MU 
      130.78        17.98        13.58        17.88        14.24         0.59 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7468 TCGA-HT-7469 
        3.72         7.04        10.59        10.78         6.67         7.82 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 
       24.26         6.38         6.05        42.74         0.10         0.10 
TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-8106 TCGA-HT-8114 
        0.23        23.61         3.68         1.71         0.10         3.88 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A618 TCGA-HW-A5KL TCGA-HW-A5KM 
        0.23        14.70         5.33         5.33         9.67         6.61 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 
       19.00         4.73         1.64        18.77        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R4 
       11.31         5.85        70.55         9.04         7.92        17.42 
TCGA-S9-A7R7 TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84O 
       83.80        49.45        15.09        19.36        40.83        29.92 
TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH 
       18.90        33.07        30.08        10.95 

$subtype3
TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       64.64        40.18         6.38         7.40         6.61       122.73 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XG 
       46.65        50.17        78.28        12.72        27.62        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DH-5143 
       12.59        11.01        16.08        27.81        13.64        14.40 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6393 TCGA-DU-6403 
       14.56        17.46        13.38        18.94        52.11        11.64 
TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 TCGA-DU-7292 
        7.96       156.23       138.28        14.99        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        2.76         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       15.12         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76O TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5964 
        7.13        79.99        57.93       134.27        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       32.19        14.93        22.55        20.61        20.09        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A4MW TCGA-FG-A710 TCGA-FG-A713 
       16.01        20.09        11.87         5.26        22.95         5.23 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 
        0.10         8.81         3.75        17.42         6.54        75.19 
TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 
       59.18        23.18         4.57         3.16        56.09        14.27 
TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       44.68         0.10        31.69         6.90        14.53        39.09 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.33         0.13         5.33         2.93        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       31.43         1.64         9.40        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 
        6.25         0.46         2.50         3.95        29.59         1.71 
TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       15.72        10.49         0.13         0.10         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 
        1.81         6.38        29.92        13.45         8.32        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-IK-8125 TCGA-P5-A5EY 
        4.31         8.61        19.59        17.82        42.77         2.37 
TCGA-P5-A5F0 TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.11         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS 
        6.31         3.91         1.91         0.23         5.03        62.17 
TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A6WQ 
       22.49         9.86        70.65        10.88         6.15         3.39 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       14.27        19.63         4.21         8.12         3.58        18.21 
TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84R 
       13.02        35.93        22.59        48.39        50.76         9.44 
TCGA-VM-A8CA TCGA-VM-A8CD 
       13.51         7.89 

$subtype4
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-A4X9 
        0.10         9.96         8.02        47.93        44.52        30.08 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DH-5144 TCGA-DH-A669 TCGA-DU-5870 TCGA-DU-5874 
       16.80         5.98         8.02        30.21       182.33        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7015 TCGA-DU-7018 
       22.42        49.02        46.06         1.22        90.77        30.67 
TCGA-DU-8168 TCGA-DU-A76R TCGA-EZ-7264 TCGA-FG-6690 TCGA-FG-7637 TCGA-FG-A60K 
       14.17        21.30        14.33        24.99        40.08         6.64 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7616 TCGA-HT-7676 
        4.21         4.08         0.13       154.19         0.23         0.16 
TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-A5R9 TCGA-HW-7491 TCGA-HW-A5KJ 
       16.24         2.96        17.52         0.07        40.18        10.55 
TCGA-KT-A74X TCGA-QH-A65R TCGA-QH-A6X8 TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW 
        5.23         5.75         4.73        32.65        59.38        28.27 
TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
      103.76        72.59        22.92         9.37         8.19         2.04 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M TCGA-VM-A8CB 
       25.32        34.36        24.26        16.50         0.10 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
  117.40   211.17   156.23   182.33 
