[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/11541557/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/11590619/LGG-TP.mergedcluster.txt"

nPatients in clinical file=433, in cluster file=516, common to both=433
[1]  12 433
[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 
141  97 192 
  1   2   3 
141  97 192 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
185  64 145  39 
  1   2   3   4 
185  64 145  39 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
52 62 69 75 
 1  2  3  4 
52 62 69 75 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 67 132  59 
  1   2   3 
 67 132  59 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
110  94  90 116  20 
  1   2   3   4   5 
110  94  90 116  20 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
111  94 104 121 
  1   2   3   4 
111  94 104 121 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
114  89 161  66 
  1   2   3   4 
114  89 161  66 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
182 162  86 
  1   2   3 
182 162  86 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
157 130 140 
  1   2   3 
157 130 140 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 72 115 167  73 
  1   2   3   4 
 72 115 167  73 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 433 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-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
         332          225          196          313          935          116 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
          NA          968          922          438          244           NA 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
        1279          846          523          523         1650          311 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
         200          105          189          548          443          531 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
          NA          407          257          207         5546          576 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
         532          461         6423         1585          682         1491 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
        2286         1401           NA           NA         2660          214 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
          NA           NA          605           NA           NA         3470 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
         242          235           NA           NA         4752         4206 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
          NA           NA           NA           NA           NA         2761 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
          NA          800           NA           NA         2869           NA 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
          NA           NA           NA         1834           NA         1277 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
          84           NA           NA          121          629          651 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
         582          516          471          431          433          383 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
         460          151          111          172          371          263 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
          82         2372          220          182           NA           NA 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
         217           NA         3787           NA         1525         2052 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
        1251         2433         1762         4084         2379         2907 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
        3978          436            7            6         1453          547 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
        1045          979          571          454          760          729 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 
         413          467          544         1219          686          627 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
         611          394          416          433          487          611 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
         455          685          472         1164          326          160 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
         569          721          449          542          499          457 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
         500          322          868          328          698         1329 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
         159          226          174            4            3          203 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
         238          268            4            1          503          114 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
         530          199          738          194          216         2287 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        1800         1826         4690          122          153          908 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
         705         3283          139          526           NA          671 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
        1399         1706         1752           NA          434            5 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
         494           23         1359          184         1300            3 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
         964          455            3            3           90          533 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
         210          442         1201          585         1189            7 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        1540           15          718         1130           10            4 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
         112          162           89           52          343          956 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
          50          494          286           NA            3          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-A5R7 
         488          478            7          319            4          426 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
           2          447            3           NA           82          396 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61A TCGA-HT-A74O TCGA-HW-7486 
          55          491          162          194            3          910 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
         409          253          585         1222         1092          131 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
         660          657          596          542          619          240 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
         633          630           NA         1301          159          144 
TCGA-P5-A5ET TCGA-P5-A5EU TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
          NA           NA            7          204           50           72 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
          70          125          179          232           23           39 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
         175           77          147          237          125          127 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
         451          442           NA           NA           67           96 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
          18          192          119          144           58            7 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
         153          106            2         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         1151         1049 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
         953          658          498          536          719          992 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
         300         2878         2546           NA         3236         1897 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
        2208         2437          987         2585          331          604 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
         484          231          461          428          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-A7R1 
         247          109          123          863          396         5000 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
          NA         3013          530         2549           NA          569 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
         152         1504         1470         1500         1058         1472 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
         365          459         1544         1045          738          589 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
         532           NA          502          910          575          287 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
         139          365         1006          915          411            3 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
          NA          815          333          823          214          706 
TCGA-W9-A837 
        1371 
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=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=324,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=3,	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=18,	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 433 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 118  22
  subtype2  60  36
  subtype3 174  17
subtype1 subtype2 subtype3 
     140       96      191 
subtype1 subtype2 subtype3 
      22       36       17 
$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-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XC 
        7.56        47.93        46.65        36.56        78.28        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64X TCGA-DB-A75O TCGA-DB-A75P 
       27.02        18.84        18.38        10.92        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       19.96        14.40        42.05        27.81        17.19         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6399 TCGA-DU-6401 
        3.45         6.21        13.38        18.94        65.75        87.45 
TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 
      114.08        62.96       156.23        14.99       105.21       117.40 
TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TU 
       26.30        44.02        23.31        15.48        15.12         3.65 
TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5307 
        7.23         7.13       124.50        50.14        67.46        57.93 
TCGA-FG-5963 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 
       17.98        14.93        24.99        23.97        13.68        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y 
       14.96        15.52        23.70        14.76        16.41        28.54 
TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
        0.13         7.82         8.81         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7603 TCGA-HT-7604 
        6.38         7.10        60.03         4.01        23.18       107.93 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
       57.60         0.16        42.74        31.69        14.96         0.10 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
       17.52        19.23         0.23        23.61         3.68        11.28 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 
       31.43        63.55        21.50         0.10         0.23         3.88 
TCGA-HT-8563 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 
       16.04        14.01         0.10         2.70         1.81         5.33 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8321 
        0.10         8.32        19.23        35.90        21.70        19.59 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.81        20.71        19.00         6.71         2.30         5.88 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-S9-A6TS 
        0.76         1.28         2.53         0.59         0.23        62.17 
TCGA-S9-A6TU TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WO 
       69.07        17.62         9.86         5.85        80.12         7.59 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
       14.07         7.92         9.37         4.04        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80        18.71         5.00        48.33        34.78        48.39 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-VM-A8C8 
       50.76        24.26        19.36        17.49        40.83        33.07 
TCGA-VM-A8CH TCGA-VV-A86M 
       10.95         7.04 

$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-A669 TCGA-DU-5847 TCGA-DU-5852 
      122.73        30.08        18.84        30.21        18.02         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6402 
        8.45         6.81        17.49       211.17        49.02         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7292 
       11.47         6.54         8.84        90.77        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       18.94        25.91        41.98         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TW 
       20.68        19.13        16.96        12.59         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-F6-A8O4 TCGA-FG-5965 
       12.20        11.41        26.76        41.13         0.20        32.19 
TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 
       18.77        13.58        20.09        10.72         5.26        10.59 
TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7606 
       10.78        43.69         5.72        16.54        17.42        17.29 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 
        0.49         1.71        16.24        12.23         2.50         4.70 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC 
       15.72         0.23         0.13         0.07        14.70         5.33 
TCGA-HT-A617 TCGA-HW-8322 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5F0 
       16.14        17.82         7.89         4.73         0.23         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A870 
        4.18        14.53        12.23         1.91         5.03         0.07 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       31.33        16.37        19.86        14.27        19.63         4.21 
TCGA-S9-A7QW TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-VM-A8CD 
        3.58       164.38        10.39        49.45        12.00         7.89 

