[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"        "-oTHNSC-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/HNSC-TP/11541491/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/11591321/HNSC-TP.mergedcluster.txt"

nPatients in clinical file=494, in cluster file=528, common to both=494
[1]  10 494
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
143 131 175  39 
  1   2   3   4 
143 131 175  39 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
85 76 91 87 68 70 17 
 1  2  3  4  5  6  7 
85 76 91 87 68 70 17 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
55 52 37 68 
 1  2  3  4 
55 52 37 68 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
78 85 49 
 1  2  3 
78 85 49 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
189 134 142 
  1   2   3 
189 134 142 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 48 156 143 118 
  1   2   3   4 
 48 156 143 118 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
205 142 145 
  1   2   3 
205 142 145 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
189 131 172 
  1   2   3 
189 131 172 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
 72 123  91 116  45 
  1   2   3   4   5 
 72 123  91 116  45 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
141 227  79 
  1   2   3 
141 227  79 
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 494 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415           NA          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
         622          918          850          351          216           NA 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
         182           NA           NA           NA          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         2161          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
        1151          392          817          993          642          758 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625           NA         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268           NA         1007         1045          173           NA 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        1081         1681           NA           NA           NA           NA 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
          NA           NA           NA          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98           NA          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
         318          611          394          735           NA          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         429           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         645          225          526          484          348          175 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
          NA          367           NA          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1207          654           NA         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
        1399          317          341          129         1253           NA 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
          NA         1000         1407         1057          985           NA 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
          NA           NA         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
          NA          707           NA          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521           NA         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125           NA          514           NA          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
          NA         1435         1191         1440         1245           NA 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105           NA          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
          NA         1036           NA          796           NA          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430           NA          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         4241          522         3930 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         3270         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         2784         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
         641         1899           NA           NA           NA           NA 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
        3835           NA           NA           NA           NA           NA 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
          NA           NA           NA           NA         3837         3381 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
          NA           NA           NA           NA           NA         3497 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        2347           NA         1444         1095          954          797 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
          NA         1099           NA           NA           NA           NA 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
          NA         4335           NA           NA           NA           NA 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
          NA          851           NA         5480           NA           NA 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
          NA           NA         1722           NA           NA           NA 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1075           NA          906           NA          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685           NA          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
         321          237          828           NA          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548           NA          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
        1131          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
           3          384           14           13           NA            6 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          NA          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
         206            2            5           25           NA           NA 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
         122          441          588          360          412           NA 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         440           NA          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         111          112           NA          254          240          910 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
          NA         1726         1559           NA         1120           NA 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
         578         1917           NA           NA           NA           NA 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
          NA          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 
         228          225          387          567          198           NA 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1663           NA         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS TCGA-UF-A7JV 
         413           NA 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=171,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=319,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBERPACKYEARSSMOKED"                 
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 494 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  46 130  95 164 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   47   130    95   164 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  46 130  95 164 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   47   130    95   164 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
171  63 156   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
171  63 156   8 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
171  63 156   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
171  63 156   8 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=86, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=25, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  79  36
  subtype2  84  32
  subtype3 113  37
  subtype4  25   8
subtype1 subtype2 subtype3 subtype4 
     115      116      150       33 
subtype1 subtype2 subtype3 subtype4 
      36       32       37        8 
$subtype1
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6868 
         102          283          415          248         1636          190 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7872 
         384          113          895          182          278          436 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4736 
           5          721          142          392          817          395 
TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5367 TCGA-CN-6013 TCGA-CN-A641 TCGA-CQ-5329 
         625         1988         1966          628          367         1422 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
        1393          317         1253         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CG 
        1959         1560         1007          509         1950          391 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 
        1971          354          379          350         1956         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7390 TCGA-CV-5435 
        1440         1960          759         1036          907         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
         584          546         2437          406         2641         1478 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-6954 
        1315         1665         1948         1969         1969         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7180 
        1969         1959         3837         1970         1945         1987 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7428 TCGA-CV-7440 TCGA-CV-A45R 
         954          797         1967         1973         1981         5480 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6516 
         906          670          110          685          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO TCGA-D6-A6EQ 
         292          701          128          539          435          368 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 
         389         1778          548          299         1131          490 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 
          92          585           14          133          403            2 
TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L 
          25           49          485          588          440          351 
TCGA-MT-A51X TCGA-P3-A5QA TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
          34         1726         1968          400          553          357 
TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A7JC 
         228          149          135          135         1326          484 
TCGA-UF-A7JD 
         735 