subtype1 subtype2 subtype3 subtype4 
  15.570   15.255   13.575   16.500 
[1] "0.0 - 117.4 (15.6)" "0.1 - 211.2 (15.3)" "0.1 - 156.2 (13.6)"
[4] "0.1 - 182.3 (16.5)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 43 65
  subtype2 37 46
  subtype3 73 80
  subtype4 25 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   65
  subtype2   37   46
  subtype3   73   80
  subtype4   25   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       43       37       73       25
  MALE         65       46       80       28
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          52               28                28
  subtype2          54               16                13
  subtype3          35               46                72
  subtype4           1               12                40
D9V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             52       54       35        1
  OLIGOASTROCYTOMA        28       16       46       12
  OLIGODENDROGLIOMA       28       13       72       40
[1] 3 4
[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
  subtype1  25  83
  subtype2  23  60
  subtype3  31 122
  subtype4   9  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   83
  subtype2   23   60
  subtype3   31  122
  subtype4    9   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        25       23       31        9
  YES       83       60      122       44
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         8
  subtype2                                0     0                         1
  subtype3                                0     0                         5
  subtype4                                0     1                         0
          vv
clus       WHITE
  subtype1    97
  subtype2    81
  subtype3   146
  subtype4    49
D9V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        0        0        1
  BLACK OR AFRICAN AMERICAN               8        1        5        0
  WHITE                                  97       81      146       49
[1] 4 4
[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
  subtype1   5  97
  subtype2   2  75
  subtype3   8 140
  subtype4   0  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   97
  subtype2    2   75
  subtype3    8  140
  subtype4    0   45
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        8        0
  NOT HISPANIC OR LATINO       97       75      140       45
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 102  23
  subtype2  71   8
  subtype3 100  10
  subtype4  50  29
subtype1 subtype2 subtype3 subtype4 
     125       79      110       79 
subtype1 subtype2 subtype3 subtype4 
      23        8       10       29 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5396 
        4.70         7.69        18.15        10.62         0.10         9.96 
TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5274 
       17.69        17.95         8.48         7.56        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-A4XD TCGA-DB-A64S 
       47.93        72.92        46.65        36.56        27.02        15.42 
TCGA-DB-A64V TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66D 
       14.73        19.96        31.82        30.31         8.02        15.75 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
        6.81       182.33        17.49        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 
       65.75        87.45        94.52       114.08       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-A5TW 
       30.67        44.02        25.91        41.98        20.68         5.65 
TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 
        7.23       124.50        50.14        67.46        41.13        78.21 
TCGA-E1-5322 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8182 
      130.78        24.99        23.97        15.35        40.08        13.68 
TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.24        14.96        15.52        24.46         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FN-7833 TCGA-HT-7468 
        7.04         6.64         7.04         4.21         0.13         6.67 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 
        0.03        16.54         7.10        60.03         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 
       29.85       107.93        17.29        22.06        45.99        57.60 
TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 
        0.23         0.16        16.24         0.76         6.05        14.96 
TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 
        0.10        17.52        19.23        50.63        23.61         3.68 
TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HW-7490 TCGA-HW-8320 
       63.55         0.23         3.88        16.04        19.23         8.94 
TCGA-HW-A5KL TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 
        9.67         0.23         6.71         2.30         5.88         1.28 
TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6X3 TCGA-R8-A6ML TCGA-S9-A6TU TCGA-S9-A6TW 
        2.53         4.18         0.59        94.03        69.07        28.27 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO TCGA-S9-A7IY 
       11.31        15.62        94.62        83.70         7.59        12.59 
TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-TM-A84B TCGA-TM-A84H 
        9.37         4.04        87.09        17.42        12.00        24.26 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CH 
       40.83        29.92        18.90        33.07        10.95 

$subtype2
TCGA-CS-4942 TCGA-CS-5390 TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 
       43.89        64.64         8.02        44.52        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64P TCGA-DB-A64Q 