$subtype3
TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6669 
       10.62        64.64         0.10         9.96         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
        6.61        81.96        75.25        72.92        50.17        44.52 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       10.29        12.72        72.95        12.59        11.01        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 
        7.40         6.44        10.29        31.82        30.31         8.02 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5870 
       17.19        54.25        10.22        14.56        17.46       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       15.16        52.11        22.42        75.16        46.06         1.22 
TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
        7.73       138.28        30.67        94.32        62.01        60.30 
TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A6S2 TCGA-DU-A6S3 
        2.76        21.40        14.17        14.24         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5311 
       77.98         5.98        21.30        44.42        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 
       78.21        95.57       130.78        14.33         0.23        47.77 
TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       34.36        15.35        17.88        22.55        20.61        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A60K 
       16.01        20.09        22.52        38.27        18.71        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-7467 
       15.02        16.44        22.95         5.23         7.43         0.10 
TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        6.67         0.13         0.03        75.19        59.18       154.19 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
        5.03        29.85         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       56.09         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
        6.05         0.10         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       39.48        39.09        50.63        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 
        5.33         2.93         1.64         9.40         0.10        33.01 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV TCGA-HT-A615 
        6.25         0.46         3.95        29.59        10.49        13.02 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-A5KJ 
       29.92        13.45        40.18         4.31        21.60        20.35 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-QH-A65R 
       42.77         5.23         1.64         2.37         7.63         5.75 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11        14.83         2.20         3.16 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
        6.31         3.91         4.73         3.48        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       32.65        59.38        18.77        37.84        34.49        21.63 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       23.64        32.61        94.62        83.70       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       72.59        32.45        84.99        10.88        15.91        15.16 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
       12.59         8.19         2.04         8.12        28.37        13.02 
TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       31.59        49.32        15.09        34.36        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA 
       18.90         9.44         4.57        12.00        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
        0.10        26.79        27.06        23.21        45.07 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  156.23   211.17   182.33 
subtype1 subtype2 subtype3 
  17.505   12.410   16.010 
[1] "0.1 - 156.2 (17.5)" "0.1 - 211.2 (12.4)" "0.0 - 182.3 (16.0)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  57  84
  subtype2  51  46
  subtype3  82 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   84
  subtype2   51   46
  subtype3   82  110
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       57       51       82
  MALE         84       46      110
[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          79               38                24
  subtype2          48               26                23
  subtype3          32               43               117
D3V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             79       48       32
  OLIGOASTROCYTOMA        38       26       43
  OLIGODENDROGLIOMA       24       23      117
[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  33 108
  subtype2  22  75
  subtype3  34 158
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33  108
  subtype2   22   75
  subtype3   34  158
     clus
vv    subtype1 subtype2 subtype3
  NO        33       22       34
  YES      108       75      158
[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     2                         8
  subtype3                                0     4                         4
          vv
clus       WHITE
  subtype1   136
  subtype2    86
  subtype3   178
D3V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        2        4
  BLACK OR AFRICAN AMERICAN               2        8        4
  WHITE                                 136       86      178
[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   5 128
  subtype2   4  88
  subtype3   7 171
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  128
  subtype2    4   88
  subtype3    7  171
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        4        7
  NOT HISPANIC OR LATINO      128       88      171
[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 155  28
  subtype2  34  30
  subtype3 132  12
  subtype4  34   5
subtype1 subtype2 subtype3 subtype4 
     183       64      144       39 
subtype1 subtype2 subtype3 subtype4 
      28       30       12        5 
$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-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       18.38        15.42        10.92         6.44        10.29        30.74 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       30.31        14.40        42.05        27.81        17.19         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
        3.45         6.21        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-7011 
      114.08         7.73        62.96       156.23        14.99       105.21 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 
      117.40        90.77        26.30        44.02        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       41.98         2.76        20.68        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O 
       12.59        15.12         3.65         5.65         7.23         7.13 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5322 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 
      130.78         0.20        32.19        14.93        24.99        17.88 
TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.24        14.96        15.52        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A711 TCGA-FN-7833 
       14.76        16.41        10.59        28.54        43.69         0.13 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       24.26         6.38        60.03       154.19         4.01         5.03 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       23.18       107.93        17.29        45.99        56.09        57.60 
TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.16         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
       17.52        19.23        50.63        23.61         3.68        11.28 
TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R7 
       63.55         2.50         0.23         3.88        16.04        14.01 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7489 
        0.10         2.70         1.81         5.33         0.10         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
       19.23        35.90        21.70        21.60        19.59        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.71        19.00         0.23         6.71         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
        7.63         0.76         2.53         0.59         1.91         0.23 
TCGA-QH-A870 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U1 
        0.07        62.17        69.07        18.77        21.63        17.62 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS 
        9.86        94.62        83.70         7.59        14.07         7.92 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.21         9.37         3.58         4.04        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80        31.59         5.00        48.33        34.78        48.39 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T 
       50.76        24.26        19.36        40.83        18.90        12.00 
TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A86M 
       33.07        10.95         7.04 

$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-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-7012 TCGA-DU-7013 
      133.74        19.89        16.83        11.47         6.54         8.84 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       10.36         7.96         5.10        23.74        19.13         4.96 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU 
       12.20        11.41        26.76        18.77        13.58        10.72 
TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7857 
        5.26        10.78         7.43         5.72         7.82         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 
        0.49         1.71        16.24        12.23         0.10         4.70 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-A5KK 
       15.72         0.23        14.70         5.33        16.14         7.89 
TCGA-KT-A7W1 TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6U0 TCGA-S9-A6UA 
        4.73        14.53        12.23         5.03        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 
       19.86        15.91        19.63        10.39        18.71        49.45 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84J TCGA-VM-A8CD 
       12.00        15.09        17.49         7.89 

$subtype3
TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       10.62        64.64         0.10         9.96         8.02         6.61 
TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       75.25        50.17        44.52        10.29        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       11.01        16.80         5.98        16.08        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       13.64         7.40        31.82         8.02        30.21        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       54.25        10.22        14.56       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 
       22.42        46.06         1.22         7.96       138.28        30.67 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 
       94.32        62.01        60.30        21.40        14.17         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 
        2.70        77.98         5.98        21.30       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 
       95.57        14.33         0.23        47.77        34.36        15.35 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-A60K 
       40.08        22.55        20.61        16.01        20.09        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 
       15.02        16.44        22.95         0.10         6.67         0.13 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 
       75.19        59.18         4.57        22.06         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       16.24        44.68         0.10         2.96         6.90        14.53 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 
       37.15         0.33         0.13         2.93         1.64         9.40 
TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HW-7486 
        6.25         3.95        10.49         0.07        13.02        29.92 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 
       13.45        40.18         4.31        17.82        20.35        42.77 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        5.23         1.64         4.11         5.75         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
        4.11        14.83         2.20         3.16         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        4.73         3.48        88.83        94.03        32.65        59.38 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB 
       37.84        34.49        31.33        23.64        32.61       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IQ 
       62.37        72.59        32.45        10.88        15.16        14.27 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
       12.59         8.19         2.04         8.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S 
      164.38        49.32        34.36        16.50        29.92         4.57 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
       13.51         0.10        26.79        27.06        23.21        45.07 

$subtype4
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-A64O TCGA-DB-A75P TCGA-DU-7298 
        7.40       122.73        72.92        18.84         3.81        18.94 
TCGA-DU-8162 TCGA-DU-A7TG TCGA-FG-5963 TCGA-FG-6691 TCGA-FG-7643 TCGA-FG-8181 
        3.98        44.42        17.98        23.97        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8189 TCGA-FG-A713 TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7607 
       13.68        22.52         5.23         7.10        29.85         3.16 
TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7880 TCGA-HT-7902 
        0.76         0.10        39.48        39.09         5.33        31.43 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8113 TCGA-HT-8558 
        0.10        21.50        33.01         0.46        29.59         1.71 
TCGA-HT-A5R5 TCGA-HT-A61A TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6WG 
        0.13         6.38         2.37         1.28         4.18        80.12 
TCGA-S9-A6WI TCGA-TM-A84R TCGA-VM-A8C9 
       84.99         9.44        30.08 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  156.23   211.17   182.33   122.73 
subtype1 subtype2 subtype3 subtype4 
  17.620   11.555   15.255   13.680 
[1] "0.0 - 156.2 (17.6)" "0.1 - 211.2 (11.6)" "0.1 - 182.3 (15.3)"
[4] "0.1 - 122.7 (13.7)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  79 106
  subtype2  31  33
  subtype3  61  84
  subtype4  21  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79  106
  subtype2   31   33
  subtype3   61   84
  subtype4   21   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       79       31       61       21
  MALE        106       33       84       18
[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          98               58                29
  subtype2          43               10                11
  subtype3           4               29               112
  subtype4          14               11                14
D4V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             98       43        4       14
  OLIGOASTROCYTOMA        58       10       29       11
  OLIGODENDROGLIOMA       29       11      112       14
[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  49 136
  subtype2  14  50
  subtype3  21 124
  subtype4   5  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49  136
  subtype2   14   50
  subtype3   21  124
  subtype4    5   34
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        49       14       21        5
  YES      136       50      124       34
[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     1                         5
  subtype2                                1     2                         4
  subtype3                                0     3                         3
  subtype4                                0     0                         2
          vv
clus       WHITE
  subtype1   177
  subtype2    57
  subtype3   134
  subtype4    35
D4V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        2        3        0
  BLACK OR AFRICAN AMERICAN               5        4        3        2
  WHITE                                 177       57      134       35
[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   6 171
  subtype2   2  58
  subtype3   6 127
  subtype4   2  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  171
  subtype2    2   58
  subtype3    6  127
  subtype4    2   34
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            6        2        6        2
  NOT HISPANIC OR LATINO      171       58      127       34
[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  6
  subtype2 31 30
  subtype3 59 10
  subtype4 64 11
subtype1 subtype2 subtype3 subtype4 
      51       61       69       75 
subtype1 subtype2 subtype3 subtype4 
       6       30       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        14.76         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        21.70         6.71         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
        5.88         7.63         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 
       38.27        10.72         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        20.71 
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        18.71        23.70 
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        21.60        19.59 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5EV 
       20.35        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        22.52         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-8015 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43         1.64         0.10        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-A5R7 TCGA-HT-A5RB TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 
       14.01         0.10        29.92        13.45        35.90         4.31 
TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F4 
        1.64         4.11         0.76 

