[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"        "-oTPRAD-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/PRAD-TP/11541653/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/11590506/PRAD-TP.mergedcluster.txt"

nPatients in clinical file=368, in cluster file=498, common to both=367
[1]  10 367
[1] "CN_CNMF"
[1] 3
  1   2   3 
207  88  68 
  1   2   3 
207  88  68 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
109 102 104  30 
  1   2   3   4 
109 102 104  30 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
42 55 62 
 1  2  3 
42 55 62 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
48 65 46 
 1  2  3 
48 65 46 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
107 123 130 
  1   2   3 
107 123 130 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
108 128 124 
  1   2   3 
108 128 124 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
115 116 132 
  1   2   3 
115 116 132 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
112  72  46  80  53 
  1   2   3   4   5 
112  72  46  80  53 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
50 61 33 80 
 1  2  3  4 
50 61 33 80 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
46 26 17 52 25 58 
 1  2  3  4  5  6 
46 26 17 52 25 58 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCHNUMBER"                           

Input Data has 29 rows and 367 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
         621         1332          671         1033          112          771 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          425 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
          60           91          731           31          396         1065 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
         943           31           62           28         1339          365 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
          31          700           31          458          731           62 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
         396          486          821          304          974         1004 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
          91          882          826         1007          595          405 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
         906         1415         1365          800         1391          880 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
         922          827          727         1184         1464         1116 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
        1476         1172         1102         1832         1416         1454 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
        1590         1962         1578         2079         1310         1115 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
        1179         1209         1832         1273         1456          884 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
         822         1491         1860         2542          663          295 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
         289          285          510          233          533          175 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
         842          191            9          727         1167          787 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
         781          625          442          430          552          596 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
         526          114          701          606         1961         1946 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
         821           NA          314          162          129          532 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
         299           93          229          668          536          393 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
         417          560          278           91          230          864 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
         469          409          273          524          494           54 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1266         2657         2465         2068         2028         2110 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
        1696          554         2089         1515         1404         1542 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
        1501         1434         1415         1443         1378         1198 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
        1363          101         1222         1215         1156         1226 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
         811          958         1155         1393          765          830 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
        1771         1726         1608         1543         1164         1185 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
         849          942         1075          857          994           NA 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
         757          643          185          941          112          601 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
          NA          162           89           61           72          440 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
         868           24          870           60           51           72 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
          89           52           22           64           81           53 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
          45           51           63          748          792           60 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
          34           98          928           45          543          747 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
          56          589          682           95          726           66 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
          69           59          546          679           48          483 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
          35          680           23           54           61           67 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
          49          167           71          106           44           38 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
         134         2391         2684         2522           NA          614 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
         374          662          518          488          503          491 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
         624          454          523          183          405          528 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
         279          279          310          206          316          437 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-KK-A59V 
         617          422          178          212          323         2859 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
        1712         1359         1879         2364         3524          913 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
        1659         4604         2056         2753         1498         3447 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
        2040         1770          840         1063          692           83 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
         804           NA          158          209          302          400 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
         822          763          483          573           97         1247 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
        3487         1436         2620          362          249          269 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
         776          394          183          472          481          917 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
        1001          459          132         3253          805         2576 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
        2879           NA         2309         1690         1853         2037 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
         663         1486          655          542          176         1131 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
         846          119         1157         1461          275           91 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
         790          972          958          972          868          930 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
         889          824         1126         1206          775         1611 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
        1491         1173         1124         2183         1890         1842 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
         512         1384         1261         1373           NA         1441 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
        1395         1155          798         3247         2170         1910 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
         213          427         1259           NA         1897          740 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1518          862           50          150           34          239 
TCGA-ZG-A9ND 
         183 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=320,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=179,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=184,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 25:'PSA_VALUE':	nDistinctValues=83,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=290,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "HISTOLOGICAL.TYPE"        
 [5] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 367 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
150 210   5 
[1] "table(vv)"
vv
 T2  T3  T4 
150 210   5 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T2  T3  T4 
150 210   5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
150 210   5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=10, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=179, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=83, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1 203   3
  subtype2  85   2
  subtype3  67   1
subtype1 subtype2 subtype3 
     206       87       68 
subtype1 subtype2 subtype3 
       3        2        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
       24.03        13.02        31.00        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 
        1.02        15.06        24.03         2.04        13.02         9.99 
TCGA-CH-5790 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       32.02        29.00        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       44.88        26.30        27.19        38.93        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5527 
       38.53        46.55        47.80        64.50        68.35        39.75 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7318 
       60.23        47.87        29.06        27.02         9.70        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 
        7.66        17.52         5.75        27.68        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8469 
       20.55        14.14        19.59         3.75        19.92        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H 
       26.99        10.32         5.33         4.24        17.49         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-FC-7708 TCGA-FC-A66V 
       21.96        17.62        12.92        13.71        28.41        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 
       69.37        55.76        18.21        68.68        49.81        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6384 
       40.18        38.01        40.31        31.50        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       27.29        58.22        38.27        35.34        28.18        32.68 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       21.14         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
        2.37        14.47         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 
        2.93         1.71         0.72         1.74         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       26.04         1.97         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 
       24.56        19.36         3.12         2.27        22.32         1.58 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HY 
        2.20         1.61         5.49         3.48         1.45         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       88.24        82.92        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       13.32        17.36         9.17         9.17         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E2 TCGA-KK-A6E3 
       14.37        20.28        93.99        44.68       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y 
       90.51        27.62        34.95        22.75        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        6.87         9.93         3.19       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       11.90         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C 
       15.81        30.15        32.91        84.69        23.93        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       66.97        48.85        21.53         5.79         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJR TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HK 
       31.96        31.96        27.09        39.65        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WX 
       38.56        41.46        45.14        71.34        60.99        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QZ 
        1.64         7.86 

$subtype2
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5788 
       35.01         1.02         2.04         0.92        44.02        26.99 
TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5521 
       33.01        33.11        23.90        36.23        52.27        51.88 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7315 
       43.07        36.66        38.76        49.02        21.80         9.50 
TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-7961 
       25.68        18.15         9.83         3.06        18.41        15.42 
TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7521 
       13.45         3.32        26.66        56.75        50.73        30.97 
TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7821 TCGA-HC-8216 
       26.01         5.33         1.97         1.48         1.84        22.42 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59X 
       78.61        43.69        10.19        13.87        10.62        56.28 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A8IB 
       61.78       115.86        54.54       113.33        58.19         2.73 
TCGA-KK-A8IF TCGA-M7-A724 TCGA-M7-A725 TCGA-TP-A8TV TCGA-VP-A872 TCGA-VP-A875 
       26.43        15.88        18.84         8.19       106.95        26.47 
TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A9DX TCGA-XK-AAIV 
       60.92        21.80        17.82        37.18        25.97        31.50 
TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       28.54        29.23        37.02        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       60.56        16.83        45.50        45.86        37.97        26.24 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK 
      106.75        62.79         7.00        14.04        41.39        62.37 
TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9ND 
       24.33        28.34         6.02 

$subtype3
TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5772 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5503 
        2.99         1.02        15.98         2.99        27.16        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5515 TCGA-EJ-5531 TCGA-EJ-7125 
       28.93        30.31        48.13        60.23        41.85        61.15 
TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 
       83.57         9.37         6.28         0.30        38.37        14.53 
TCGA-EJ-7792 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       17.29        23.05        64.47         9.14         2.99         7.56 
TCGA-FC-A5OB TCGA-G9-6338 TCGA-G9-6351 TCGA-G9-6365 TCGA-G9-6369 TCGA-G9-6378 
        8.98        66.67        46.16        44.81        39.95        37.97 
TCGA-G9-6498 TCGA-G9-7510 TCGA-G9-7519 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7737 
       52.87        38.96        27.91         2.01        28.54         2.10 
TCGA-HC-7738 TCGA-HC-7744 TCGA-HC-7750 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
        2.66         1.68         1.12        23.87         2.17         1.94 
TCGA-HC-8261 TCGA-HC-A6AP TCGA-HC-A6HX TCGA-J4-8198 TCGA-J9-A52C TCGA-KK-A6E0 
       17.95         2.33         1.25        20.19         5.85        30.02 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IM 
       49.25        67.07        13.15        27.02        25.08        41.00 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 TCGA-VP-A87B TCGA-X4-A8KS TCGA-XA-A8JR 
       15.09         4.34        94.65        75.91        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XK-AAJA TCGA-Y6-A8TL TCGA-YL-A8SH TCGA-YL-A8SI 
       38.04        48.03        30.58        25.48        28.77        47.38 
TCGA-ZG-A8QX TCGA-ZG-A8QY 
        4.93         1.12 