$subtype2
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6870 
         462         1983          276          520          644          451 
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DL 
          63          236          855          918          850          623 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         142          133          536          687         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 
        1955          624         1157         1230          993         1250 
TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 
        1330         1081         1980         1966          630          933 
TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         629         1970         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63T 
         394          735          429          443          391          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
         526          348         1466         1000          707          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-7364 
        2562          358          514         1969          234         1435 
TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7398 
        1245          105         1979           30         1954          156 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 
         181         1955          522         1950         3295         1978 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-7091 TCGA-CV-7097 
         215         1970         1952         1959         1959         1970 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 
        1939         1952         1095         1976         1099         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A461 
        1957         1947         1972         1937         1959         1954 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EP 
        1075          317          237          106          376          424 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-A623 
         338          516         1965          575          324            6 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-KU-A66T 
           5           37           55          111          360          552 
TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 
         240         1954          198          157          168         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
        1319         1252         1278         1043         1894         1497 
TCGA-UF-A7JH TCGA-UF-A7JS 
         665          413 

$subtype3
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-A4IH 
         722         1288         1762          725          623          622 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         216         1976          314          187         2878          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-C9-A480 TCGA-CN-4722 
         558          310          423          638            4          799 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
        1151          642         1960          811         1268         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 
         173         1980         1975          683          290          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A49C 
         629           45          432           98          202          645 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         484          175          223         1207          654         1660 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1399          341          129         1179         1750         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-5248 
        1274          877         1963          893          303         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6492 TCGA-CR-7376 TCGA-CR-7377 
         362          311          345          479          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
         796          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 
         946          908          898          930          216         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6436 TCGA-CV-6942 
         911         1472         1958          701         1899         3835 
TCGA-CV-6943 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 
        1948         1936         1959         1979         1444         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q 
        1974         1948         1937         1984          851         1945 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JO 
        1960         1940         1946         1722         1977         1959 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
         646          606         1950          321           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         154          568          483         1030          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A61V TCGA-F7-A620 
         369          368          340          658          384           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 
         407           58          414          206           25           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          24           11           10           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D 
         441          360          224          378          168           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         111          254          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-UF-A7JJ 
        1917          245          225          387          567          214 

$subtype4
TCGA-BA-5559 TCGA-BA-A6DA TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6996 TCGA-CN-6998 
        1747          351         1007         1977          432           46 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A6V3 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD 
         535          904          298         1353         1960          998 
TCGA-CQ-A4CE TCGA-CR-6467 TCGA-CR-7373 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 
         785         1777          889         2886         2327          519 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6952 TCGA-CV-7434 TCGA-CV-A6JD TCGA-CV-A6JZ 
        1840          641         1966         1958         1970          714 
TCGA-D6-A6EM TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-IQ-A61H TCGA-MT-A51W 
         232         1081           15            3          412           14 
TCGA-MT-A67A TCGA-MT-A67G TCGA-QK-A6IG 
         392          112          218 