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 
   14.96    16.83    20.35    15.72 
[1] "0.1 - 82.0 (15.0)"  "0.1 - 156.2 (16.8)" "0.0 - 211.2 (20.4)"
[4] "0.1 - 138.3 (15.7)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 19 33
  subtype2 33 29
  subtype3 20 49
  subtype4 39 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   33
  subtype2   33   29
  subtype3   20   49
  subtype4   39   36
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       33       20       39
  MALE         33       29       49       36
[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          20               21                11
  subtype2          31               11                20
  subtype3          20               21                28
  subtype4          15               17                43
D5V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             20       31       20       15
  OLIGOASTROCYTOMA        21       11       21       17
  OLIGODENDROGLIOMA       11       20       28       43
[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 37
  subtype2 20 42
  subtype3 30 39
  subtype4 19 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   37
  subtype2   20   42
  subtype3   30   39
  subtype4   19   56
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        15       20       30       19
  YES       37       42       39       56
[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    49
  subtype2                         2    60
  subtype3                         3    65
  subtype4                         3    72
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        3        2        3        3
  WHITE                           49       60       65       72
[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 48
  subtype2  2 56
  subtype3  4 60
  subtype4  4 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   48
  subtype2    2   56
  subtype3    4   60
  subtype4    4   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        4        4
  NOT HISPANIC OR LATINO       48       56       60       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"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 57  9
  subtype2 92 39
  subtype3 50  9
subtype1 subtype2 subtype3 
      66      131       59 
subtype1 subtype2 subtype3 
       9       39        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        14.76         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        21.70        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 
       38.27        10.72         5.26        18.71        23.70         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 
       21.60        19.59        20.35         7.89        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F6 
       42.77         0.23         2.30         7.63         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        22.52         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-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 
        0.13        31.43         0.10        21.50        33.01         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 
        3.95        29.59         1.71        15.72        10.49        14.01 
TCGA-HT-A5RB TCGA-HW-7493 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F4 
        0.10        35.90         1.64         2.37         0.76 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  138.28   211.17   134.27 
subtype1 subtype2 subtype3 
  15.435   18.150   15.480 
[1] "0.0 - 138.3 (15.4)" "0.1 - 211.2 (18.1)" "0.1 - 134.3 (15.5)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 28 39
  subtype2 54 78
  subtype3 29 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   39
  subtype2   54   78
  subtype3   29   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       54       29
  MALE         39       78       30
[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          53               33                46
  subtype3          15               14                30
D6V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             18       53       15
  OLIGOASTROCYTOMA        23       33       14
  OLIGODENDROGLIOMA       26       46       30
[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 84
  subtype3 16 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   47
  subtype2   48   84
  subtype3   16   43
     clus
vv    subtype1 subtype2 subtype3
  NO        20       48       16
  YES       47       84       43
[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   126
  subtype3                         1    58
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        5        5        1
  WHITE                           62      126       58
[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   6 117
  subtype3   3  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   61
  subtype2    6  117
  subtype3    3   55
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        6        3
  NOT HISPANIC OR LATINO       61      117       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"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  92  17
  subtype2  57  36
  subtype3  82   7
  subtype4 101  15
  subtype5  20   0
subtype1 subtype2 subtype3 subtype4 subtype5 
     109       93       89      116       20 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       36        7       15        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-DB-A75M TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A7UU 
       10.92        10.29        30.74        30.31        27.81         3.45 
TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 
        6.21        13.38         6.81        18.94        17.49        49.02 
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-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 
       44.02        25.91        41.98        20.68        16.96        15.48 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 
       15.12         5.65         7.23         7.13       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5322 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
       67.46       130.78        32.19        24.99        23.97        17.88 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX 
       13.68        14.24        14.96        15.52        38.27        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7472 
       23.70        14.76        16.41        28.54         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 TCGA-HT-7609 
       16.54         6.38        60.03         4.01       107.93        45.99 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 
       57.60         0.16        17.52        19.23        50.63        23.61 
TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A74O 
        3.68        63.55         2.50         0.23         3.88         0.10 
TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.23        21.60        19.59        20.81        20.71        19.00 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5F1 TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A870 
        0.23         6.71         5.88         0.59         0.23         0.07 
TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WG 
       69.07        21.63        17.62        94.62        83.70        80.12 
TCGA-S9-A6WO TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 
        7.59         3.58         4.04        99.06        17.42        31.59 
TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH 
       24.26        40.83        18.90        12.00        33.07        10.95 
TCGA-VV-A86M 
        7.04 

$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        42.05        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        10.72         5.26        10.59 
TCGA-FG-A70Z TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7601 
       10.78         7.43         5.72         7.82        24.26         5.03 
TCGA-HT-7616 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 
        0.23         0.76        42.74         0.10        39.48         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 
        0.49         1.71        16.24        12.23         0.10         4.70 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 
       16.04         0.23        14.70         5.33        16.14         5.33 
TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A6CV 
        7.89         4.73         1.64         2.30         1.28        14.53 
TCGA-QH-A6CX TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN 
       12.23        18.77        16.37         5.85        19.86        15.91 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V 
        7.92        19.63         9.37        10.39        83.80        18.71 
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-VM-A8C9 TCGA-VM-A8CD 
       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-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
        7.40        31.82         8.02        17.19        54.25        10.22 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        52.11        22.42        46.06         1.22 
TCGA-DU-6410 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S8 
        7.96        30.67        94.32        21.40        14.17         5.98 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-7634 TCGA-FG-7637 
       78.21        95.57        14.33         0.23        15.35        40.08 
TCGA-FG-8186 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7468 
       16.01        17.82        15.02        16.44        22.95         6.67 
TCGA-HT-7471 TCGA-HT-7481 TCGA-HT-7606 TCGA-HT-7677 TCGA-HT-7687 TCGA-HT-7692 
        0.13        59.18        17.29        16.24         0.10         2.96 
TCGA-HT-7875 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HW-7491 
        0.33         9.40         6.25         0.07        13.02        40.18 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A65Z 
       17.82        20.35         5.23         5.75         7.79         4.11 
TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        6.31         4.73         3.48        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        37.84        34.49        23.64        32.61       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7J1 TCGA-S9-A7J2 
       62.37        72.59        32.45        15.16         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
        8.12        13.02        49.32        34.36        16.50        29.92 
TCGA-TM-A84S TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
        4.57         0.10        26.79        27.06        23.21 