subtype1 subtype2 subtype3 
    0.72     0.76     0.30 
subtype1 subtype2 subtype3 
  151.36   115.86    94.65 
subtype1 subtype2 subtype3 
   21.86    26.47    25.28 
[1] "0.7 - 151.4 (21.9)" "0.8 - 115.9 (26.5)" "0.3 - 94.7 (25.3)" 
D1V2, continuous
          vv
clus        T2  T3  T4
  subtype1 102 101   2
  subtype2  12  74   2
  subtype3  36  31   1
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2      102       12       36
  T3      101       74       31
  T4        2        2        1
[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"
D1V4, binary
          cls
clus         0   1
  subtype1 152  15
  subtype2  62  22
  subtype3  49   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  152   15
  subtype2   62   22
  subtype3   49    7
   clus
vv  subtype1 subtype2 subtype3
  0      152       62       49
  1       15       22        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"
D1V5, binary
          cls
clus         0   1
  subtype1   8 199
  subtype2   4  84
  subtype3   1  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  199
  subtype2    4   84
  subtype3    1   67
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        8        4        1
  PROSTATE ADENOCARCINOMA ACINAR TYPE         199       84       67
[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        R0  R1  R2  RX
  subtype1 156  35   3   5
  subtype2  46  36   1   3
  subtype3  41  19   1   3
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      156       46       41
  R1       35       36       19
  R2        3        1        1
  RX        5        3        3
[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"
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    90
  subtype2     0                         1    29
  subtype3     0                         3    27
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        3        1        3
  WHITE                           90       29       27
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 109   0
  subtype2  99   3
  subtype3 100   2
  subtype4  30   0
subtype1 subtype2 subtype3 subtype4 
     109      102      102       30 
subtype1 subtype2 subtype3 subtype4 
       0        3        2        0 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5762 TCGA-CH-5763 
       20.42         6.97        13.97        24.03        44.02        12.00 
TCGA-CH-5771 TCGA-CH-5789 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 TCGA-EJ-5502 
       13.02         9.99        13.32        29.79        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 
       45.73        30.31        27.19        38.93        36.69        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5531 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 
       60.23        46.55        41.85        27.68         6.28        23.90 
TCGA-EJ-7785 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       20.55        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
        5.33         4.24        17.49         7.53        21.96        17.62 
TCGA-EJ-A65G TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 
        9.14        28.41        17.23         1.78        41.62        67.99 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6366 
       68.68        49.81        46.16        50.70        47.15         3.32 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.18        38.01        37.97        45.80        25.15        27.29 
TCGA-G9-7519 TCGA-G9-7522 TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7233 TCGA-HC-7737 
       27.91        35.34        30.94         2.93         1.71         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7817 
        1.74         1.48         2.07        24.59         1.12        30.51 
TCGA-HC-8216 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8266 TCGA-HC-A6AQ TCGA-HC-A6AS 
       22.42         2.17         1.94         1.15         3.48         1.45 
TCGA-HC-A6HX TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O 
        1.25        82.92        12.30        17.03        16.04        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A83L TCGA-J9-A52C TCGA-KK-A6E3 TCGA-KK-A7B2 TCGA-M7-A71Y TCGA-M7-A720 
       10.39         5.85        67.59        22.75         5.19         9.93 
TCGA-M7-A723 TCGA-QU-A6IP TCGA-VN-A88I TCGA-VN-A88N TCGA-VP-A878 TCGA-VP-A87C 
       25.08        86.14         8.84        15.52        94.65        55.56 
TCGA-VP-A87E TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
       66.97        37.18        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SB TCGA-YL-A8SK TCGA-ZG-A8QW 
        2.99        52.96        49.02        45.50        37.97         1.64 
TCGA-ZG-A8QZ 
        7.86 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5751 
       43.79        33.96         3.68         2.99         1.02        35.01 
TCGA-CH-5761 TCGA-CH-5767 TCGA-CH-5772 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5504 
        0.92        15.06        15.98         2.99        27.16        28.93 
TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5532 
       48.13        36.23        47.80        52.27        64.50        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7331 
       27.02        49.02        61.15        83.57         9.37         0.30 
TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A65E TCGA-EJ-A65J 
       38.37        14.53        64.47        26.99        13.71         2.99 
TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 
        7.56        15.42        13.45         8.98        16.24        81.04 
TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6494 TCGA-G9-6496 
       66.67        18.21        39.95        40.31        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7523 TCGA-HC-7075 
       52.87        50.73        38.96        30.97        28.18        19.76 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7738 
        5.33         2.01        28.54         0.79         0.72         2.66 
TCGA-HC-8256 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A6AL 
        3.12        17.95         1.58        15.88         0.76         2.20 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HI-7168 TCGA-J4-A83J TCGA-J9-A52D TCGA-KK-A59X 
        5.49         2.33        78.61        10.19         6.97        56.28 
TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A8IB 
       77.72        30.02        49.25        67.07        58.19         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-M7-A725 
       26.43        20.65        13.15        27.02        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R 
        3.19        41.00        47.21        15.81        30.15        15.09 
TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-Y6-A8TL 
       75.91        21.80        48.85         5.79        38.04        25.48 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A8SQ 
       36.95        71.77        60.56        28.77       106.75        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A8QY 
        7.00        41.39        60.99        62.37         4.93         1.12 

$subtype3
TCGA-2A-A8VV TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5750 
       22.06        22.06         1.02        12.99         1.97        13.02 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5768 
       31.00         1.02         2.04         1.02         1.02        24.03 
TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5496 
        2.04        26.99        32.02        33.01        29.00        19.56 
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       23.90        48.53        51.88        68.35        43.07        36.66 
TCGA-EJ-5530 TCGA-EJ-5542 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       60.23        29.06        16.77         7.66        17.52         5.75 
TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D 
       25.68        14.14        10.32         9.83         3.06        12.92 
TCGA-G9-6332 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6362 TCGA-G9-6363 
       87.35        69.37        55.76        49.35        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7525 TCGA-H9-7775 
       39.39        44.81        26.66        31.50        32.68         6.08 
TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
        3.68         2.37        14.47        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7818 
        2.37         1.68        26.04         1.97         3.22         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-A48F 
       17.85        24.56        19.36         2.27        22.32        22.36 
TCGA-HC-A631 TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K 
        1.78         4.41        88.24        43.69        20.19        21.76 
TCGA-J4-A67N TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
       16.54         9.17         9.17         6.77        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 
       13.87        10.62        44.68        54.54        90.51       113.33 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-QU-A6IN TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       27.62        34.95       114.64        25.51        12.95         6.02 
TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D 
       32.91       106.95        26.47        84.69        23.93        60.92 
TCGA-VP-A87K TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SP 
       21.53        38.56        16.83        41.46        45.86        71.34 

$subtype4
TCGA-2A-A8W3 TCGA-CH-5745 TCGA-CH-5765 TCGA-EJ-5495 TCGA-EJ-5499 TCGA-EJ-5526 
       25.35         2.99        23.01        33.11        46.52        38.76 
TCGA-EJ-5527 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7783 TCGA-EJ-7789 
       39.75        21.80         9.70         9.50        25.87        18.15 
TCGA-EJ-8469 TCGA-EJ-A65F TCGA-G9-6361 TCGA-HC-7232 TCGA-HC-7821 TCGA-HC-8257 
       63.98        18.41        46.52         2.93         1.84        23.87 
TCGA-HC-A632 TCGA-HC-A6AN TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E2 
        2.01         1.61        93.99        61.78       115.86       151.36 
TCGA-M7-A71Z TCGA-XJ-A9DX TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A9WH 
        6.87        25.97        62.14        45.14        26.24        14.04 

subtype1 subtype2 subtype3 subtype4 
    1.12     0.30     1.02     1.61 
subtype1 subtype2 subtype3 subtype4 
   94.65   106.75   114.64   151.36 
subtype1 subtype2 subtype3 subtype4 
   20.52    27.02    22.19    25.61 
[1] "1.1 - 94.7 (20.5)"  "0.3 - 106.8 (27.0)" "1.0 - 114.6 (22.2)"
[4] "1.6 - 151.4 (25.6)"
D2V2, continuous
          vv
clus       T2 T3 T4
  subtype1 58 49  0
  subtype2 42 57  3
  subtype3 42 60  2
  subtype4  3 27  0
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       58       42       42        3
  T3       49       57       60       27
  T4        0        3        2        0
[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"
D2V4, binary
          cls
clus        0  1
  subtype1 78  8
  subtype2 76 12
  subtype3 73 13
  subtype4 22  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78    8
  subtype2   76   12
  subtype3   73   13
  subtype4   22    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       78       76       73       22
  1        8       12       13        7
[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"
D2V5, binary
          cls
clus         0   1
  subtype1   5 104
  subtype2   2 100
  subtype3   5  99
  subtype4   2  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  104
  subtype2    2  100
  subtype3    5   99
  subtype4    2   28
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        5        2        5        2
  PROSTATE ADENOCARCINOMA ACINAR TYPE         104      100       99       28
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 78 21  1  4
  subtype2 57 35  2  3
  subtype3 77 19  2  3
  subtype4 20  8  0  1
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       78       57       77       20
  R1       21       35       19        8
  R2        1        2        2        0
  RX        4        3        3        1
[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"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    47
  subtype2     0                         1    38
  subtype3     0                         3    51
  subtype4     1                         1    11
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        1
  BLACK OR AFRICAN AMERICAN        2        1        3        1
  WHITE                           47       38       51       11
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 42  0
  subtype2 55  0
  subtype3 60  1
subtype1 subtype2 subtype3 
      42       55       61 
subtype1 subtype2 subtype3 
       0        0        1 
$subtype1
TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
        2.99        22.06         1.02        13.97         1.97         2.99 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5767 
        1.02        13.02         1.02        44.02        12.00        15.06 
TCGA-CH-5768 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 
       24.03         9.99        32.02        33.01        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       19.56        13.32        26.30        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5524 
       38.93        48.13        60.23        46.55        47.80        43.07 
TCGA-EJ-5527 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7330 TCGA-EJ-7783 TCGA-EJ-7785 
       39.75        47.87        29.06         6.28        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7791 TCGA-EJ-8468 TCGA-EJ-A46E TCGA-HC-7736 TCGA-HC-7748 
       14.53        19.59        64.47        17.49         0.72        26.04 