       10.29        12.72        18.84        72.95        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5874 TCGA-DU-6393 
       16.08        27.81        30.21         7.79        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7294 TCGA-DU-8168 
       22.42         1.22         7.96       156.23        94.32        14.17 
TCGA-DU-A5TS TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5319 
       15.12         5.98         7.13        21.30       134.27        95.57 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-A6J1 
       14.33        47.77        17.88        22.55        20.61         4.08 
TCGA-FG-A710 TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7692 TCGA-HT-7884 TCGA-HT-8108 
       22.95         0.13       154.19         2.96        11.28         2.50 
TCGA-HT-A5R9 TCGA-HT-A614 TCGA-HT-A615 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ 
        0.07         2.70        13.02        40.18        17.82        10.55 
TCGA-KT-A74X TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6X4 
        5.23         5.75         4.83         7.79         4.11         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TX 
        3.91         4.73         0.23        32.65        59.38        28.14 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL 
       20.05       103.76        62.37        72.59        22.92        10.88 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        6.15         3.39         8.19         2.04         8.12         3.58 
TCGA-S9-A7QY TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84S 
       18.21        25.32        22.59        34.36        16.50         4.57 
TCGA-VM-A8CB 
        0.10 

$subtype3
TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5278 
       40.18         6.38         7.40         6.61       122.73        50.17 
TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W TCGA-DH-5143 
       27.62        18.38        12.59        11.01        13.64        14.40 
TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-7009 
        3.85        14.56        17.46        13.38        18.94       138.28 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       26.30        18.94        62.01        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A6S2 TCGA-DU-A6S3 
        3.98        21.40        16.96        15.48         8.65         2.70 
TCGA-DU-A6S6 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
       77.98        79.99        57.93        34.36        32.19        14.93 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A713 
       20.09        12.95        16.01        20.09        11.87         5.23 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.10         8.81         3.75        17.42         6.54        24.26 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
       75.19        59.18        23.18         4.57         3.16        56.09 
TCGA-HT-7620 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
       14.27        44.68         0.10        31.69         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
       39.48        39.09        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 
        2.93        31.43         1.64         9.40        21.50        33.01 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV 
        6.25         0.46         3.95        29.59         1.71        10.49 
TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
        0.13         0.10         1.81         5.33         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 
       13.45         8.32        35.90         4.31         8.61        19.59 
TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
       42.77         2.37         4.11         2.20         3.16         1.91 
TCGA-R8-A6MK TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WI 
       88.83        62.17        22.49         9.86        70.55        70.65 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CF TCGA-TM-A84F 
       14.27        19.63        13.02        35.93        48.39        50.76 
TCGA-TM-A84R TCGA-VM-A8CA 
        9.44        13.51 

$subtype4
TCGA-CS-5395 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A64O TCGA-DB-A64X TCGA-DH-A66B 
       21.01        23.84        12.43        18.84        10.92        29.62 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 
       18.02         6.74         8.45       211.17         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
      133.74        19.89        16.83         7.73        11.47        62.96 
TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 
       14.99         6.54         8.84        10.36         7.96         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       23.74        19.13        14.24        12.59         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 
       12.20        11.41        26.76        17.98        18.77        13.58 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7478 
        0.59         5.26        10.59        10.78         7.82         6.38 
TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
       42.74         0.10         0.23         0.49         1.71        16.24 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA 
       12.23         0.10         4.70        15.72         0.23        14.70 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 
        5.33        16.14         7.89         6.61        19.00         4.73 
TCGA-P5-A5EX TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 
        1.64         2.96         5.03        18.77        21.63        16.37 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7R2 