subtype1 subtype2 subtype3 subtype4 
       2        5        4        3 
subtype1 subtype2 subtype3 subtype4 
    5480     3295     3835     2886 
subtype1 subtype2 subtype3 subtype4 
     670      721      692      785 
[1] "2.0 - 5480.0 (670.0)" "5.0 - 3295.0 (721.0)" "4.0 - 3835.0 (692.0)"
[4] "3.0 - 2886.0 (785.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       7       20        22        77         5         1
  subtype2       6       16        18        68         4         0
  subtype3      11       32        27        73         1         0
  subtype4       2        7         7        17         2         0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          7        6       11        2
  STAGE II        20       16       32        7
  STAGE III       22       18       27        7
  STAGE IVA       77       68       73       17
  STAGE IVB        5        4        1        2
  STAGE IVC        1        0        0        0
[1] 6 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       T0+T1 T2 T3 T4
  subtype1    12 38 30 53
  subtype2     9 28 30 48
  subtype3    23 51 23 50
  subtype4     3 10 11 11
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       12        9       23        3
  T2          38       28       51       10
  T3          30       30       23       11
  T4          53       48       50       11
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 48 18 53  2
  subtype2 44 12 46  3
  subtype3 67 24 41  1
  subtype4 11  9 12  2
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       48       44       67       11
  N1       18       12       24        9
  N2       53       46       41       12
  N3        2        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"
          vv
clus       M0 M1 MX
  subtype1 45  1 15
  subtype2 38  0 15
  subtype3 66  0 21
  subtype4 18  0  7
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       45       38       66       18
  M1        1        0        0        0
  MX       15       15       21        7
[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"
D1V7, binary
          cls
clus         0   1
  subtype1  38 105
  subtype2  27 104
  subtype3  53 122
  subtype4  14  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38  105
  subtype2   27  104
  subtype3   53  122
  subtype4   14   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       38       27       53       14
  MALE        105      104      122       25
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   143
  subtype2                                   127
  subtype3                                   168
  subtype4                                    39
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
  subtype4                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   4
  subtype3                                                   6
  subtype4                                                   0
D1V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            143      127
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        4
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            168       39
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6        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"
D1V9, binary
          cls
clus         0   1
  subtype1  24 119
  subtype2  23 108
  subtype3  29 146
  subtype4   3  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  119
  subtype2   23  108
  subtype3   29  146
  subtype4    3   36
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        24       23       29        3
  YES      119      108      146       36
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                        16
  subtype2                                0     1                        16
  subtype3                                1     4                         9
  subtype4                                0     1                         3
          vv
clus       WHITE
  subtype1   114
  subtype2   112
  subtype3   155
  subtype4    34
D1V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   5        1        4        1
  BLACK OR AFRICAN AMERICAN              16       16        9        3
  WHITE                                 114      112      155       34
[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"
D1V13, binary
          cls
clus         0   1
  subtype1  10 125
  subtype2   5 112
  subtype3   8 157
  subtype4   1  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  125
  subtype2    5  112
  subtype3    8  157
  subtype4    1   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           10        5        8        1
  NOT HISPANIC OR LATINO      125      112      157       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 50 24
  subtype2 52 14
  subtype3 54 20
  subtype4 48 24
  subtype5 53 11
  subtype6 39 15
  subtype7  8  8
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      74       66       74       72       64       54       16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      24       14       20       24       11       15        8 
$subtype1
TCGA-4P-AA8J TCGA-BA-5557 TCGA-BA-A4II TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-4217 
         102          623          918          216         1976          187 
TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4738 
         436         1955            4         1151          642         1960 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6022 
         173         1980         1966          594          629          202 
TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5331 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6227 
         432          654         1399         1974         1407         1959 
TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-6474 
        1179         1353         1963          893          303         1971 
TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
        1969          379          479          972         1968          796 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1954         1951          913          946          908          898 
TCGA-CR-7397 TCGA-CV-5971 TCGA-CV-6943 TCGA-CV-6961 TCGA-CV-7238 TCGA-CV-7410 
         216          701         1948         1959         1444         1948 
TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JO 
        1984         1961         1960         1722         1977         1959 
TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM 
         606          321           77          106          539          232 
TCGA-DQ-5630 TCGA-F7-8489 TCGA-F7-A620 TCGA-H7-A6C4 TCGA-HD-8634 TCGA-IQ-7632 
        1030          658           13          414           24          441 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-AA3K TCGA-UF-A718 
         168           14          400          357          168         1326 
TCGA-UF-A7JA TCGA-UF-A7JJ 
        1894          214 

$subtype2
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DL 
         462          520          644          895          182          623 
TCGA-BB-7864 TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
         687         1153         1230          817          993          625 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6988 TCGA-CN-A49A 
        1330          811         1045         1081          318          391 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 
         225          526          484          348          367          298 
TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7372 
        1959         1950          707          358         1435          759 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 
         156          911         2886         1959         1957         1969 
TCGA-CV-7091 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7428 TCGA-CV-7435 
        1959         1095          797         1960         1973         1959 
TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JU TCGA-CX-7086 TCGA-D6-6823 
        1981         1940         1954          110          237          701 
TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-H7-A6C5 
         435          338          324         1131          384          403 
TCGA-HD-7917 TCGA-HD-8224 TCGA-IQ-7631 TCGA-KU-A66S TCGA-QK-A8Z7 TCGA-QK-AA3J 
          37           55          122          224          198          157 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1663         1319         1252          735         1497          665 