$subtype2
TCGA-CH-5738 TCGA-CH-5764 TCGA-CH-5771 TCGA-CH-5772 TCGA-EJ-5498 TCGA-EJ-5499 
        6.97         1.02        13.02        15.98        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5503 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-7115 
       44.88        45.73        36.69        48.53        38.53        27.02 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7328 TCGA-EJ-7331 
       61.15         9.70         9.50         9.37        27.68         0.30 
TCGA-EJ-7781 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8470 
       23.90        17.29         3.75        23.05        19.92        26.99 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46F TCGA-EJ-A65E TCGA-EJ-A65M TCGA-FC-7708 
        5.33         4.24         9.83        13.71         7.56        28.41 
TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6364 
       41.62        55.76        18.21        46.16        50.70        39.39 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6499 
       40.18        38.01        40.31        25.15        58.22        50.73 
TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7079 TCGA-HC-7210 TCGA-HC-7232 
       35.34        28.18         6.08         2.93        28.54         2.93 
TCGA-HC-7233 TCGA-HC-7740 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 
        1.71         1.74        78.61        88.24        82.92        12.30 
TCGA-KK-A59Y 
       44.68 

$subtype3
TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5765 
       12.99        35.01        31.00         2.04         0.92        23.01 
TCGA-CH-5766 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5507 
        1.02         2.04        26.99         2.99        27.16        23.90 
TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5525 
       36.23        52.27        64.50        51.88        68.35        36.66 
TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-7321 TCGA-EJ-7782 TCGA-EJ-7784 
       38.76        60.23        41.85         7.66        38.37        25.68 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46G TCGA-FC-7961 
       14.14        18.15        63.98        10.32         3.06        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-G9-6338 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       13.45         8.98        66.67        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       45.30        44.81         3.32        26.66        31.50        37.97 
TCGA-G9-6496 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7525 TCGA-HC-7081 TCGA-HC-7211 
       56.75        38.96        30.97        32.68         2.37         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-7817 TCGA-HC-8264 TCGA-HI-7171 
       28.60         1.97         1.68        30.51         1.58        43.69 
TCGA-J4-8198 TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       20.19         5.85        10.62        93.99        56.28        61.78 
TCGA-KK-A5A1 
       77.72 

subtype1 subtype2 subtype3 
    0.72     0.30     0.79 
subtype1 subtype2 subtype3 
   64.47    88.24    93.99 
subtype1 subtype2 subtype3 
   24.95    27.02    30.51 
[1] "0.7 - 64.5 (25.0)" "0.3 - 88.2 (27.0)" "0.8 - 94.0 (30.5)"
D3V2, continuous
          vv
clus       T2 T3 T4
  subtype1 18 23  0
  subtype2 27 27  1
  subtype3 13 45  4
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       18       27       13
  T3       23       27       45
  T4        0        1        4
[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"
D3V4, binary
          cls
clus        0  1
  subtype1 38  4
  subtype2 43  2
  subtype3 42 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    4
  subtype2   43    2
  subtype3   42   11
   clus
vv  subtype1 subtype2 subtype3
  0       38       43       42
  1        4        2       11
[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"
D3V5, binary
          cls
clus        0  1
  subtype1  0 42
  subtype2  1 54
  subtype3  1 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   42
  subtype2    1   54
  subtype3    1   61
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        0        1        1
  PROSTATE ADENOCARCINOMA ACINAR TYPE          42       54       61
[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       R0 R1 R2 RX
  subtype1 36  4  0  1
  subtype2 40  9  0  2
  subtype3 36 20  1  1
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       36       40       36
  R1        4        9       20
  R2        0        0        1
  RX        1        2        1
[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"
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    39
  subtype2     2                         1    42
  subtype3     0                         5    40
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        0        1        5
  WHITE                           39       42       40
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 48  0
  subtype2 63  1
  subtype3 46  0
subtype1 subtype2 subtype3 
      48       64       46 
subtype1 subtype2 subtype3 
       0        1        0 
$subtype1
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 
        2.99         1.02        13.02         1.02        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 
        1.02        23.01         1.02        15.06        24.03        13.02 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99        32.02        33.01        29.00        33.11        19.56 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5508 TCGA-EJ-5509 
       44.88        26.30        28.93        30.31        38.93        48.13 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5524 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7314 
       46.55        47.80        43.07        41.85        47.87         9.70 
TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7791 
        9.37         6.28        25.87        20.55        14.53        19.59 
TCGA-EJ-8468 TCGA-EJ-A46E TCGA-HC-7210 TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7748 
       64.47        17.49        28.54         0.72         1.74        26.04 

$subtype2
TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5769 
       12.99        35.01        31.00         2.04         0.92         2.04 
TCGA-CH-5788 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5514 
       26.99         2.99        27.16        27.19        23.90        36.23 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 
       52.27        64.50        51.88        68.35        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-7321 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-7789 
       60.23         7.66        38.37        25.68        14.14        18.15 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46G TCGA-EJ-A65E TCGA-FC-7961 
       63.98        26.99        10.32         3.06        13.71        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6356 TCGA-G9-6361 
       13.45         8.98        66.67        18.21        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 
       47.44        45.30        44.81         3.32        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6496 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7525 TCGA-HC-7079 
       37.97        56.75        38.96        30.97        32.68         2.93 
TCGA-HC-7081 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-7817 
        2.37         0.79        28.60         1.97         1.68        30.51 
TCGA-HC-8264 TCGA-HI-7171 TCGA-J4-8198 TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
        1.58        43.69        20.19         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       56.28        44.68        61.78        77.72 

$subtype3
TCGA-CH-5772 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5503 TCGA-EJ-5510 
       15.98        13.32        29.79        46.52        45.73        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-EJ-7115 
       48.53        38.53        60.23        39.75        29.06        27.02 
TCGA-EJ-7125 TCGA-EJ-7315 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7792 
       61.15         9.50        27.68         0.30        23.90        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46F 
        3.75        23.05        19.92         5.33         4.24         9.83 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6353 
        7.56        28.41        41.62        55.76        46.16        50.70 
TCGA-G9-6364 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6384 TCGA-G9-6494 
       39.39        40.18        38.01        40.31        25.15        58.22 
TCGA-G9-6499 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7232 TCGA-HC-7233 
       50.73        35.34        28.18         6.08         2.93         1.71 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 
       78.61        88.24        82.92        12.30 