$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-DB-A75L TCGA-DB-A75P TCGA-DH-5143 
       18.38        11.01        13.64         6.44         3.81        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-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       26.30         7.96        18.94        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
        2.76         3.98         8.65         2.70        77.98        11.41 
TCGA-DU-A76R TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-F6-A8O4 
       21.30        44.42        79.99        57.93       134.27         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       47.77        34.36        14.93        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 
       12.95        22.52        43.69         5.23         0.10         8.81 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7603 
        3.75        17.42         6.54        75.19       154.19        23.18 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7688 
        4.57         3.16        22.06        56.09        44.68        31.69 
TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7877 
        0.10         6.90        14.53        39.09        37.15         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        5.33         2.93         1.64         0.10        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-A5R7 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HW-7487 TCGA-HW-7489 
        0.13        14.01         0.10         1.81        13.45         8.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 
       35.90         4.31        21.70        42.77         2.37         4.11 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC 
        7.63         0.76         2.20         3.16         1.91         5.03 
TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ 
       62.17        31.33         9.86        84.99        10.88        14.27 
TCGA-S9-A7IZ TCGA-S9-A7R1 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R 
        4.21       164.38        48.33        34.78        48.39         9.44 
TCGA-VM-A8CA TCGA-W9-A837 
       13.51        45.07 

$subtype5
TCGA-DB-A64O TCGA-DB-A64V TCGA-DH-A7UT TCGA-FG-8187 TCGA-HT-7479 TCGA-HT-7602 
       18.84        14.73         6.58        20.09         7.10        29.85 
TCGA-HT-7620 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-A614 
       14.27         6.05        14.96        11.28        31.43         2.70 
TCGA-HW-7486 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6CU TCGA-QH-A6X5 TCGA-S9-A6WQ 
       29.92         2.53         4.83        14.83         3.91        14.07 
TCGA-S9-A7IY TCGA-S9-A7QY 
       12.59        28.37 

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   164.38    31.43 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.940   12.230   16.440   14.745   14.170 
[1] "0.0 - 130.8 (18.9)" "0.1 - 211.2 (12.2)" "0.1 - 182.3 (16.4)"
[4] "0.1 - 164.4 (14.7)" "2.5 - 31.4 (14.2)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 43 67
  subtype2 46 48
  subtype3 41 49
  subtype4 51 65
  subtype5  9 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   67
  subtype2   46   48
  subtype3   41   49
  subtype4   51   65
  subtype5    9   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       43       46       41       51        9
  MALE         67       48       49       65       11
[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          55               36                19
  subtype2          66               13                15
  subtype3           3               17                70
  subtype4          31               32                53
  subtype5           3               10                 7
D7V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5
  ASTROCYTOMA             55       66        3       31        3
  OLIGOASTROCYTOMA        36       13       17       32       10
  OLIGODENDROGLIOMA       19       15       70       53        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 81
  subtype2 22 72
  subtype3 11 79
  subtype4 25 91
  subtype5  2 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   81
  subtype2   22   72
  subtype3   11   79
  subtype4   25   91
  subtype5    2   18
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        29       22       11       25        2
  YES       81       72       79       91       18
[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     2                         4
  subtype3                                0     3                         0
  subtype4                                0     1                         5
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1   103
  subtype2    86
  subtype3    84
  subtype4   107
  subtype5    20
D7V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        2        3        1        0
  BLACK OR AFRICAN AMERICAN               5        4        0        5        0
  WHITE                                 103       86       84      107       20
[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   4  99
  subtype2   2  86
  subtype3   4  77
  subtype4   6 105
  subtype5   0  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   99
  subtype2    2   86
  subtype3    4   77
  subtype4    6  105
  subtype5    0   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        2        4        6        0
  NOT HISPANIC OR LATINO       99       86       77      105       20
[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  93  17
  subtype2  60  33
  subtype3  94  10
  subtype4 105  15
subtype1 subtype2 subtype3 subtype4 
     110       93      104      120 
subtype1 subtype2 subtype3 subtype4 
      17       33       10       15 
$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-DB-A75M TCGA-DB-A75O TCGA-DH-A66D TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5853 
       10.29        30.74        27.81         6.58         6.21        13.38 
TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
        6.81        18.94        17.49        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
       87.45        94.52       114.08       117.40        90.77        26.30 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS 
       44.02        25.91        41.98        20.68        15.48        15.12 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
        5.65         7.23         7.13       124.50        50.14        67.46 
TCGA-E1-5322 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 
      130.78        32.19        24.99        23.97        13.68        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       14.96        15.52        38.27        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       16.41        28.54         0.13         0.03        16.54         7.10 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 
       60.03         4.01       107.93        45.99        57.60         0.16 
TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 
        6.05        14.96        17.52        19.23        50.63        23.61 
TCGA-HT-7879 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 
        3.68        31.43        63.55         2.50         0.23         3.88 
TCGA-HT-A614 TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
        2.70         0.10        19.23        21.60        19.59        20.81 
TCGA-HW-A5KM TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A65S 
       20.71         0.23         6.71         2.30         5.88         2.53 
TCGA-QH-A6X3 TCGA-QH-A870 TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 
        0.59         0.07        69.07        21.63        17.62        94.62 
TCGA-S9-A6U9 TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R3 
       83.70        80.12         7.59        14.07         4.04        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84T TCGA-VM-A8C8 
       17.42        31.59        24.26        40.83        12.00        33.07 
TCGA-VM-A8CH TCGA-VV-A86M 
       10.95         7.04 

$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-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 
       30.31        42.05         3.45        18.02         6.74         8.45 
TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
      211.17         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 
       11.47        62.96        14.99         6.54         8.84        10.36 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
        5.10        23.74        19.13        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5963 TCGA-FG-6688 
        3.65        12.20        26.76        41.13        17.98        18.77 
TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87N 
       13.58        10.72         5.26        10.59        10.78         7.43 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7606 
        5.72         7.82        24.26         6.38         5.03        17.29 
TCGA-HT-7616 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 
        0.23         0.76        42.74         0.10        39.48         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 
        0.49         1.71        16.24        12.23         0.10         4.70 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 
       16.04         0.23        14.70         5.33        16.14         5.33 
TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5F6 TCGA-QH-A6CV 
        7.89        19.00         4.73         1.64         1.28        14.53 
TCGA-QH-A6CX TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN 
       12.23        18.77        16.37         5.85        19.86        15.91 
TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
        7.92         9.37        10.39        83.80        18.71         5.00 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J 
       49.45        12.00        15.09        50.76        19.36        17.49 
TCGA-TM-A84Q TCGA-VM-A8C9 TCGA-VM-A8CD 
       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-DB-A75K TCGA-DH-5141 TCGA-DH-5144 
       16.08        27.81        14.73         7.40        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5870 TCGA-DU-5874 
       30.21        17.19        54.25        10.22       182.33        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7018 
       52.11        22.42        46.06         1.22         7.96        30.67 
TCGA-DU-7294 TCGA-DU-8168 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 
       94.32        14.17         5.98        21.30       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7637 
       95.57        14.33         0.23        34.36        15.35        40.08 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 
       16.01        20.09        17.82        15.02        16.44        22.95 
TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7602 TCGA-HT-7608 TCGA-HT-7620 TCGA-HT-7677 
        6.67         0.13        29.85        22.06        14.27        16.24 
TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A4DV TCGA-HT-A5R9 
        0.10         2.96         9.40         6.25        10.49         0.07 
TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X 
       13.02        29.92        40.18        17.82        20.35         5.23 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6X4 
        5.75         4.83         7.79         4.11        14.83         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        3.91         4.73         3.48        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        37.84        34.49        23.64        32.61       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IY 
       62.37        72.59        32.45        10.88        15.16        12.59 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-TM-A7C5 
        8.19         2.04         8.12        28.37       164.38        49.32 
TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CB TCGA-VM-A8CE 
       34.36        16.50        29.92         4.57         0.10        26.79 
TCGA-VV-A829 TCGA-VW-A7QS 
       27.06        23.21 