        5.85         9.30         9.04         7.92         4.21        10.39 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-VM-A8C9 
       83.80        31.59        49.45        15.09        19.36        30.08 
TCGA-VM-A8CD 
        7.89 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  182.33   156.23   138.28   211.17 
subtype1 subtype2 subtype3 subtype4 
  17.420   15.160   14.465   11.410 
[1] "0.0 - 182.3 (17.4)" "0.1 - 156.2 (15.2)" "0.1 - 138.3 (14.5)"
[4] "0.1 - 211.2 (11.4)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1 47 80
  subtype2 38 41
  subtype3 53 58
  subtype4 40 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   80
  subtype2   38   41
  subtype3   53   58
  subtype4   40   40
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       47       38       53       40
  MALE         80       41       58       40
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          52               38                37
  subtype2           9               19                51
  subtype3          25               33                53
  subtype4          56               12                12
D10V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             52        9       25       56
  OLIGOASTROCYTOMA        38       19       33       12
  OLIGODENDROGLIOMA       37       51       53       12
[1] 3 4
[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
  subtype1 38 89
  subtype2  9 70
  subtype3 24 87
  subtype4 17 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   89
  subtype2    9   70
  subtype3   24   87
  subtype4   17   63
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        38        9       24       17
  YES       89       70       87       63
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         4
  subtype2                                0     1                         2
  subtype3                                0     0                         4
  subtype4                                1     1                         4
          vv
clus       WHITE
  subtype1   122
  subtype2    72
  subtype3   106
  subtype4    73
D10V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   0        1        0        1
  BLACK OR AFRICAN AMERICAN               4        2        4        4
  WHITE                                 122       72      106       73
[1] 4 4
[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
  subtype1   5 115
  subtype2   1  69
  subtype3   6 102
  subtype4   3  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  115
  subtype2    1   69
  subtype3    6  102
  subtype4    3   71
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        1        6        3
  NOT HISPANIC OR LATINO      115       69      102       71
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1  73  15
  subtype2  49  24
  subtype3  45   5
  subtype4 104  12
  subtype5  26   8
  subtype6   9   5
  subtype7  17   1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      88       73       50      116       34       14       18 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      15       24        5       12        8        5        1 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        4.70        43.89        18.15        17.95         8.48         7.56 
TCGA-DB-5273 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A64S 
       81.96        36.56        30.08        12.72        27.02        15.42 
TCGA-DH-5142 TCGA-DH-A66D TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6401 
       30.31        15.75         6.81        49.02        65.75        87.45 
TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 
       94.52         7.73        14.99       117.40        90.77        44.02 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TW TCGA-DU-A6S7 
       25.91        41.98        20.68        15.48         5.65         7.23 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
       50.14        67.46       130.78        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        24.46         3.72 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
        7.04         7.04         0.13         0.03        16.54         7.10 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 
       60.03         4.01         5.03       107.93        17.29        22.06 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7689 
       45.99        57.60         0.16         6.05        42.74        14.96 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8114 
       19.23        50.63         3.68        63.55         0.23         3.88 
TCGA-HW-8320 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-P5-A5EV TCGA-P5-A5EW TCGA-QH-A6X3 
        8.94         9.67         6.61         0.23         6.71         0.59 
TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO 
       69.07        21.63        11.31        94.62        83.70         7.59 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84H 
        3.58         4.04        87.09        17.42        31.59        24.26 
TCGA-TM-A84L TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CH 
       40.83        18.90        33.07        10.95 

$subtype2
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 TCGA-DB-5274 TCGA-DB-A64O 
        7.69        10.62        21.01        17.69        75.25        18.84 
TCGA-DH-5140 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-6396 TCGA-DU-6402 
       19.96        29.62        18.02         6.74        75.16         7.04 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7013 
       19.89        16.83        11.47        62.96         6.54         8.84 
TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR 
       10.36         5.10        23.74        19.13        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7T8 TCGA-E1-5318 