subtype1 subtype2 subtype3 
    0.72     0.79     0.30 
subtype1 subtype2 subtype3 
   64.47    93.99    88.24 
subtype1 subtype2 subtype3 
  20.070   27.895   29.425 
[1] "0.7 - 64.5 (20.1)" "0.8 - 94.0 (27.9)" "0.3 - 88.2 (29.4)"
D4V2, continuous
          vv
clus       T2 T3 T4
  subtype1 22 25  0
  subtype2 15 46  4
  subtype3 21 24  1
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       22       15       21
  T3       25       46       24
  T4        0        4        1
[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"
D4V4, binary
          cls
clus        0  1
  subtype1 43  4
  subtype2 43 12
  subtype3 37  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    4
  subtype2   43   12
  subtype3   37    1
   clus
vv  subtype1 subtype2 subtype3
  0       43       43       37
  1        4       12        1
[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"
D4V5, binary
          cls
clus        0  1
  subtype1  0 48
  subtype2  2 63
  subtype3  0 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   48
  subtype2    2   63
  subtype3    0   46
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        0        2        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE          48       63       46
[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       R0 R1 R2 RX
  subtype1 43  4  0  0
  subtype2 36 20  1  3
  subtype3 33  9  0  1
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       43       36       33
  R1        4       20        9
  R2        0        1        0
  RX        0        3        1
[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"
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    45
  subtype2     0                         5    40
  subtype3     2                         1    36
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        2
  BLACK OR AFRICAN AMERICAN        0        5        1
  WHITE                           45       40       36
[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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 104   3
  subtype2 121   2
  subtype3 127   1
subtype1 subtype2 subtype3 
     107      123      128 
subtype1 subtype2 subtype3 
       3        2        1 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5762 
       20.42         6.97        13.97         2.99        24.03        44.02 
TCGA-CH-5763 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5497 TCGA-EJ-5498 
       12.00        13.02         9.99         2.99        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 
       46.52        44.88        26.30        45.73        27.19        38.93 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5531 
       36.69        38.53        60.23        68.35        38.76        41.85 
TCGA-EJ-7115 TCGA-EJ-7318 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7783 
       27.02        16.77        27.68         6.28        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8470 
       20.55        19.59         3.75        23.05        19.92        26.99 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-FC-7708 
        5.33         4.24        17.49         7.53        21.96        28.41 
TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 
       17.23         1.78        41.62        67.99        69.37        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 
       46.16        50.70        47.15        44.81        40.18        38.01 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7522 
       45.80        25.15        27.29        38.27        38.96        35.34 
TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7740 
       30.94         2.93        28.54         0.79         0.72         1.74 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-8258 
        2.07        24.59        26.04        30.51         1.48         2.17 
TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A6AQ TCGA-HC-A6AS 
        1.94        22.32        15.88         1.15         3.48         1.45 
TCGA-HC-A6HX TCGA-HI-7170 TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 
        1.25        82.92        16.04        14.93         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A83K TCGA-J9-A52C TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y 
       17.36         6.77         5.85        22.75        20.65         5.19 
TCGA-M7-A720 TCGA-QU-A6IP TCGA-VN-A88I TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C 
        9.93        86.14         8.84        94.65        23.93        55.56 
TCGA-X4-A8KQ TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJR TCGA-XK-AAJT 
       37.18        48.03         9.04         2.99        27.09        37.02 
TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8SK TCGA-YL-A9WJ TCGA-YL-A9WX 
       39.65        52.96        37.97        60.99        49.91 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5751 
       43.79        33.96         3.68         2.99         1.02        35.01 
TCGA-CH-5767 TCGA-CH-5772 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-5504 TCGA-EJ-5505 
       15.06        15.98        26.99        27.16        28.93        30.31 
TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5532 TCGA-EJ-7123 
       48.13        36.23        47.80        52.27        47.87        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-7786 
       61.15        83.57        21.80         9.37         0.30        14.53 
TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-8468 TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65G 
       18.15        17.29        64.47        17.62        13.71         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD 
        2.99         7.56        15.42        13.45         8.98        16.24 
TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6366 TCGA-G9-6369 
       81.04        66.67        18.21        68.68         3.32        39.95 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       40.31        37.97        58.22        56.75        52.87        50.73 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7075 TCGA-HC-7078 
       27.91        30.97        28.18        26.01        19.76         5.33 
TCGA-HC-7080 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-7750 
        2.01         1.71         2.10         2.66         1.48         1.12 
TCGA-HC-7752 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8264 
        3.22        22.42         3.12         2.27        17.95         1.58 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HI-7168 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67O 
        5.49         2.33        78.61        88.24        12.30        16.14 
TCGA-J4-A67Q TCGA-J4-A83J TCGA-J4-A83L TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 
       20.52        10.19        10.39        56.28        61.78        30.02 
TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-KK-A8IF 
       67.59        49.25        67.07        58.19         2.73        26.43 
TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO 
       13.15        25.08        15.88         3.19        41.00        47.21 
TCGA-TP-A8TV TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VP-A87B 
        8.19        15.52        15.81        30.15        15.09        75.91 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       66.97        21.80        17.82         5.79         3.91        38.04 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-Y6-A8TL 
       25.97        31.50        28.54        30.58        29.23        25.48 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SH 
       36.95        71.77        62.14        60.56        45.50        28.77 
TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-ZG-A8QW 
       47.38       106.75        62.79         7.00        41.39         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
        4.93         1.12         6.02 

$subtype3
TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
       22.06        25.35        22.06         1.02        12.99         1.97 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 
       13.02        31.00         1.02         2.04         0.92         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 
       23.01         1.02        24.03         2.04        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5516 
       29.00        33.11        19.56        23.90        48.53        46.55 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       64.50        51.88        43.07        36.66        39.75        60.23 
TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       29.06         9.70         9.50         7.66        17.52         5.75 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46F 
       38.37        25.68        14.14        63.98        10.32         9.83 
TCGA-EJ-A46G TCGA-EJ-A65D TCGA-EJ-A65F TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 
        3.06        12.92        18.41        87.35        55.76        49.35 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-6377 
       46.52        47.44        45.30        39.39        26.66        31.50 
TCGA-G9-7525 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7081 
       32.68        24.89        21.14         6.08         3.68         2.37 
TCGA-HC-7209 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       14.47        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7744 TCGA-HC-7749 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
        1.68         1.97        17.85        24.56         1.84        19.36 
TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       23.87        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6HY TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L 
        1.61         4.41        43.69        20.19        21.76        17.03 
TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83M TCGA-J4-A83N 
       16.54        17.19         9.17         9.17        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 
       13.87        10.62        93.99        44.68       115.86        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-M7-A71Z 
      151.36        90.51       113.33        27.62        34.95         6.87 
TCGA-M7-A725 TCGA-QU-A6IN TCGA-TP-A8TT TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       18.84       114.64        11.90        25.51        12.95         6.02 
TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D TCGA-VP-A87J 
       32.91       106.95        26.47        84.69        60.92        48.85 
TCGA-VP-A87K TCGA-XK-AAIW TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC 
       21.53        31.96        49.02        38.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL 
       45.14        45.86        26.24        71.34        14.04        24.33 
TCGA-YL-A9WY TCGA-ZG-A8QZ 
       28.34         7.86 