$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-DB-A75L 
       27.62        18.84        18.38        13.64        10.92         6.44 
TCGA-DB-A75P TCGA-DH-5143 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6542 TCGA-DU-7008 
        3.81        14.40        14.56        17.46         7.73       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 
      138.28       105.21         7.96        18.94        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A6S2 
       23.31         2.76         3.98        21.40        16.96         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 
        2.70        77.98        11.41        44.42        79.99        57.93 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
        0.20        47.77        14.93        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 
       20.09        12.95        22.52        43.69         5.23         0.10 
TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7481 
        8.81         3.75        17.42         6.54        75.19        59.18 
TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7681 
      154.19        23.18         4.57         3.16        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-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 
        0.33         0.13         5.33         2.93        11.28         1.64 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 
        0.10        21.50        33.01         0.46         3.95        29.59 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A616 
        1.71        15.72         0.13        14.01         0.10         1.81 
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        21.70        42.77 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A6CY TCGA-QH-A6CZ 
        2.37         4.11         7.63         0.76         2.20         3.16 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
        1.91         0.23         5.03        62.17        31.33         9.86 
TCGA-S9-A6WI TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QZ 
       84.99        14.27        19.63         4.21         3.58        13.02 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-VM-A8CA TCGA-W9-A837 
       48.33        34.78        48.39         9.44        13.51        45.07 

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 
  18.825   12.230   16.470   14.465 
[1] "0.0 - 130.8 (18.8)" "0.1 - 211.2 (12.2)" "0.1 - 182.3 (16.5)"
[4] "0.1 - 156.2 (14.5)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 43 68
  subtype2 45 49
  subtype3 46 58
  subtype4 56 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   68
  subtype2   45   49
  subtype3   46   58
  subtype4   56   65
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       43       45       46       56
  MALE         68       49       58       65
[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          52               40                19
  subtype2          67               13                14
  subtype3           3               22                79
  subtype4          36               33                52
D8V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             52       67        3       36
  OLIGOASTROCYTOMA        40       13       22       33
  OLIGODENDROGLIOMA       19       14       79       52
[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 82
  subtype2 22 72
  subtype3 12 92
  subtype4 26 95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   82
  subtype2   22   72
  subtype3   12   92
  subtype4   26   95
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        29       22       12       26
  YES       82       72       92       95
[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     2                         3
  subtype3                                0     3                         1
  subtype4                                0     1                         5
          vv
clus       WHITE
  subtype1   104
  subtype2    87
  subtype3    96
  subtype4   113
D8V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   0        2        3        1
  BLACK OR AFRICAN AMERICAN               5        3        1        5
  WHITE                                 104       87       96      113
[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   3 100
  subtype2   3  87
  subtype3   4  90
  subtype4   6 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  100
  subtype2    3   87
  subtype3    4   90
  subtype4    6  110
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        3        4        6
  NOT HISPANIC OR LATINO      100       87       90      110
[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  94  19
  subtype2  64  25
  subtype3 139  21
  subtype4  57   9
subtype1 subtype2 subtype3 subtype4 
     113       89      160       66 
subtype1 subtype2 subtype3 subtype4 
      19       25       21        9 
$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-DB-A75O TCGA-DH-5140 
       10.29        27.02        18.84        14.73        30.74        19.96 
TCGA-DH-5141 TCGA-DH-A66F TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5854 TCGA-DU-5855 
       31.82        17.19         6.21        18.02         8.45         6.81 
TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7012 TCGA-DU-7014 
       17.49        75.16        94.52         7.73         6.54       117.40 
TCGA-DU-7290 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
       10.36        25.91        41.98         5.10        23.74        19.13 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-E1-5318 TCGA-E1-5319 
        4.96         5.65        12.20         7.23        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-FG-A70Y TCGA-FG-A87Q TCGA-FN-7833 
       38.27        23.70        16.41        28.54         5.72         0.13 
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-7680 TCGA-HT-7689 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        0.76        14.96        39.48        19.23        50.63         0.49 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-A4DS 
       16.24        63.55         4.70         0.23        16.04         0.23 
TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-A5KK TCGA-P5-A5EV 
       16.14         0.10        19.23        21.60         7.89         0.23 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A6CS 
        6.71         2.30         5.88         1.28         2.53         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A870 TCGA-S9-A6TU TCGA-S9-A6TX 
       14.83        14.53         0.59         0.07        69.07        34.49 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WO 
       32.61        94.62        83.70        62.37        19.86         7.59 
TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 
       14.07        12.59         4.04        10.39        99.06        31.59 
TCGA-TM-A84B TCGA-TM-A84S TCGA-TM-A84T TCGA-VV-A829 TCGA-VV-A86M 
       12.00         4.57        12.00        27.06         7.04 

$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        42.05        27.81        17.19 
TCGA-DH-A7UU TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 
        3.45       211.17        65.75        87.45         7.04       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7013 
       19.89        16.83       114.08        11.47        62.96         8.84 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A76L TCGA-DU-A7T8 TCGA-E1-5302 
       14.24        12.59         3.65        26.76       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-6692 TCGA-FG-7636 
       67.46        41.13       130.78        17.98        13.58        17.88 
TCGA-FG-8185 TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.24        10.72        18.71        14.76        10.59        10.78 
TCGA-FG-A87N TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7684 
        7.43         6.67         7.82        24.26         6.38         6.05 
TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7857 TCGA-HT-7873 
       42.74         0.10         0.10        17.52         0.23        23.61 
TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-8106 TCGA-HT-8114 TCGA-HT-A5RA TCGA-HT-A5RC 
        3.68         1.71         0.10         3.88        14.70         5.33 
TCGA-HT-A618 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX 
        5.33        20.81        20.71        19.00         4.73         1.64 
TCGA-QH-A6CX TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6UA 
       12.23        18.77        21.63        16.37        17.62         5.85 
TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
       80.12        15.91         7.92        17.42        83.80        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
        5.00        49.45        15.09        19.36        17.49        40.83 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH 
       29.92        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-5278 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XG TCGA-DB-A4XH 
       50.17        78.28        12.72        27.62        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P 
       11.01        16.08        27.81        13.64         6.44         3.81 
TCGA-DH-5143 TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DU-5849 TCGA-DU-5851 
       14.40        54.25        10.22         6.58        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6393 TCGA-DU-6403 TCGA-DU-6410 
        6.74        13.38        18.94        52.11        11.64         7.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 
      156.23       138.28        14.99        26.30         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 
       44.02        62.01        60.30        23.31         2.76         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A6S2 
       20.68        21.40        16.96        15.48        15.12         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7TG 
        2.70        77.98         5.98        11.41         7.13        44.42 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       79.99        57.93       134.27         0.20        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-A711 
       16.01        20.09        22.52         5.26        22.95        43.69 
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-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
       14.27        44.68         0.10        31.69         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       39.09        37.15         0.33         0.13         5.33         2.93 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43         1.64         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 
       12.23         6.25         0.46         2.50         3.95        29.59 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB 
        1.71        15.72        10.49         0.13        14.01         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 
        2.70        13.02         1.81         6.38        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-IK-8125 
        8.32        35.90         4.31        21.70        19.59        42.77 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65V TCGA-QH-A6CY 
        2.37         4.11         7.63         0.76         4.83         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        3.16         6.31         3.91         1.91         0.23         5.03 
TCGA-R8-A6MK TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL 
       88.83        62.17        31.33         9.86        84.99        10.88 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QW 
       15.16        14.27        19.63         4.21         8.12         3.58 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F 
       28.37        13.02        48.33        34.78        48.39        50.76 
TCGA-TM-A84R TCGA-VM-A8CA TCGA-VM-A8CD TCGA-W9-A837 
        9.44        13.51         7.89        45.07 