        4.96         3.65        12.20        26.76       124.50        78.21 
TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A60K TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7616 
       13.58         0.59         6.64        24.26         6.38         0.23 
TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
        0.76         0.10         0.23         0.49         1.71        16.24 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5R9 
       12.23         0.10         4.70        16.04         0.23         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7490 TCGA-HW-A5KK 
       14.70         5.33        16.14         5.33        19.23         7.89 
TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.73         1.64         2.30         5.88         1.28         2.53 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-S9-A6UA 
        4.18         2.96        18.77        28.27        16.37         5.85 
TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A7IY TCGA-TM-A7C3 TCGA-TM-A84B TCGA-VM-A8C9 
       70.55         9.30        12.59        49.45        12.00        30.08 
TCGA-VM-A8CD 
        7.89 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5275 TCGA-DB-A4XA 
       64.64         0.10         9.96         8.02        47.93        10.29 
TCGA-DB-A4XG TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64X TCGA-DH-5141 TCGA-DH-5144 
       72.95        16.80         5.98        10.92        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5870 TCGA-DU-6394 TCGA-DU-7018 TCGA-DU-8168 
       30.21         7.79       182.33        22.42        30.67        14.17 
TCGA-DU-A76R TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-7637 TCGA-FG-A6IZ TCGA-HT-7468 
       21.30        95.57        14.33        40.08         4.21         6.67 
TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7875 TCGA-HT-8012 TCGA-HW-7491 TCGA-KT-A74X 
        0.10         2.96         0.33         9.40        40.18         5.23 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6X8 TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TX 
        7.79         4.11         4.73        94.03        59.38        28.14 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A7J0 
       15.62        20.05       103.76        72.59        22.92         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
        8.19         2.04        25.32        34.36        16.50        29.92 
TCGA-TM-A84S TCGA-VM-A8CB 
        4.57         0.10 

$subtype4
TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       40.18         6.38         7.40         6.61       122.73        46.65 
TCGA-DB-5278 TCGA-DB-5281 TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L 
       50.17        78.28        27.62        18.38        12.59        11.01 
TCGA-DB-A64R TCGA-DB-A64W TCGA-DH-5143 TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 
       16.08        13.64        14.40         3.85        14.56        17.46 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 
      156.23       138.28        26.30         7.96        18.94        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-A6S2 
       60.30        23.31         2.76         3.98        21.40         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76O TCGA-E1-5307 
        2.70        77.98         5.98        11.41         7.13        57.93 
TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7638 TCGA-FG-7641 
      134.27        47.77        34.36        14.93        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A4MW TCGA-FG-A6J1 TCGA-FG-A710 
       20.09        12.95        11.87         5.26         4.08        22.95 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        5.23         0.10         8.81         3.75        17.42         6.54 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
       75.19        59.18        23.18         4.57         3.16        56.09 
TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
       44.68        31.69         6.90        14.53        39.09        37.15 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 
        0.13         5.33         2.93         1.64        21.50        33.01 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 
        6.25         0.46         3.95        29.59         1.71        15.72 
TCGA-HT-A5R5 TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A61A TCGA-HW-7487 
        0.13         0.10        13.02         1.81         6.38        13.45 
TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-A5KJ TCGA-IK-8125 
        8.32        35.90         4.31         8.61        10.55        42.77 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
        2.37         4.11         5.75         2.20         3.16         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI 
        0.23         5.03        62.17        22.49         9.86        70.65 
TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J3 
       10.88         6.15        14.27        19.63         4.21         8.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F 
       18.21        13.02        35.93        22.59        48.39        50.76 
TCGA-TM-A84R TCGA-VM-A8CA 
        9.44        13.51 

$subtype5
TCGA-CS-6188 TCGA-DB-5279 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-5872 
       23.84        44.52        13.38         8.45        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-6408 
       15.16        52.11        46.06         1.22        11.64       114.08 
TCGA-DU-6410 TCGA-DU-7294 TCGA-DU-8166 TCGA-E1-5305 TCGA-FG-5965 TCGA-FG-6688 
        7.96        94.32        16.96        79.99        32.19        18.77 