subtype1 subtype2 subtype3 
    0.72     0.30     0.76 
subtype1 subtype2 subtype3 
   94.65   106.75   151.36 
subtype1 subtype2 subtype3 
   24.03    25.48    22.21 
[1] "0.7 - 94.7 (24.0)"  "0.3 - 106.8 (25.5)" "0.8 - 151.4 (22.2)"
D5V2, continuous
          vv
clus       T2 T3 T4
  subtype1 52 52  1
  subtype2 57 63  3
  subtype3 38 91  1
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       52       57       38
  T3       52       63       91
  T4        1        3        1
[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"
D5V4, binary
          cls
clus        0  1
  subtype1 80  8
  subtype2 88 15
  subtype3 92 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80    8
  subtype2   88   15
  subtype3   92   22
   clus
vv  subtype1 subtype2 subtype3
  0       80       88       92
  1        8       15       22
[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"
D5V5, binary
          cls
clus         0   1
  subtype1   4 103
  subtype2   3 120
  subtype3   6 124
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  103
  subtype2    3  120
  subtype3    6  124
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        4        3        6
  PROSTATE ADENOCARCINOMA ACINAR TYPE         103      120      124
[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       R0 R1 R2 RX
  subtype1 77 21  0  3
  subtype2 77 37  2  3
  subtype3 88 31  3  4
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       77       77       88
  R1       21       37       31
  R2        0        2        3
  RX        3        3        4
[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"
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    52
  subtype2     0                         3    40
  subtype3     0                         4    55
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        0        3        4
  WHITE                           52       40       55
[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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 105   3
  subtype2 127   1
  subtype3 120   2
subtype1 subtype2 subtype3 
     108      128      122 
subtype1 subtype2 subtype3 
       3        1        2 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5762 TCGA-CH-5763 
       20.42         6.97        13.97         2.99        44.02        12.00 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       13.02         9.99         2.99        29.79        46.52        44.88 
TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5531 
       45.73        27.19        36.69        38.53        60.23        41.85 
TCGA-EJ-7115 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       27.02        27.68         6.28         0.30        23.90        25.87 
TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8470 TCGA-EJ-A46B 
       19.59         3.75        23.05        19.92        26.99         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65M 
        4.24        17.49         7.53        21.96        17.62         7.56 
TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 
       17.23         1.78        41.62        67.99        69.37        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 
       46.16        50.70        47.15        44.81        40.18        38.01 
TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6499 TCGA-G9-7509 
       31.50        45.80        25.15        27.29        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7522 TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7211 TCGA-HC-7233 
       38.96        35.34        30.94         2.93         0.79         1.71 
TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-7818 
        0.72         1.74         2.07        24.59        30.51         1.48 
TCGA-HC-7820 TCGA-HC-8216 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8266 TCGA-HC-A6AP 
       24.56        22.42         2.17         1.94         1.15         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7170 TCGA-J4-A67M TCGA-J4-A67O 
        3.48         1.45         1.25        82.92        16.04        16.14 
TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A83J TCGA-J9-A52C TCGA-KK-A6E3 
       14.93         6.02        13.32        10.19         5.85        67.59 
TCGA-KK-A6E5 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 
       49.25        22.75         2.73        20.65         5.19         9.93 
TCGA-M7-A723 TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-VP-A878 TCGA-VP-A879 
       25.08        41.00        47.21        86.14        94.65        23.93 
TCGA-VP-A87C TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJT 
       55.56        38.04        48.03         9.04         2.99        37.02 
TCGA-XK-AAJU TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A9WJ TCGA-YL-A9WX 
       39.65        71.77        45.50        37.97        60.99        49.91 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5748 
       43.79        33.96         3.68        25.35         2.99         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5767 TCGA-CH-5772 
       13.02        35.01         1.02         0.92        15.06        15.98 
TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 
       26.99        27.16        26.30        28.93        30.31        48.13 
TCGA-EJ-5511 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5532 TCGA-EJ-7123 
       48.53        47.80        52.27        64.50        47.87        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7782 
       61.15        83.57        21.80         9.37        16.77        38.37 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-8468 TCGA-EJ-8474 
       14.53        14.14        18.15        17.29        64.47        10.32 
TCGA-EJ-A46G TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7961 TCGA-FC-A4JI 
        3.06        13.71         9.14         2.99        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 
        8.98        16.24        81.04        66.67        18.21        68.68 
TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       39.95        40.31        37.97        58.22        56.75        52.87 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7080 
       27.91        30.97        28.18        19.76         5.33         2.01 
TCGA-HC-7210 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7750 
       28.54         2.10         2.66         1.48         1.97         1.12 
TCGA-HC-7752 TCGA-HC-8256 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV 
        3.22         3.12        17.95         1.58        15.88         0.76 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HI-7168 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q 
        2.20         5.49        78.61        88.24        12.30        20.52 
TCGA-J4-A6G3 TCGA-J4-A83L TCGA-J4-A83M TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       17.36        10.39        14.37        93.99        56.28        61.78 
TCGA-KK-A6E0 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A8IF TCGA-M7-A721 
       30.02        67.07        58.19        27.62        26.43        13.15 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88N 
       15.88        18.84         3.19         8.19         8.84        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H 
       15.81        30.15        15.09        75.91        66.97        21.80 
TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A9DX TCGA-XK-AAIW 
       48.85        17.82         5.79         3.91        25.97        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-Y6-A8TL TCGA-YL-A8HJ 
       28.54        30.58        29.23        27.09        25.48        52.96 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI 
       36.95        62.14        60.56        41.46        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-ZG-A8QX 
       45.86       106.75        62.79         7.00        41.39         4.93 
TCGA-ZG-A8QY TCGA-ZG-A9ND 
        1.12         6.02 

$subtype3
TCGA-2A-A8VV TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
       22.06        22.06         1.02        12.99         1.97        24.03 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 
       31.00         2.04         1.02        23.01         1.02        24.03 
TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
        2.04        32.02        33.01        29.00        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5521 
       13.32        23.90        38.93        36.23        46.55        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       29.06         9.70         9.50         7.66        17.52         5.75 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F 
       25.68        20.55        63.98         9.83        12.92        18.41 
TCGA-FC-7708 TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 
       28.41        87.35        55.76        49.35        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-7525 TCGA-G9-A9S0 
       45.30        39.39         3.32        26.66        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 
       24.89        21.14         6.08         3.68         2.37        14.47 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7744 
       28.60         1.97         1.68         2.37         2.93         1.68 
TCGA-HC-7748 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8259 
       26.04        17.85         1.84        19.36        23.87         2.27 
TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6HY 
       22.32        22.36         1.78         2.01         1.61         4.41 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67S 
       43.69        20.19        21.76        17.03        16.54        17.19 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52E 
        9.17         9.17         6.77        20.28        13.87        10.62 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E6 
       44.68       115.86        54.54       151.36        90.51       113.33 
TCGA-KK-A7B1 TCGA-M7-A71Z TCGA-QU-A6IN TCGA-TP-A8TT TCGA-VN-A88K TCGA-VN-A88L 
       34.95         6.87       114.64        11.90        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D 
        6.02        32.91       106.95        26.47        84.69        60.92 
TCGA-VP-A87K TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA 
       21.53        37.18        31.50        49.02        38.56        16.83 
TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL TCGA-YL-A9WY 
       45.14        26.24        71.34        14.04        24.33        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QZ 
        1.64         7.86 

subtype1 subtype2 subtype3 
    0.30     0.76     1.02 
subtype1 subtype2 subtype3 
   94.65   106.75   151.36 
subtype1 subtype2 subtype3 
  24.245   25.415   22.685 
[1] "0.3 - 94.7 (24.2)"  "0.8 - 106.8 (25.4)" "1.0 - 151.4 (22.7)"
D6V2, continuous
          vv
clus       T2 T3 T4
  subtype1 55 50  1
  subtype2 52 73  3
  subtype3 40 83  1
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       55       52       40
  T3       50       73       83
  T4        1        3        1
[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"
D6V4, binary
          cls
clus        0  1
  subtype1 82  8
  subtype2 95 14
  subtype3 83 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82    8
  subtype2   95   14
  subtype3   83   23
   clus
vv  subtype1 subtype2 subtype3
  0       82       95       83
  1        8       14       23
[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"
D6V5, binary
          cls
clus         0   1
  subtype1   4 104
  subtype2   4 124
  subtype3   5 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  104
  subtype2    4  124
  subtype3    5  119
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        4        4        5
  PROSTATE ADENOCARCINOMA ACINAR TYPE         104      124      119
[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       R0 R1 R2 RX
  subtype1 73 25  0  2
  subtype2 86 35  3  2
  subtype3 83 29  2  6
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       73       86       83
  R1       25       35       29
  R2        0        3        2
  RX        2        2        6
[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"
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    49
  subtype2     0                         5    42
  subtype3     1                         2    56
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        1
  BLACK OR AFRICAN AMERICAN        0        5        2
  WHITE                           49       42       56
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 112   3
  subtype2 115   0
  subtype3 128   3
subtype1 subtype2 subtype3 
     115      115      131 
subtype1 subtype2 subtype3 
       3        0        3 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5745 
       20.42        22.06        25.35         1.02        13.97         2.99 
TCGA-CH-5746 TCGA-CH-5754 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5771 
       24.03         2.04        12.00         1.02         1.02        13.02 
TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99        33.01         2.99        29.00        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 TCGA-EJ-5505 
       13.32        29.79        46.52        44.88        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5515 TCGA-EJ-5516 
       27.19        38.93        48.13        36.69        60.23        46.55 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 
       51.88        68.35        43.07        38.76        39.75        41.85 
TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H 
       29.06        21.80         5.33         4.24        17.49         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65M TCGA-FC-7961 
       21.96        17.62        13.71        18.41         7.56        15.42 
TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6353 
       17.23         1.78        41.62        67.99        69.37        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6379 TCGA-G9-7509 TCGA-G9-A9S7 TCGA-H9-A6BX 
       49.35        47.15        45.80        38.27        21.14        30.94 
TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-8216 TCGA-HC-8260 TCGA-HC-8265 TCGA-HC-A6AN 
       24.59        30.51        22.42         1.94        15.88         1.61 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-J4-A67L 
        2.33         3.48         1.45         1.25         4.41        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.04        16.54        16.14        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       13.32        17.36         6.77        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A6DY TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-M7-A720 TCGA-M7-A721 
        5.85       115.86        22.75         2.73         9.93        13.15 
TCGA-M7-A723 TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88Q TCGA-VP-A878 TCGA-VP-A879 
       25.08        86.14        11.90        32.91        94.65        23.93 
TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       55.56        37.18        27.81        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HK TCGA-YL-A8SH TCGA-YL-A8SJ 
       31.96        39.65        25.48        49.02        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
       37.97       106.75        60.99        62.37        49.91        28.34 
TCGA-ZG-A8QZ 
        7.86 