$subtype4
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 
        0.10         9.96         8.02        47.93        46.65        44.52 
TCGA-DB-A4X9 TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A669 
       30.08        16.80         5.98         7.40         8.02        30.21 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        22.42        49.02        46.06         1.22 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8168 TCGA-DU-A76R TCGA-EZ-7264 
       90.77        30.67        94.32        14.17        21.30        14.33 
TCGA-F6-A8O3 TCGA-FG-6690 TCGA-FG-7637 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
        0.23        24.99        40.08        17.82        15.02        16.44 
TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7692 
        0.13       154.19         0.23         0.16        16.24         2.96 
TCGA-HT-8012 TCGA-HT-A5R9 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X 
        9.40         0.07        40.18        17.82        20.35         5.23 
TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6ML 
        5.75         7.79         4.11         4.73         3.48        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE 
       32.65        59.38        37.84        23.64       106.39        72.59 
TCGA-S9-A6WH TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7R1 TCGA-TM-A7C5 
       32.45         9.37         8.19         2.04       164.38        49.32 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS 
       34.36        24.26        16.50         0.10        26.79        23.21 

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 
   16.04    17.49    14.14    17.82 
[1] "0.0 - 117.4 (16.0)" "0.1 - 211.2 (17.5)" "0.1 - 156.2 (14.1)"
[4] "0.1 - 182.3 (17.8)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 47 67
  subtype2 38 51
  subtype3 77 84
  subtype4 30 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   67
  subtype2   38   51
  subtype3   77   84
  subtype4   30   36
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       47       38       77       30
  MALE         67       51       84       36
[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          58               31                25
  subtype2          57               16                16
  subtype3          41               45                75
  subtype4           2               14                50
D9V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             58       57       41        2
  OLIGOASTROCYTOMA        31       16       45       14
  OLIGODENDROGLIOMA       25       16       75       50
[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  89
  subtype2  23  66
  subtype3  30 131
  subtype4  10  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   89
  subtype2   23   66
  subtype3   30  131
  subtype4   10   56
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        25       23       30       10
  YES       89       66      131       56
[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     1                         1
  subtype3                                0     1                         5
  subtype4                                0     3                         0
          vv
clus       WHITE
  subtype1   102
  subtype2    86
  subtype3   152
  subtype4    60
D9V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        1        1        3
  BLACK OR AFRICAN AMERICAN               8        1        5        0
  WHITE                                 102       86      152       60
[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   5 103
  subtype2   2  81
  subtype3   8 147
  subtype4   1  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  103
  subtype2    2   81
  subtype3    8  147
  subtype4    1   56
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        8        1
  NOT HISPANIC OR LATINO      103       81      147       56
[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 153  28
  subtype2 145  16
  subtype3  56  30
subtype1 subtype2 subtype3 
     181      161       86 
subtype1 subtype2 subtype3 
      28       16       30 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.69        17.95         8.48         7.56 
TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        8.02        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        30.08        10.29        12.72        27.02        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K 
       16.80         5.98        15.42        27.81        14.73         7.40 
TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 
       30.74        19.96        31.82        30.31         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5855 
       42.05        27.81        17.19         6.58         6.21         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 
       46.06        65.75        87.45        94.52       114.08       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 
       90.77        30.67        94.32        44.02        25.91        41.98 
TCGA-DU-8163 TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       20.68         5.65         7.23        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       67.46        41.13        78.21        95.57       130.78        14.33 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8182 TCGA-FG-8185 
       24.99        23.97        15.35        40.08        13.68        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       14.96        15.52        38.27        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7468 
       17.82        16.41        15.02        28.54         0.13         6.67 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 
        0.13         0.03        16.54         7.10        60.03         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-7616 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 
       57.60         0.23         0.16        16.24         0.76         6.05 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 
       14.96         0.10         2.96        17.52        19.23        50.63 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
       23.61         3.68        63.55         0.23         3.88        16.04 
TCGA-HT-A614 TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8322 
        2.70         0.10        19.23        40.18        21.60        17.82 
TCGA-HW-A5KL TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.81         5.23         0.23         6.71         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
        7.63         1.28         2.53         4.83         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 
       14.83         0.59         3.91         4.73         3.48         0.07 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       94.03        32.65        69.07        37.84        34.49        21.63 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       17.62        23.64        32.61        94.62        83.70       106.39 
TCGA-S9-A6WD TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7J1 
       62.37         7.59        15.16        14.07        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-TM-A84B 
        2.04         8.12         4.04        99.06        17.42        12.00 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S 
       34.36        24.26        40.83        29.92        18.90         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       12.00        33.07        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS 
       23.21 

$subtype2
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-5279 TCGA-DB-5281 TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       44.52        78.28        27.62        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 
       11.01        16.08        13.64         6.44         3.81        14.40 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       17.19        54.25        10.22        14.56        17.46        13.38 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       15.16        52.11         1.22         7.96       156.23       138.28 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       26.30         7.96        18.94        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TS 
        2.76         3.98        21.40        16.96        14.17        15.12 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7TG 
        8.65         2.70        77.98         5.98         7.13        44.42 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       79.99        57.93       134.27         0.23         0.20        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       34.36        32.19        14.93        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A6J1 
       20.09        12.95        16.01        20.09        22.52        16.44 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 
       22.95        43.69         5.23         0.10         8.81         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
       17.42         6.54        24.26        75.19        59.18       154.19 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7681 
       23.18         4.57         3.16        56.09        14.27        44.68 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
        0.10        31.69         6.90        14.53        39.09        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.33         0.13         5.33         2.93        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64         9.40         0.10        21.50        33.01         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV 
        0.46         2.50         3.95        29.59         1.71        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 
        0.13        14.01         0.07         0.10        13.02         1.81 
TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 
        5.33         6.38        29.92        13.45         8.32        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 
        4.31        21.70        20.35        42.77         2.37         4.11 
TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
        0.76         5.75         7.79         2.20         3.16         6.31 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
        1.91         0.23        59.38        62.17        31.33         9.86 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ 
       72.59        80.12        32.45        84.99        10.88        14.27 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       19.63         4.21         3.58        28.37        13.02       164.38 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84M 
       48.33        49.32        34.78        48.39        50.76        16.50 
TCGA-TM-A84R TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-W9-A837 
        9.44        13.51         0.10         7.89        45.07 