TCGA-FG-7634 TCGA-FG-8186 TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7677 TCGA-HT-7690 
       15.35        16.01         0.13       154.19        16.24         0.10 
TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8108 
       17.52        39.48        23.61        11.28        31.43         2.50 
TCGA-HW-7486 TCGA-HW-8321 TCGA-HW-8322 TCGA-IK-7675 
       29.92        19.59        17.82        19.00 

$subtype6
TCGA-CS-6665 TCGA-DB-A4XE TCGA-DU-6392 TCGA-DU-6404 TCGA-E1-5304 TCGA-FG-5963 
       12.43        18.84       211.17       133.74        41.13        17.98 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R7 
       10.59        10.78         7.82         9.04         7.92        83.80 
TCGA-TM-A84C TCGA-TM-A84I 
       15.09        19.36 

$subtype7
TCGA-DB-5276 TCGA-DB-A64U TCGA-DB-A64V TCGA-DU-A5TS TCGA-FG-8187 TCGA-FG-A4MY 
       72.92        27.81        14.73        15.12        20.09         9.67 
TCGA-HT-7602 TCGA-HT-7620 TCGA-HT-A4DV TCGA-HT-A614 TCGA-QH-A65V TCGA-QH-A6X4 
       29.85        14.27        10.49         2.70         4.83         6.31 
TCGA-QH-A6X5 TCGA-R8-A6MK TCGA-R8-A6MO TCGA-S9-A6WD TCGA-S9-A6WQ TCGA-S9-A7R2 
        3.91        88.83        32.65        62.37         3.39        10.39 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.03     0.07     0.10     0.10     0.10     7.82     2.70 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  130.78   124.50   182.33   156.23   154.19   211.17    88.83 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  17.650   10.620   14.975   13.235   18.295   16.535   14.500 
[1] "0.0 - 130.8 (17.6)" "0.1 - 124.5 (10.6)" "0.1 - 182.3 (15.0)"
[4] "0.1 - 156.2 (13.2)" "0.1 - 154.2 (18.3)" "7.8 - 211.2 (16.5)"
[7] "2.7 - 88.8 (14.5)" 
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 35 53
  subtype2 34 40
  subtype3 20 30
  subtype4 56 61
  subtype5 17 17
  subtype6  8  6
  subtype7  8 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   53
  subtype2   34   40
  subtype3   20   30
  subtype4   56   61
  subtype5   17   17
  subtype6    8    6
  subtype7    8   12
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       35       34       20       56       17        8        8
  MALE         53       40       30       61       17        6       12
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          48               26                14
  subtype2          45               16                13
  subtype3           3                9                38
  subtype4          27               30                60
  subtype5           7               11                16
  subtype6          10                2                 2
  subtype7           2                8                10
D11V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASTROCYTOMA             48       45        3       27        7       10
  OLIGOASTROCYTOMA        26       16        9       30       11        2
  OLIGODENDROGLIOMA       14       13       38       60       16        2
                   clus
vv                  subtype7
  ASTROCYTOMA              2
  OLIGOASTROCYTOMA         8
  OLIGODENDROGLIOMA       10
[1] 3 7
[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
  subtype1 27 61
  subtype2 12 62
  subtype3  7 43
  subtype4 24 93
  subtype5 11 23
  subtype6  5  9
  subtype7  2 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   61
  subtype2   12   62
  subtype3    7   43
  subtype4   24   93
  subtype5   11   23
  subtype6    5    9
  subtype7    2   18
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        27       12        7       24       11        5        2
  YES       61       62       43       93       23        9       18
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         4
  subtype2                                1     1                         2
  subtype3                                0     0                         0
  subtype4                                0     0                         4
  subtype5                                0     0                         2
  subtype6                                0     0                         1
  subtype7                                0     1                         1
          vv
clus       WHITE
  subtype1    83
  subtype2    69
  subtype3    48
  subtype4   111
  subtype5    31
  subtype6    13
  subtype7    18
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        1        0        0        0
  BLACK OR AFRICAN AMERICAN               4        2        0        4        2
  WHITE                                  83       69       48      111       31
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               1        1
  WHITE                                  13       18
[1] 4 7
[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
  subtype1   1  80
  subtype2   2  66
  subtype3   2  42
  subtype4   7 106
  subtype5   2  31
  subtype6   0  14
  subtype7   1  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   80
  subtype2    2   66
  subtype3    2   42
  subtype4    7  106
  subtype5    2   31
  subtype6    0   14
  subtype7    1   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        2        7        2        0
  NOT HISPANIC OR LATINO       80       66       42      106       31       14
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       18
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 96 24
  subtype2 95 12
  subtype3 83  6
  subtype4 49 28
subtype1 subtype2 subtype3 subtype4 
     120      107       89       77 
subtype1 subtype2 subtype3 subtype4 
      24       12        6       28 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-6186 
        4.70         7.69        43.89        18.15        10.62        17.69 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