$subtype3
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4224 TCGA-BB-4227 
         283          248          384          113          278          133 
TCGA-CN-4725 TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
        1157          395         1988         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-6020 TCGA-CN-6998 TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6223 
         683           98           46         1422         1253         1057 
TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4CE TCGA-CR-6477 
         985         1560         1007         1274          785          514 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7401 TCGA-CV-5436 TCGA-CV-5439 
        1956         1191         1036         1077          584          546 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-7090 
         406         2641         1478         1315         1665         3837 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-A45R TCGA-CV-A6JE 
        1945         1987         1979          954         5480         1075 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-8569 
         906          670          646          685          292          128 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7592 
         368          389         1778         1081         1965          299 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-8502 TCGA-HD-7753 
         490           15          585            3          133            5 
TCGA-IQ-7630 TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51X 
         485          440          351          360          552           34 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6II 
        1726         1954          578          553          228          225 
TCGA-UF-A7JC TCGA-UF-A7JS 
         484          413 

$subtype4
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 
         415          276          190          451          236          850 
TCGA-BA-A6DA TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4723 
         351          142          536          428          624          721 
TCGA-CN-4735 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6021 
        1250          630          933          629          432         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
        1110          224          611          394          735          429 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-7370 TCGA-CR-7371 
         317         1000          391          950          105         1979 
TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
          30          392          907         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-7101 
        1438         1978          215         1969         1969         1939 
TCGA-CV-7235 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 
        1952         1967         1976         1099         1955         1957 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7446 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6516 
        1947         1972         1958          317          828          773 
TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 TCGA-F7-A50I 
         568          376          424          516          575           92 
TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61H 
          14            6           25          111          360          412 
TCGA-MZ-A7D7 TCGA-P3-A6T4 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A71E TCGA-UF-A7J9 
         240         1968          135          135         1278         1043 

$subtype5
TCGA-BA-4077 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH 
        1983         1762         1747           63          855          622 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-CN-4741 
        2878          140          558          310          638         1268 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         290          628          443          535          904          645 
TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         175          223         1466         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7385 
         362          311          345          234         1245          997 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-6433 
         181         1472          522         2327         1958          641 
TCGA-CV-6441 TCGA-CV-7100 TCGA-CV-7406 TCGA-CV-A460 TCGA-DQ-7590 TCGA-DQ-7591 
        1970         1959         1974         1946          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 
         369          368          340          206           25           44 
TCGA-HD-A634 TCGA-HL-7533 TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          10         1057          378          112          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A6V9 
        1559         1120          245          567 

$subtype6
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DJ TCGA-BB-7863 
         722         1288          725         1636          314          423 
TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4734 TCGA-CN-5363 TCGA-CN-6018 TCGA-CQ-5324 
           5          799          758         1977           45         1207 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 
        1660         1393          341          129         1750         1309 
TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CR-6484 TCGA-CR-7373 TCGA-CR-7386 TCGA-CR-7395 
         877          998          354          889         1430          930 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6952 
        2437          519         1840         1899         3835         1966 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1970         1936         1937         1958          851         1945 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CV-A6K2 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-A6EK 
        1970          714         1950          491          154          483 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
         407           58            2           11           49           33 
TCGA-IQ-A61E TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A6T2 TCGA-QK-A6IG TCGA-QK-A8Z9 
         588          392          111         1917          218          149 