$subtype3
TCGA-CS-5395 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A64O TCGA-DB-A64X TCGA-DH-A7UU 
       21.01        23.84        12.43        18.84        10.92         3.45 
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-8158 TCGA-DU-8161 
       14.99         6.54         8.84        10.36         5.10        23.74 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       19.13        15.48        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-FG-A87N TCGA-FG-A87Q 
       10.72         5.26        10.59        10.78         7.43         5.72 
TCGA-HT-7469 TCGA-HT-7478 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 
        7.82         6.38        42.74         0.10        39.48         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 
        0.49         1.71        16.24        12.23         0.10         4.70 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-8321 
       15.72         0.23        14.70         5.33        16.14        19.59 
TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-QH-A6CV 
        7.89        20.71        19.00         4.73         1.64        14.53 
TCGA-QH-A6CX TCGA-QH-A6XC TCGA-R8-A6MK TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA 
       12.23         5.03        88.83        18.77        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 
       19.86        15.91         7.92         9.37        10.39        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I 
       31.59        18.71         5.00        49.45        15.09        19.36 
TCGA-TM-A84J TCGA-VM-A8C9 
       17.49        30.08 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  182.33   164.38   211.17 
subtype1 subtype2 subtype3 
   17.82    14.56    12.33 
[1] "0.0 - 182.3 (17.8)" "0.1 - 164.4 (14.6)" "0.1 - 211.2 (12.3)"
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1  72 110
  subtype2  78  84
  subtype3  42  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72  110
  subtype2   78   84
  subtype3   42   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       72       78       42
  MALE        110       84       44
[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"
D10V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          63               54                65
  subtype2          37               39                86
  subtype3          58               13                15
D10V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             63       37       58
  OLIGOASTROCYTOMA        54       39       13
  OLIGODENDROGLIOMA       65       86       15
[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"
D10V6, binary
          cls
clus         0   1
  subtype1  42 140
  subtype2  28 134
  subtype3  18  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42  140
  subtype2   28  134
  subtype3   18   68
     clus
vv    subtype1 subtype2 subtype3
  NO        42       28       18
  YES      140      134       68
[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     2                         5
  subtype2                                0     2                         5
  subtype3                                1     2                         4
          vv
clus       WHITE
  subtype1   172
  subtype2   150
  subtype3    78
D10V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   2        2        2
  BLACK OR AFRICAN AMERICAN               5        5        4
  WHITE                                 172      150       78
[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"
D10V8, binary
          cls
clus         0   1
  subtype1   6 163
  subtype2   7 146
  subtype3   3  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  163
  subtype2    7  146
  subtype3    3   78
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        7        3
  NOT HISPANIC OR LATINO      163      146       78
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 116  41
  subtype2 115  14
  subtype3 120  19
subtype1 subtype2 subtype3 
     157      129      139 
subtype1 subtype2 subtype3 
      41       14       19 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 
        4.70         7.69        10.62        21.01        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5279 
       17.95         8.48         7.56        81.96        72.92        44.52 
TCGA-DB-A64O TCGA-DB-A75O TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
       18.84        30.74        18.02         6.74         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7290 TCGA-DU-7301 
       62.96         6.54         8.84       117.40        10.36        25.91 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 
       41.98         5.10        23.74        20.68        19.13        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76L 
       14.24        12.59         4.96        12.20         7.23        26.76 
TCGA-E1-5319 TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       95.57        17.98        18.77        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MU 
       15.35        13.68        14.24        14.96        15.52        10.72 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
        7.43         5.72         0.13         7.82         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       16.54         7.10        60.03       154.19         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-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 
        0.23        14.27         0.16        16.24         0.76         6.05 
TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       42.74        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23         0.23        50.63         0.49        23.61 
TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 
        3.68         1.71        16.24        63.55        12.23         0.10 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA 
        4.70         0.23         3.88        16.04         0.23        14.70 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7490 TCGA-HW-8320 
        5.33        16.14         0.10        29.92        19.23        21.60 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5F1 
       19.59         7.89        19.00         4.73         1.64         5.88 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A870 TCGA-S9-A6TU 
        4.18        14.53        12.23         0.59         0.07        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U5 TCGA-S9-A6UA 
       18.77        37.84        21.63        16.37        32.61         5.85 
TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 
       80.12        19.86        15.91        10.39        99.06        83.80 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84I 
       18.71         5.00        49.45        12.00        15.09        19.36 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD 
       29.92        18.90         4.57        33.07        30.08         7.89 
TCGA-VV-A829 
       27.06 

$subtype2
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 
       43.89        18.15        64.64         0.10         9.96         8.02 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       75.25        47.93        46.65        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-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-A64X TCGA-DB-A75K TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       10.92         7.40        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7US 
        8.02        30.21        42.05        27.81        17.19        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-6393 TCGA-DU-7008 TCGA-DU-7015 
        6.58         3.45         6.21        52.11       156.23        90.77 
TCGA-DU-7018 TCGA-DU-7299 TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S8 
       30.67        44.02        15.12         3.65         5.65         5.98 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5318 
      124.50        50.14        67.46        41.13        79.99        78.21 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-7637 TCGA-FG-A4MT TCGA-FG-A4MX 
      130.78        14.33         0.23        40.08        38.27        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7477 TCGA-HT-A5R5 
       10.59        28.54        22.95         6.67        24.26         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HW-7491 TCGA-HW-A5KJ 
        0.07         0.10         2.70        13.02        40.18        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ 
       20.81        20.71         5.23         0.23         6.71         2.30 
TCGA-P5-A5F2 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        7.63         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CU TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK 
       14.83         6.31         3.91         4.73         3.48        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TX TCGA-S9-A6U1 TCGA-S9-A6U2 
       94.03        32.65        59.38        34.49        17.62        23.64 
TCGA-S9-A6U8 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WO 
       94.62       106.39        62.37        72.59        32.45         7.59 
TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       15.16        12.59         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 
        3.58         4.04       164.38        17.42        31.59        49.32 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M TCGA-TM-A84T TCGA-VM-A8CB TCGA-VM-A8CE 
       34.36        24.26        16.50        12.00         0.10        26.79 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS 
       10.95         7.04        23.21 

$subtype3
TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6665 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       40.18         6.38        12.43         7.40         6.61       122.73 
TCGA-DB-5278 TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P 
       50.17        12.59        11.01        13.64         6.44         3.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5874 
       17.19        54.25        14.56        17.46        13.38        15.16 
TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 
      211.17         1.22         7.96       138.28        14.99        26.30 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        18.94        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S2 
        2.76         3.98        21.40        16.96        14.17         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7TG 
        2.70        77.98        11.41         7.13        21.30        44.42 
TCGA-E1-5307 TCGA-E1-5311 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       57.93       134.27         0.20        47.77        34.36        32.19 
TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       14.93        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A711 
       16.01        20.09        22.52         5.26        10.78        43.69 
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-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 
        6.38        75.19        59.18        23.18         4.57         3.16 
TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
       56.09        44.68         0.10        31.69         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       39.09        37.15         0.33         0.13         5.33         2.93 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43         1.64         9.40         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 
       33.01         6.25         0.46         2.50         3.95        29.59 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A616 TCGA-HT-A618 
        1.71        15.72        10.49        14.01         1.81         5.33 
TCGA-HT-A61A TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        6.38        13.45         8.32        35.90         4.31        21.70 
TCGA-HW-8322 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-QH-A6CY 
       17.82        42.77         2.37         4.11         0.76         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TY 
        3.16         1.91         0.23         5.03        62.17        31.33 
TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.86        84.99        10.88        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA 
       19.63         4.21        28.37        13.02        48.33        34.78 
TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84R TCGA-VM-A8CA 
       48.39        50.76        17.49        40.83         9.44        13.51 
TCGA-W9-A837 
       45.07 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  182.33   164.38   211.17 
subtype1 subtype2 subtype3 
   16.14    17.19    14.07 
[1] "0.0 - 182.3 (16.1)" "0.1 - 164.4 (17.2)" "0.1 - 211.2 (14.1)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 59 98
  subtype2 62 68
  subtype3 71 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   98
  subtype2   62   68
  subtype3   71   69
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       59       62       71
  MALE         98       68       69
[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"
D11V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          78               39                40
  subtype2          42               31                57
  subtype3          37               35                68
D11V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             78       42       37
  OLIGOASTROCYTOMA        39       31       35
  OLIGODENDROGLIOMA       40       57       68
[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"
D11V6, binary
          cls
clus         0   1
  subtype1  43 114
  subtype2  18 112
  subtype3  27 113
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43  114
  subtype2   18  112
  subtype3   27  113
     clus
vv    subtype1 subtype2 subtype3
  NO        43       18       27
  YES      114      112      113
[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                                1     2                         6
  subtype2                                0     3                         3
  subtype3                                0     1                         5
          vv
clus       WHITE
  subtype1   145
  subtype2   120
  subtype3   132
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   2        3        1
  BLACK OR AFRICAN AMERICAN               6        3        5
  WHITE                                 145      120      132
[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"
D11V8, binary
          cls
clus         0   1
  subtype1   4 144
  subtype2   7 109
  subtype3   5 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  144
  subtype2    7  109
  subtype3    5  131
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        7        5
  NOT HISPANIC OR LATINO      144      109      131
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1  62   9
  subtype2 102  13
  subtype3 145  21
  subtype4  42  31
subtype1 subtype2 subtype3 subtype4 
      71      115      166       73 
subtype1 subtype2 subtype3 subtype4 
       9       13       21       31 
$subtype1
TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-6186 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-A4XD 
        4.70        10.62        17.69         8.48         7.56        27.02 
TCGA-DB-A64S TCGA-DB-A75O TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7014 
       15.42        30.74         6.21        75.16         7.73       117.40 
TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-A5TW TCGA-DU-A6S7 
       90.77        44.02        25.91        41.98         5.65         7.23 
TCGA-E1-5303 TCGA-FG-6691 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       67.46        23.97        14.24        14.96        15.52        38.27 
TCGA-FG-A4MY TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 
       23.70         0.13         0.03        16.54         7.10        60.03 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 
        4.01         5.03        29.85       107.93        17.29        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-8563 
       50.63        23.61         3.68        63.55         0.23        16.04 
TCGA-HT-A74O TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW 
        0.10        20.81        20.71        19.00         0.23         6.71 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A6X3 TCGA-QH-A870 TCGA-S9-A6TU TCGA-S9-A6TZ 
        2.30         5.88         0.59         0.07        69.07        21.63 
TCGA-S9-A6U1 TCGA-S9-A6WO TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A84B 
       17.62         7.59         4.04        99.06        31.59        12.00 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       12.00        33.07        10.95        27.06         7.04 