       17.95         8.48         7.56        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB 
       46.65        44.52        36.56        78.28        10.29        12.72 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A64V TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66B 
       27.02        15.42        14.73        19.96        30.31        29.62 
TCGA-DH-A66D TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 
       15.75         6.81       182.33        18.94        17.49        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 
       75.16        46.06        65.75        87.45        94.52       114.08 
TCGA-DU-6542 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 
        7.73       117.40        90.77        44.02        25.91        41.98 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-E1-5302 
       14.24        12.59         5.65         7.23       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 TCGA-FG-6690 
       67.46        41.13       134.27        78.21       130.78        24.99 
TCGA-FG-6691 TCGA-FG-7637 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 
       23.97        40.08        13.68        14.24        14.96        15.52 
TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FN-7833 TCGA-HT-7472 
       24.46         9.67         6.64         7.04         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       16.54        24.26         7.10        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
        5.03        29.85       107.93        17.29        22.06        45.99 
TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 TCGA-HT-7855 
       57.60         0.76         6.05        14.96        17.52        19.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8114 
       50.63        23.61         3.68        63.55         0.23         3.88 
TCGA-HT-8563 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       16.04        19.23         8.94         9.67         6.61        19.00 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S 
        0.23         6.71         2.30         5.88         1.28         2.53 
TCGA-QH-A6X3 TCGA-R8-A6MK TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U9 
        0.59        88.83        69.07        21.63        11.31        83.70 
TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R3 
       70.55         7.59        12.59         9.37         4.04        87.09 
TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CH 
       31.59        12.00        24.26        18.90        33.07        10.95 

$subtype2
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-5278 
       64.64         0.10         9.96         8.02        75.25        50.17 
TCGA-DB-A4X9 TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       30.08        27.62        18.84        18.38        72.95        12.59 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DH-5141 TCGA-DH-5143 
       16.80         5.98        16.08        27.81        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5853 
        8.02        30.21         7.79         3.85        14.56        13.38 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7018 
       15.16        52.11        22.42         1.22         7.96        30.67 
TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-8168 TCGA-DU-A5TS 
       26.30        94.32        23.31        20.68        14.17        15.12 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 
        5.98         7.13        21.30        95.57        14.33        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ 
       34.36        32.19        15.35        22.55         7.04         4.21 
TCGA-FG-A6J1 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 
        4.08         6.67         0.13         0.23         0.16        16.24 
TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7884 TCGA-HT-8012 TCGA-HT-8108 
        0.10         0.10         2.96        11.28         9.40         2.50 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 
       10.49         0.13         0.07         2.70        13.02         5.33 
TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-QH-A65V TCGA-QH-A65X 
       40.18        17.82        10.55         5.23         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-R8-A6ML 
        4.11         6.31         3.91         4.73         0.23        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 
       32.65        59.38        62.17        28.27        28.14        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       20.05        94.62       103.76        62.37        72.59        22.92 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        6.15         3.39         4.21         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84G TCGA-TM-A84L 
        3.58        18.21        25.32        22.59        34.36        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB 
       16.50        29.92         4.57        13.51         0.10 

$subtype3
TCGA-CS-5393 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-A64L TCGA-DB-A64W 
       40.18         7.40         6.61       122.73        11.01        13.64 
TCGA-DU-5851 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 
       17.46       156.23       138.28        18.94        62.01        60.30 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A6S2 TCGA-DU-A6S3 
        2.76         3.98        21.40        16.96         8.65         2.70 
TCGA-DU-A6S6 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7641 
       77.98        79.99        57.93        14.93        17.88        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A710 