$subtype7
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-5355 TCGA-CN-5361 TCGA-CQ-7067 TCGA-CQ-A4C7 
         142          392         1007         1681          509         1960 
TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7369 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-7095 
         350         1440         1960         1948         1952         1970 
TCGA-CV-7432 TCGA-DQ-5631 TCGA-MT-A67D TCGA-QK-A6IJ 
        1937          548           56          387 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       4       37        3        6       10        2       56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1984     2886     5480     3295     2878     3835     1970 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   895.5    721.0    658.0    617.5    643.0    825.0   1223.5 
[1] "4.0 - 1984.0 (895.5)"   "37.0 - 2886.0 (721.0)"  "3.0 - 5480.0 (658.0)"  
[4] "6.0 - 3295.0 (617.5)"   "10.0 - 2878.0 (643.0)"  "2.0 - 3835.0 (825.0)"  
[7] "56.0 - 1970.0 (1223.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       9       14        12        44         0         0
  subtype2       3       14        11        38         3         1
  subtype3       6       14        18        42         2         0
  subtype4       2        8        12        50         3         0
  subtype5       2        8        10        20         1         0
  subtype6       3       15         8        37         3         0
  subtype7       1        3         3         9         0         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          9        3        6        2        2        3        1
  STAGE II        14       14       14        8        8       15        3
  STAGE III       12       11       18       12       10        8        3
  STAGE IVA       44       38       42       50       20       37        9
  STAGE IVB        0        3        2        3        1        3        0
  STAGE IVC        0        1        0        0        0        0        0
[1] 6 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    15 26 14 25
  subtype2     7 17 16 31
  subtype3     8 27 24 24
  subtype4     4 18 17 37
  subtype5     9 18  9  8
  subtype6     3 19 12 32
  subtype7     1  5  3  7
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1       15        7        8        4        9        3        1
  T2          26       17       27       18       18       19        5
  T3          14       16       24       17        9       12        3
  T4          25       31       24       37        8       32        7
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 32 13 31  0
  subtype2 39  8 20  1
  subtype3 31 10 32  1
  subtype4 21  9 36  3
  subtype5 13  9 16  1
  subtype6 31 10 14  2
  subtype7  4  4  7  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       32       39       31       21       13       31        4
  N1       13        8       10        9        9       10        4
  N2       31       20       32       36       16       14        7
  N3        0        1        1        3        1        2        0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 44  0  8
  subtype2 28  1  9
  subtype3 33  0  9
  subtype4 19  0  9
  subtype5 16  0 14
  subtype6 21  0  9
  subtype7  7  0  0
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       44       28       33       19       16       21        7
  M1        0        1        0        0        0        0        0
  MX        8        9        9        9       14        9        0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 28 57
  subtype2 13 63
  subtype3 29 62
  subtype4 18 69
  subtype5  9 59
  subtype6 34 36
  subtype7  3 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   57
  subtype2   13   63
  subtype3   29   62
  subtype4   18   69
  subtype5    9   59
  subtype6   34   36
  subtype7    3   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       28       13       29       18        9       34        3
  MALE         57       63       62       69       59       36       14
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    85
  subtype2                                    73
  subtype3                                    90
  subtype4                                    85
  subtype5                                    63
  subtype6                                    70
  subtype7                                    17
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
  subtype4                                                           0
  subtype5                                                           0
  subtype6                                                           0
  subtype7                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   3
  subtype3                                                   0
  subtype4                                                   2
  subtype5                                                   5
  subtype6                                                   0
  subtype7                                                   0
D2V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             85       73
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        3
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             90       85
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        2
                                                             clus
vv                                                            subtype5 subtype6
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             63       70
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                5        0
                                                             clus
vv                                                            subtype7
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             17
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1 15 70
  subtype2 10 66
  subtype3 14 77
  subtype4 19 68
  subtype5 13 55
  subtype6  7 63
  subtype7  3 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   70
  subtype2   10   66
  subtype3   14   77
  subtype4   19   68
  subtype5   13   55
  subtype6    7   63
  subtype7    3   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        15       10       14       19       13        7        3
  YES       70       66       77       68       55       63       14
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         5
  subtype2                                0     0                        12
  subtype3                                1     1                         4
  subtype4                                0     2                        13
  subtype5                                0     0                         3
  subtype6                                0     4                         5
  subtype7                                0     0                         2
          vv
clus       WHITE
  subtype1    70
  subtype2    60
  subtype3    81
  subtype4    71
  subtype5    65
  subtype6    60
  subtype7    14
D2V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0        0
  ASIAN                                   4        0        1        2        0
  BLACK OR AFRICAN AMERICAN               5       12        4       13        3
  WHITE                                  70       60       81       71       65
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   4        0
  BLACK OR AFRICAN AMERICAN               5        2
  WHITE                                  60       14
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
          cls
clus        0  1
  subtype1  3 76
  subtype2  2 63
  subtype3  8 79
  subtype4  4 77
  subtype5  3 60
  subtype6  3 66
  subtype7  1 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   76
  subtype2    2   63
  subtype3    8   79
  subtype4    4   77
  subtype5    3   60
  subtype6    3   66
  subtype7    1   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        2        8        4        3        3
  NOT HISPANIC OR LATINO       76       63       79       77       60       66
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       16
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 21 21
  subtype2 28 17
  subtype3 16 14
  subtype4 27 25
subtype1 subtype2 subtype3 subtype4 
      42       45       30       52 
subtype1 subtype2 subtype3 subtype4 
      21       17       14       25 
$subtype1
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6870 
         462          248          722          725          623          451 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721         1157          142         1230         1151          392 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 
         642         1250         1960         1330         1980         1977 
TCGA-CN-5366 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5329 TCGA-CQ-6219 TCGA-CQ-6222 
        1966           45           98         1422         1974         1407 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6942 TCGA-CV-6945 
         522          546         1958          701         3835         1969 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7254 
        1969         1959         3837         1936         1959         1976 
TCGA-CV-7406 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6823 TCGA-DQ-7592 TCGA-IQ-7630 
        1974         1981          828          701          299          485 