$subtype2
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 
        7.69        43.89        18.15        64.64         0.10         9.96 
TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        8.02        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A64P TCGA-DB-A64Q 
       78.28        10.29        12.72        27.62        16.80         5.98 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DH-5140 TCGA-DH-5141 
       27.81        14.73        10.92         7.40        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-7018 TCGA-DU-A5TP TCGA-DU-A5TR 
       10.22         6.58         3.45        30.67        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5311 
       15.12         3.65       124.50        50.14        41.13       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6690 
       78.21        95.57       130.78        14.33         0.23        24.99 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       15.35        40.08        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A70Y TCGA-HT-7468 TCGA-HT-7477 TCGA-HT-7483 TCGA-HT-7608 
       15.02        28.54         6.67        24.26       154.19        22.06 
TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R9 
        0.23        16.24         2.96         3.88        10.49         0.07 
TCGA-HT-A615 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KJ TCGA-KT-A74X 
       13.02        19.23        40.18        21.60        20.35         5.23 
TCGA-P5-A5F2 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        7.63         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK 
       14.83         6.31         3.91         4.73         3.48        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       94.03        32.65        59.38        18.77        37.84        34.49 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       23.64        32.61        94.62       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 
       80.12        15.16        14.07        12.59         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7R4 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84H 
        2.04         3.58        17.42        49.32        34.36        24.26 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-VM-A8CB TCGA-VM-A8CE 
       16.50        29.92        18.90         4.57         0.10        26.79 
TCGA-VW-A7QS 
       23.21 

$subtype3
TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       40.18        17.95        12.43         7.40         6.61       122.73 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4X9 TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       50.17        44.52        30.08        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64W TCGA-DB-A75L TCGA-DH-5143 
       12.59        11.01        16.08        13.64         6.44        14.40 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 
       17.19        54.25        14.56        17.46        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        46.06        65.75         1.22        87.45 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7019 
       94.52       114.08         7.96       156.23       138.28        26.30 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       94.32        18.94        62.01        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        8.65         2.70        77.98         5.98         7.13        21.30 
TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       44.42        79.99        57.93         0.20        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       32.19        14.93        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A6J1 
       12.95        13.68        16.01        20.09        22.52        16.44 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 
       22.95        43.69         5.23         0.10         8.81         0.13 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54         6.38        75.19        59.18 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7676 
       23.18         4.57         3.16        56.09        14.27         0.16 
TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 
       44.68         0.10        31.69         0.10         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       39.09        37.15         0.33         0.13         5.33         2.93 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43         1.64         9.40         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 
       33.01         6.25         0.46         2.50         3.95        29.59 
TCGA-HT-8558 TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 
        1.71         0.13        14.01         0.10         2.70         1.81 
TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 
        5.33         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        21.70        19.59        17.82        42.77         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
        4.11         0.76         5.75         2.20         3.16         1.91 
TCGA-QH-A6XA TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WH TCGA-S9-A6WI 
        0.23        62.17        31.33         9.86        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QY 
       10.88        14.27        19.63         4.21         8.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F 
       13.02       164.38        48.33        34.78        48.39        50.76 
TCGA-TM-A84L TCGA-TM-A84R TCGA-VM-A8CA TCGA-W9-A837 
       40.83         9.44        13.51        45.07 

$subtype4
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-DB-A64O TCGA-DB-A75P TCGA-DU-5847 
       21.01         6.38        23.84        18.84         3.81        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        6.74         8.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       16.83        11.47        62.96        14.99         6.54         8.84 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       10.36         7.96         5.10        23.74        19.13         4.96 
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-FG-A87N TCGA-FG-A87Q 
       10.72         5.26        10.59        10.78         7.43         5.72 
TCGA-HT-7469 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 
        7.82        42.74         0.10        39.48         0.23         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8564 
        1.71        16.24        12.23         0.10         4.70        15.72 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-A5KK TCGA-KT-A7W1 
        0.23        14.70         5.33        16.14         7.89         4.73 
TCGA-P5-A5EX TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6U0 TCGA-S9-A6UA 
        1.64        14.53        12.23         5.03        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V 
       19.86        15.91         7.92        10.39        83.80        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8C9 
        5.00        49.45        15.09        19.36        17.49        30.08 
TCGA-VM-A8CD 
        7.89 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  117.40   154.19   211.17   133.74 
subtype1 subtype2 subtype3 subtype4 
   16.04    17.82    16.70    11.47 
[1] "0.0 - 117.4 (16.0)" "0.1 - 154.2 (17.8)" "0.1 - 211.2 (16.7)"
[4] "0.1 - 133.7 (11.5)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 28 44
  subtype2 42 73
  subtype3 85 82
  subtype4 37 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   44
  subtype2   42   73
  subtype3   85   82
  subtype4   37   36
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28       42       85       37
  MALE         44       73       82       36
[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          40               21                11
  subtype2          30               31                54
  subtype3          35               44                88
  subtype4          52                9                12
D12V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             40       30       35       52
  OLIGOASTROCYTOMA        21       31       44        9
  OLIGODENDROGLIOMA       11       54       88       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"
D12V6, binary
          cls
clus         0   1
  subtype1  16  56
  subtype2  20  95
  subtype3  37 130
  subtype4  15  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   56
  subtype2   20   95
  subtype3   37  130
  subtype4   15   58
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        16       20       37       15
  YES       56       95      130       58
[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                         2
  subtype2                                0     3                         3
  subtype3                                0     1                         5
  subtype4                                1     2                         4
          vv
clus       WHITE
  subtype1    69
  subtype2   107
  subtype3   157
  subtype4    64
D12V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   0        3        1        2
  BLACK OR AFRICAN AMERICAN               2        3        5        4
  WHITE                                  69      107      157       64
[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   5  62
  subtype2   2 102
  subtype3   7 155
  subtype4   2  65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   62
  subtype2    2  102
  subtype3    7  155
  subtype4    2   65
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        7        2
  NOT HISPANIC OR LATINO       62      102      155       65
[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"