$subtype2
TCGA-2A-A8VO TCGA-CH-5738 TCGA-CH-5762 TCGA-CH-5767 TCGA-CH-5772 TCGA-EJ-5502 
       43.79         6.97        44.02        15.06        15.98        26.30 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 
       48.53        38.53        36.23        47.80        52.27        60.23 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7317 
       47.87        27.02        61.15        83.57         9.70         9.37 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
        5.75        27.68         6.28         0.30        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
       20.55        14.53        14.14        19.59        17.29        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A65G TCGA-FC-7708 TCGA-G9-6333 
       19.92        64.47        26.99         9.14        28.41        81.04 
TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6361 
       66.67        55.76        18.21        68.68        46.16        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       38.01        40.31        26.66        37.97        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       58.22        50.73        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 
       28.18         6.08        19.76         2.93         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       28.54         1.68         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 
        2.66         1.74         1.48         1.68         2.07        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8258 TCGA-HC-8259 
        1.97         1.12         1.48        24.56         2.17         2.27 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HI-7168 TCGA-HI-7169 
       17.95        22.32         1.58         1.15        78.61        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A6M7 TCGA-J4-A83L 
       82.92        20.19        12.30        20.52         9.17        10.39 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A7B1 TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88O 
       67.59        90.51        34.95         8.84        12.95        15.81 
TCGA-VN-A88P TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-AA1N TCGA-XA-A8JR TCGA-YL-A8HJ 
       30.15        66.97        21.80        17.82         3.91        52.96 
TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI TCGA-YL-A8SQ TCGA-ZG-A8QW TCGA-ZG-A8QX 
       71.77        45.50        47.38        62.79         1.64         4.93 
TCGA-ZG-A8QY 
        1.12 

$subtype3
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5744 
       33.96         3.68         2.99        22.06        12.99         1.97 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5765 
        1.02        13.02        31.00         1.02         0.92        23.01 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5790 TCGA-EJ-5494 TCGA-EJ-5504 
       24.03         2.04        26.99        32.02        27.16        28.93 
TCGA-EJ-5507 TCGA-EJ-5519 TCGA-EJ-5525 TCGA-EJ-7123 TCGA-EJ-7315 TCGA-EJ-7318 
       23.90        64.50        36.66        49.02         9.50        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-7793 
        7.66        17.52        38.37        25.68        18.15         3.75 
TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D TCGA-EJ-A65J 
       63.98        10.32         9.83         3.06        12.92         2.99 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6332 TCGA-G9-6348 TCGA-G9-6362 
       13.45         8.98        16.24        87.35        49.81        47.44 
TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       31.50        56.75        52.87        32.68        26.01        24.89 
TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        3.68         5.33         2.01         0.79        28.60         1.97 
TCGA-HC-7231 TCGA-HC-7752 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
        2.37         3.22        17.85         1.84        19.36         3.12 
TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       23.87        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AO TCGA-HI-7171 TCGA-J4-A67K TCGA-J4-A83I TCGA-J4-A83J TCGA-J9-A52D 
        5.49        43.69        21.76         9.17        10.19         6.97 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       10.62        93.99        56.28        44.68        61.78        77.72 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
       30.02        54.54       151.36        49.25        67.07        58.19 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Z TCGA-M7-A722 TCGA-M7-A724 TCGA-M7-A725 
       26.43        20.65         6.87        27.02        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-TP-A8TV TCGA-VN-A88K 
        3.19        41.00       114.64        47.21         8.19        25.51 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
        6.02        15.52        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       84.69        75.91        60.92        48.85        21.53         5.79 
TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       38.04        25.97        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       29.23        27.09        37.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SP 
       60.56        16.83        41.46        45.14        26.24        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-ZG-A9ND 
        7.00        14.04        41.39        24.33         6.02 

subtype1 subtype2 subtype3 
    1.02     0.30     0.76 
subtype1 subtype2 subtype3 
  115.86    90.51   151.36 
subtype1 subtype2 subtype3 
   22.42    24.56    24.03 
[1] "1.0 - 115.9 (22.4)" "0.3 - 90.5 (24.6)"  "0.8 - 151.4 (24.0)"
D7V2, continuous
          vv
clus       T2 T3 T4
  subtype1 47 66  0
  subtype2 60 52  4
  subtype3 42 90  0
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       47       60       42
  T3       66       52       90
  T4        0        4        0
[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"
D7V4, binary
          cls
clus        0  1
  subtype1 83 13
  subtype2 86  5
  subtype3 94 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   83   13
  subtype2   86    5
  subtype3   94   26
   clus
vv  subtype1 subtype2 subtype3
  0       83       86       94
  1       13        5       26
[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"
D7V5, binary
          cls
clus         0   1
  subtype1   7 108
  subtype2   1 115
  subtype3   6 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  108
  subtype2    1  115
  subtype3    6  126
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        7        1        6
  PROSTATE ADENOCARCINOMA ACINAR TYPE         108      115      126
[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       R0 R1 R2 RX
  subtype1 78 28  0  4
  subtype2 82 23  3  2
  subtype3 82 40  2  5
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       78       82       82
  R1       28       23       40
  R2        0        3        2
  RX        4        2        5
[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"
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    39
  subtype2     1                         3    69
  subtype3     0                         4    38
D7V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        0        3        4
  WHITE                           39       69       38
[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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 109   2
  subtype2  71   1
  subtype3  45   1
  subtype4  79   1
  subtype5  51   1
subtype1 subtype2 subtype3 subtype4 subtype5 
     111       72       46       80       52 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        1        1        1        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8W3 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
       20.42        25.35         6.97         1.02        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5769 
        2.99         2.04        44.02        12.00         1.02         2.04 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 
       13.02         9.99        33.01         2.99        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 
       19.56        13.32        29.79        46.52        44.88        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       38.53        60.23        46.55        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7312 TCGA-EJ-7321 
       43.07        38.76        39.75        41.85        21.80         7.66 
TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E 
        5.33        17.49         7.53        21.96        17.62        13.71 
TCGA-FC-7961 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 
       15.42        17.23         1.78        41.62        87.35        67.99 
TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       69.37        49.81        50.70        49.35        47.15        47.44 
TCGA-G9-6364 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6384 TCGA-G9-6496 
       39.39        40.18        39.95        38.01        25.15        56.75 
TCGA-G9-7509 TCGA-H9-A6BX TCGA-HC-7817 TCGA-HC-8260 TCGA-HC-A6AP TCGA-HC-A6AQ 
       38.27        30.94        30.51         1.94         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67S 
        1.45         1.25        17.03        16.04        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M 
        6.02        13.32        17.36        10.19         6.77        14.37 
TCGA-J9-A52C TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7B1 
        5.85       115.86        54.54        67.59        49.25        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-M7-A720 TCGA-M7-A721 TCGA-QU-A6IP TCGA-TP-A8TV 
       22.75         2.73         9.93        13.15        86.14         8.19 
TCGA-VN-A88Q TCGA-VP-A878 TCGA-VP-A879 TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.91        94.65        23.93        27.81        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJU TCGA-YL-A8HK TCGA-YL-A8SJ TCGA-YL-A8SK 
        2.99        31.96        39.65        49.02        45.86        37.97 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QZ 
       60.99         1.64         7.86 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5772 TCGA-EJ-5502 TCGA-EJ-5504 
       43.79        33.96         3.68        15.98        26.30        28.93 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 TCGA-EJ-5532 
       48.53        36.23        47.80        52.27        60.23        47.87 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7785 
       61.15        83.57         9.37         6.28         0.30        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-A65G 
       14.53        14.14        18.15        19.59        17.29         9.14 
TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6363 TCGA-G9-6365 
       66.67        55.76        18.21        68.68        45.30        44.81 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7519 
       40.31        37.97        27.29        58.22        52.87        27.91 
TCGA-G9-7521 TCGA-G9-7523 TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7233 TCGA-HC-7740 
       30.97        28.18         3.68        19.76         1.71         1.74 
TCGA-HC-7750 TCGA-HC-8258 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67O 
        1.12         2.17        88.24        82.92        12.30        16.14 
TCGA-J4-A67Q TCGA-J4-A6M7 TCGA-J4-A83L TCGA-J9-A52E TCGA-KK-A6E4 TCGA-KK-A6E8 
       20.52         9.17        10.39        10.62        90.51        58.19 
TCGA-KK-A8IF TCGA-VN-A88I TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A87E 
       26.43         8.84        15.81        30.15         4.34        66.97 
TCGA-VP-AA1N TCGA-XA-A8JR TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8S8 
       17.82         3.91        25.48        52.96        71.77        62.14 
TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-ZG-A8QX 
       45.50        28.77        47.38        71.34        62.79         4.93 

$subtype3
TCGA-2A-A8VV TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5765 
       22.06        12.99        24.03        13.02         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5790 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-EJ-7314 
        1.02        24.03        32.02        36.66        29.06         9.70 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-A46D TCGA-EJ-A65J 
       16.77         5.75        23.90        25.68         4.24         2.99 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-HC-7745 
       26.66        31.50        45.80        32.68        21.14         2.07 
TCGA-HC-7748 TCGA-HC-8216 TCGA-HC-A6HY TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67N 
       26.04        22.42         4.41        20.19        21.76        16.54 
TCGA-J9-A52B TCGA-KK-A59Y TCGA-KK-A8IL TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IN 
       13.87        44.68        20.65        25.08        18.84       114.64 
TCGA-TP-A8TT TCGA-VN-A88L TCGA-VN-A88M TCGA-VP-A876 TCGA-VP-A87K TCGA-X4-A8KQ 
       11.90        12.95         6.02        84.69        21.53        37.18 
TCGA-XK-AAJ3 TCGA-YL-A8SO TCGA-YL-A9WL TCGA-YL-A9WX 
       28.54       106.75        24.33        49.91 