       20.09        12.95        16.01        20.09        11.87        22.95 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        5.23         0.10         8.81         3.75        17.42         6.54 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
       75.19        59.18        23.18         4.57         3.16        56.09 
TCGA-HT-7620 TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       14.27        44.68        31.69         6.90        14.53        39.09 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
       37.15         0.33         0.13         5.33         2.93        31.43 
TCGA-HT-8010 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 
        1.64        21.50        33.01         6.25         0.46         3.95 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A TCGA-HW-7486 
       29.59         1.71         0.10         1.81         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 
       13.45         8.32        35.90         4.31         8.61        42.77 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
        2.37         4.11         5.75         2.20         3.16         1.91 
TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX 
       22.49         9.86        70.65        10.88        14.27        19.63 
TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84R 
       13.02        35.93        48.39        50.76         9.44 

$subtype4
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A64O TCGA-DB-A64X 
       21.01         6.38        23.84        12.43        18.84        10.92 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 
       18.02         6.74         8.45       211.17         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 
      133.74        19.89        16.83        11.47        62.96        14.99 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 
        6.54         8.84        10.36         7.96         5.10        23.74 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76K 
       19.13        15.48         4.96         3.65        12.20        11.41 
TCGA-DU-A76L TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW 
       26.76        17.98        18.77        13.58         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 TCGA-HT-7478 TCGA-HT-7686 
        3.72        10.59        10.78         7.82         6.38        42.74 
TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
        0.10        39.48         0.23         0.49         1.71        16.24 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA 
       12.23         0.10         4.70        15.72         0.23        14.70 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-8321 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX 
        5.33        16.14        19.59         7.89         4.73         1.64 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA 
        4.18         2.96         5.03        18.77        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 
        9.30         9.04         7.92        10.39        17.42        83.80 
TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-VM-A8C9 TCGA-VM-A8CD 
       49.45        15.09        19.36        30.08         7.89 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  182.33   103.76   156.23   211.17 
subtype1 subtype2 subtype3 subtype4 
   18.92    14.40    14.27    10.92 
[1] "0.0 - 182.3 (18.9)" "0.1 - 103.8 (14.4)" "0.1 - 156.2 (14.3)"
[4] "0.1 - 211.2 (10.9)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 44 78
  subtype2 51 57
  subtype3 44 45
  subtype4 39 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   78
  subtype2   51   57
  subtype3   44   45
  subtype4   39   39
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       44       51       44       39
  MALE         78       57       45       39
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          56               39                27
  subtype2          11               28                69
  subtype3          19               24                46
  subtype4          56               11                11
D12V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             56       11       19       56
  OLIGOASTROCYTOMA        39       28       24       11
  OLIGODENDROGLIOMA       27       69       46       11
[1] 3 4
[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
  subtype1 36 86
  subtype2 16 92
  subtype3 18 71
  subtype4 18 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   86
  subtype2   16   92
  subtype3   18   71
  subtype4   18   60
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        36       16       18       18
  YES       86       92       71       60
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                0     1                         1
  subtype3                                0     0                         4
  subtype4                                1     1                         4
          vv
clus       WHITE
  subtype1   115
  subtype2   102
  subtype3    85
  subtype4    71
D12V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   0        1        0        1
  BLACK OR AFRICAN AMERICAN               5        1        4        4
  WHITE                                 115      102       85       71
[1] 4 4
[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
  subtype1   4 109
  subtype2   4  95
  subtype3   5  82
  subtype4   2  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  109
  subtype2    4   95
  subtype3    5   82
  subtype4    2   71
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        4        5        2
  NOT HISPANIC OR LATINO      109       95       82       71
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