$subtype4
TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-7325 TCGA-EJ-8469 
       31.00         0.92        26.99        27.16        17.52        63.98 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A65M TCGA-FC-A4JI 
        9.83         3.06        12.92        18.41         7.56        13.45 
TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6361 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-HC-7080 
        8.98        16.24        46.52        26.01        24.89         2.01 
TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8264 TCGA-HC-8265 
        2.93         1.48        19.36        23.87         1.58        15.88 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HI-7168 TCGA-J4-A83I TCGA-J4-A83N TCGA-J9-A52D TCGA-KK-A59V 
        5.49        78.61         9.17        20.28         6.97        93.99 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E7 
       56.28        61.78        77.72        30.02       151.36        67.07 
TCGA-M7-A71Z TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO 
        6.87        27.02        15.88         3.19        41.00        47.21 
TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87C 
       25.51        15.52        15.09        26.47        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XJ-A9DX 
       60.92        21.80        48.85         5.79        38.04        25.97 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.50        31.96        30.58        29.23        27.09        37.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       38.56        36.95        60.56        16.83        41.46        45.14 
TCGA-YL-A8SL TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY 
       26.24         7.00        14.04        41.39        62.37        28.34 
TCGA-ZG-A8QY TCGA-ZG-A9ND 
        1.12         6.02 

$subtype5
TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5748 TCGA-CH-5767 TCGA-EJ-7115 TCGA-EJ-7123 
        2.99        22.06         1.02        15.06        27.02        49.02 
TCGA-EJ-7315 TCGA-EJ-7328 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7793 TCGA-EJ-7794 
        9.50        27.68        38.37        25.87         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-FC-7708 TCGA-G9-6333 
       19.92        64.47        26.99        10.32        28.41        81.04 
TCGA-G9-6351 TCGA-G9-6366 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7522 TCGA-H9-7775 
       46.16         3.32        50.73        38.96        35.34         6.08 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        5.33         2.93         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 
       28.60         1.97         1.68         2.37         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7818 
        2.66         1.68        24.59         1.97         3.22         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8259 TCGA-HC-8261 
       17.85        24.56         1.84         3.12         2.27        17.95 
TCGA-HC-8262 TCGA-HC-8266 TCGA-HI-7171 TCGA-VP-A872 
       22.32         1.15        43.69       106.95 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.02     0.30     1.02     0.76     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 
  115.86    90.51   114.64   151.36   106.95 
subtype1 subtype2 subtype3 subtype4 subtype5 
  27.190   28.045   22.240   25.200   14.765 
[1] "1.0 - 115.9 (27.2)" "0.3 - 90.5 (28.0)"  "1.0 - 114.6 (22.2)"
[4] "0.8 - 151.4 (25.2)" "0.7 - 107.0 (14.8)"
D8V2, continuous
          vv
clus       T2 T3 T4
  subtype1 47 63  0
  subtype2 37 31  4
  subtype3 17 29  0
  subtype4 18 62  0
  subtype5 30 23  0
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T2       47       37       17       18       30
  T3       63       31       29       62       23
  T4        0        4        0        0        0
[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"
D8V4, binary
          cls
clus        0  1
  subtype1 82 13
  subtype2 55  2
  subtype3 33  7
  subtype4 54 20
  subtype5 39  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   13
  subtype2   55    2
  subtype3   33    7
  subtype4   54   20
  subtype5   39    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       82       55       33       54       39
  1       13        2        7       20        2
[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"
D8V5, binary
          cls
clus         0   1
  subtype1   6 106
  subtype2   1  71
  subtype3   1  45
  subtype4   5  75
  subtype5   1  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  106
  subtype2    1   71
  subtype3    1   45
  subtype4    5   75
  subtype5    1   52
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        6        1        1        5
  PROSTATE ADENOCARCINOMA ACINAR TYPE         106       71       45       75
                                        clus
vv                                       subtype5
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        1
  PROSTATE ADENOCARCINOMA ACINAR TYPE          52
[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       R0 R1 R2 RX
  subtype1 82 24  0  4
  subtype2 46 21  1  2
  subtype3 32 10  0  2
  subtype4 44 30  2  2
  subtype5 38  6  2  1
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       82       46       32       44       38
  R1       24       21       10       30        6
  R2        0        1        0        2        2
  RX        4        2        2        2        1
[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"
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    51
  subtype2     0                         3    30
  subtype3     0                         0    18
  subtype4     0                         0     9
  subtype5     1                         3    38
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        1
  BLACK OR AFRICAN AMERICAN        1        3        0        0        3
  WHITE                           51       30       18        9       38
[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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 49  1
  subtype2 59  2
  subtype3 33  0
  subtype4 77  2
subtype1 subtype2 subtype3 subtype4 
      50       61       33       79 
subtype1 subtype2 subtype3 subtype4 
       1        2        0        2 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       20.42        22.06        25.35         2.99         6.97        22.06 
TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       12.99        24.03        13.02        44.02        12.00         1.02 
TCGA-CH-5766 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5497 
        1.02        15.98         9.99         2.99        29.00        13.32 
TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5522 
       28.93        27.19        38.53        46.55        47.80        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-EJ-A46D 
       43.07        38.76        39.75        29.06         5.33         4.24 
TCGA-EJ-A46I TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-7509 TCGA-HC-A6AP 
       21.96         1.78        41.62        67.99        38.27         2.33 
TCGA-J4-A6G1 TCGA-J4-A83K TCGA-M7-A720 TCGA-VN-A88L TCGA-VP-A878 TCGA-VP-A879 
       13.32         6.77         9.93        12.95        94.65        23.93 
TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJU TCGA-Y6-A8TL 
       27.81        48.03         9.04         2.99        39.65        25.48 
TCGA-YL-A8SR TCGA-ZG-A8QZ 
        7.00         7.86 

$subtype2
TCGA-CH-5752 TCGA-EJ-5525 TCGA-EJ-A46G TCGA-EJ-A65F TCGA-EJ-A65J TCGA-FC-7961 
       31.00        36.66         3.06        18.41         2.99        15.42 
TCGA-G9-6339 TCGA-G9-6354 TCGA-G9-6379 TCGA-G9-6498 TCGA-G9-A9S4 TCGA-G9-A9S7 
       69.37        49.35        45.80        52.87        24.89        21.14 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6HX 
        0.76         1.78         2.01         2.20         1.61         1.25 
TCGA-HC-A6HY TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G3 
        4.41        17.03        16.04        14.93         6.02        17.36 
TCGA-J4-A83J TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       10.19        14.37        13.87         5.85        10.62        93.99 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        61.78        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A8IB TCGA-KK-A8IL 
      151.36        90.51        49.25        67.07         2.73        20.65 
TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-VP-A872 TCGA-VP-A87K 
       18.84        41.00        47.21        86.14       106.95        21.53 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT 
       17.82        37.18        31.96        28.54        30.58        37.02 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A9WH 
       71.77        62.14        45.14        28.77       106.75        14.04 
TCGA-ZG-A9ND 
        6.02 

$subtype3
TCGA-CH-5769 TCGA-EJ-5514 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-A46H TCGA-G9-6347 
        2.04        36.23        19.59        17.29         7.53        68.68 
TCGA-G9-6361 TCGA-G9-6365 TCGA-G9-7519 TCGA-G9-7523 TCGA-H9-A6BX TCGA-HC-7817 
       46.52        44.81        27.91        28.18        30.94        30.51 
TCGA-HC-8264 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A83L TCGA-KK-A7B1 
        1.58        88.24        12.30        20.52        10.39        34.95 
TCGA-KK-A7B2 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88P TCGA-VP-A87C TCGA-VP-A87E 
       22.75         8.84        25.51        30.15        55.56        66.97 
TCGA-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
        3.91        52.96        49.02        47.38        45.86        37.97 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
        1.64         4.93         1.12 

$subtype4
TCGA-EJ-5494 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 
       27.16        27.02        49.02        61.15         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.37         7.66         5.75        27.68         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46E TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6342 
       10.32        17.49        28.41        81.04        66.67        55.76 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6369 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7510 
       46.16        50.70        39.95        31.50        50.73        38.96 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.34        26.01         6.08        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 
        2.93         2.37        14.47        28.54        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7740 
        1.68         2.37         2.93         1.71         2.10         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8258 TCGA-HC-8260 
        1.12         1.48        24.56         1.84         2.17         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HI-7168 TCGA-HI-7170 
       17.95        22.32        15.88         1.15        78.61        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A83I TCGA-M7-A723 TCGA-TP-A8TT TCGA-XK-AAIV 
       43.69        20.19         9.17        25.08        11.90        31.50 
TCGA-YL-A9WY 
       28.34 

subtype1 subtype2 subtype3 subtype4 
    1.02     0.76     1.12     0.30 
subtype1 subtype2 subtype3 subtype4 
   94.65   151.36    88.24    82.92 
subtype1 subtype2 subtype3 subtype4 
   22.01    28.54    28.18    19.92 
[1] "1.0 - 94.7 (22.0)"  "0.8 - 151.4 (28.5)" "1.1 - 88.2 (28.2)" 
[4] "0.3 - 82.9 (19.9)" 
D9V2, continuous
          vv
clus       T2 T3 T4
  subtype1 24 25  0
  subtype2 17 44  0
  subtype3 15 17  1
  subtype4 36 43  0
D9V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       24       17       15       36
  T3       25       44       17       43
  T4        0        0        1        0
[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"
D9V4, binary
          cls
clus        0  1
  subtype1 34  7
  subtype2 49  6
  subtype3 21  6
  subtype4 60  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    7
  subtype2   49    6
  subtype3   21    6
  subtype4   60    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       34       49       21       60
  1        7        6        6        7
[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"
D9V5, binary
          cls
clus        0  1
  subtype1  3 47
  subtype2  4 57
  subtype3  1 32
  subtype4  0 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   47
  subtype2    4   57
  subtype3    1   32
  subtype4    0   80
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        3        4        1        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE          47       57       32       80
[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       R0 R1 R2 RX
  subtype1 36 10  0  3
  subtype2 31 26  0  3
  subtype3 21  8  1  1
  subtype4 56 14  1  2
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       36       31       21       56
  R1       10       26        8       14
  R2        0        0        1        1
  RX        3        3        1        2
[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"
D9V7, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
D9V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    27
  subtype2     0                         0     3
  subtype3     0                         0     7
  subtype4     1                         3    54
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        3
  WHITE                           27        3        7       54
[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"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 45  1
  subtype2 25  1
  subtype3 16  1
  subtype4 51  1
  subtype5 25  0
  subtype6 56  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      46       26       17       52       25       57 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        1        1        1        0        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-EJ-7793 TCGA-EJ-A46B TCGA-EJ-A46D 
       20.42        22.06        25.35         3.75         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65F TCGA-G9-6329 TCGA-G9-6333 
       17.49         7.53        21.96        18.41        41.62        81.04 
TCGA-G9-6339 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6499 TCGA-G9-7509 TCGA-H9-A6BX 
       69.37        50.70        49.35        50.73        38.27        30.94 
TCGA-HC-7817 TCGA-HC-8260 TCGA-HC-A6AP TCGA-HC-A6HX TCGA-J4-A67L TCGA-J4-A67M 
       30.51         1.94         2.33         1.25        17.03        16.04 
TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J9-A52C TCGA-KK-A7B1 TCGA-KK-A7B2 
       14.93        13.32         6.77         5.85        34.95        22.75 
TCGA-KK-A8IB TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-VN-A88L TCGA-VP-A878 
        2.73         9.93        25.08        86.14        12.95        94.65 
TCGA-VP-A879 TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       23.93        37.18        27.81        48.03         9.04         2.99 
TCGA-XK-AAJU TCGA-YL-A8HK TCGA-YL-A8SK TCGA-ZG-A8QZ 
       39.65        49.02        37.97         7.86 

$subtype2
TCGA-EJ-7125 TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 
       61.15         9.37         0.30        14.53        14.14        17.29 
TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6369 TCGA-G9-7519 TCGA-G9-7523 TCGA-HC-7075 
       66.67        68.68        39.95        27.91        28.18        19.76 
TCGA-HC-7750 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A83L TCGA-VN-A88I 
        1.12        88.24        12.30        20.52        10.39         8.84 
TCGA-VN-A88P TCGA-VP-A87E TCGA-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8S8 TCGA-YL-A8SH 
       30.15        66.97         3.91        52.96        62.14        28.77 
TCGA-YL-A8SI TCGA-ZG-A8QX 
       47.38         4.93 

$subtype3
TCGA-CH-5769 TCGA-EJ-5514 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7231 
        2.04        36.23        30.97        26.01        21.14         2.37 
TCGA-J4-A83I TCGA-TP-A8TT TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A87C TCGA-XK-AAIV 
        9.17        11.90        25.51       106.95        55.56        31.50 
TCGA-YL-A8SF TCGA-YL-A9WH TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY 
       45.14        14.04        28.34         1.64         1.12 

$subtype4
TCGA-CH-5737 TCGA-CH-5752 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5525 TCGA-EJ-7123 
        2.99        31.00         2.99        27.16        36.66        49.02 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-FC-7961 TCGA-FC-A8O0 TCGA-G9-6379 TCGA-G9-6498 
        3.06         2.99        15.42         1.78        45.80        52.87 
TCGA-G9-A9S4 TCGA-HC-7078 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       24.89         5.33         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6HY TCGA-J4-A67T TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J9-A52B 
        1.61         4.41         6.02        17.36        10.19        13.87 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
       10.62        93.99        44.68        61.78        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 
       30.02        54.54       151.36        90.51        49.25        67.07 
TCGA-KK-A8IL TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IO TCGA-VP-A87K TCGA-VP-AA1N 
       20.65        18.84        41.00        47.21        21.53        17.82 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HO 
       31.96        28.54        30.58        37.02        25.48        71.77 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SR TCGA-ZG-A9ND 
       45.86       106.75         7.00         6.02 

$subtype5
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 
        6.97        22.06        12.99        24.03        13.02        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5794 
       12.00         1.02         1.02        15.98         9.99        29.00 
TCGA-EJ-5497 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 
       13.32        28.93        27.19        38.53        46.55        47.80 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-G9-6336 
       68.35        43.07        38.76        39.75        29.06        67.99 
TCGA-G9-6365 
       44.81 

$subtype6
TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       27.02         9.70         9.50         7.66         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7791 
        6.28        38.37        25.87        25.68        20.55        19.59 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-FC-7708 TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6377 TCGA-G9-7510 
       28.41        55.76        46.16        46.52        31.50        38.96 
TCGA-G9-7522 TCGA-H9-7775 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       35.34         6.08         2.93         2.37        14.47        28.54 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 
       28.60         1.97         1.68         2.93         1.71         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8258 TCGA-HC-8261 
        1.97         1.48        24.56         1.84         2.17        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HI-7168 TCGA-HI-7170 
       22.32         1.58        15.88         1.15        78.61        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A83M 
       43.69        20.19        14.37 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.25     0.30     1.12     0.76     1.02     1.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   94.65    88.24   106.95   151.36    68.35    82.92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.010   24.215   25.510   26.320   28.930   19.590 
[1] "1.2 - 94.7 (22.0)"  "0.3 - 88.2 (24.2)"  "1.1 - 107.0 (25.5)"
[4] "0.8 - 151.4 (26.3)" "1.0 - 68.3 (28.9)"  "1.1 - 82.9 (19.6)" 
D10V2, continuous
          vv
clus       T2 T3 T4
  subtype1 24 21  0
  subtype2 17  9  0
  subtype3  3 14  0
  subtype4 14 38  0
  subtype5  8 15  1
  subtype6 26 32  0
D10V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T2       24       17        3       14        8       26
  T3       21        9       14       38       15       32
  T4        0        0        0        0        1        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus        0  1
  subtype1 27  5
  subtype2 20  0
  subtype3  8  8
  subtype4 43  5
  subtype5 19  5
  subtype6 47  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    5
  subtype2   20    0
  subtype3    8    8
  subtype4   43    5
  subtype5   19    5
  subtype6   47    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       27       20        8       43       19       47
  1        5        0        8        5        5        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  4 42
  subtype2  1 25
  subtype3  1 16
  subtype4  2 50
  subtype5  0 25
  subtype6  0 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   42
  subtype2    1   25
  subtype3    1   16
  subtype4    2   50
  subtype5    0   25
  subtype6    0   58
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        4        1        1        2
  PROSTATE ADENOCARCINOMA ACINAR TYPE          42       25       16       50
                                        clus
vv                                       subtype5 subtype6
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        0        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE          25       58
[1] 2 6
[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       R0 R1 R2 RX
  subtype1 34  7  0  3
  subtype2 20  4  1  0
  subtype3 10  6  0  1
  subtype4 25 24  0  2
  subtype5 17  7  0  1
  subtype6 38 10  1  2
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       34       20       10       25       17       38
  R1        7        4        6       24        7       10
  R2        0        1        0        0        0        1
  RX        3        0        1        2        1        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
D10V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     5
  subtype2     0                         0    11
  subtype3     0                         0     3
  subtype4     0                         0     8
  subtype5     0                         0    25
  subtype6     1                         3    39
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        0        0        0
  WHITE                            5       11        3        8       25
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           39
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