$subtype2
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6869 
         276         1288         1762          520         1747          644 
TCGA-BA-6871 TCGA-BB-4217 TCGA-CN-4730 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
          63          187          817         1268         1007         1045 
TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6024 
        1681          290          630          628         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-5324 TCGA-CQ-5332 
         318          611          394          429         1207          317 
TCGA-CQ-6228 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
        1959         1955         1950         3295         1978         2886 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 
         641         1970         1969         1957         1959         1970 
TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1095         1967         1099         1955         1957         1947 
TCGA-CV-7433 TCGA-D6-6827 TCGA-DQ-7591 
        1984          568          622 

$subtype3
TCGA-BA-6872 TCGA-BA-6873 TCGA-CN-4722 TCGA-CN-5365 TCGA-CN-6011 TCGA-CN-6021 
         384          113          799         1980          933         1970 
TCGA-CQ-5323 TCGA-CQ-5331 TCGA-CQ-7068 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 
        1466         1399         1309         2327          519         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6952 
        1315         1665         1899         1952         1959         1966 
TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1987          797         1960         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6825 TCGA-IQ-7632 
        1937         1958          237          773          491          441 

$subtype4
TCGA-CN-4731 TCGA-CN-4734 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 
         993          758          395          625          811         1988 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
         173         1081         1966         1975          683          629 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 
         594          629          432          202          735          432 
TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
          46          654         1660         1393          129         1253 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5436 
        1000          985         1959         1179         1007          584 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6934 
        2437          406         2641         1478          215         1948 
TCGA-CV-6943 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1948         1970         1939         1945         1979         1952 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7410 TCGA-CV-7435 TCGA-CV-7446 TCGA-CV-7568 
        1444          954         1948         1959         1958         1961 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 
         321          292           77          154 

subtype1 subtype2 subtype3 subtype4 
      45       63      113       46 
subtype1 subtype2 subtype3 subtype4 
    3837     3295     2327     2641 
subtype1 subtype2 subtype3 subtype4 
  1193.5   1110.0   1752.5    996.5 
[1] "45.0 - 3837.0 (1193.5)"  "63.0 - 3295.0 (1110.0)" 
[3] "113.0 - 2327.0 (1752.5)" "46.0 - 2641.0 (996.5)"  
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       1       14         9        28         1
  subtype2       2        4         7        33         1
  subtype3       3        8         6        16         1
  subtype4       3       13         9        40         1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        2        3        3
  STAGE II        14        4        8       13
  STAGE III        9        7        6        9
  STAGE IVA       28       33       16       40
  STAGE IVB        1        1        1        1
[1] 5 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       T0+T1 T2 T3 T4
  subtype1     3 19 12 19
  subtype2     3  6 14 25
  subtype3     3 13  6 13
  subtype4     4 21 21 22
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        3        3        3        4
  T2          19        6       13       21
  T3          12       14        6       21
  T4          19       25       13       22
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 20  5 19  1
  subtype2 15  3 25  1
  subtype3 17  5  8  1
  subtype4 20  8 27  1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       20       15       17       20
  N1        5        3        5        8
  N2       19       25        8       27
  N3        1        1        1        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"
          vv
clus       M0
  subtype1  9
  subtype2  6
  subtype3  1
  subtype4  6
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V7, binary
          cls
clus        0  1
  subtype1 13 42
  subtype2  7 45
  subtype3 15 22
  subtype4 27 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   42
  subtype2    7   45
  subtype3   15   22
  subtype4   27   41
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       13        7       15       27
  MALE         42       45       22       41
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    55
  subtype2                                    52
  subtype3                                    37
  subtype4                                    68
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V9, binary
          cls
clus        0  1
  subtype1 21 34
  subtype2 20 32
  subtype3  4 33
  subtype4 16 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   34
  subtype2   20   32
  subtype3    4   33
  subtype4   16   52
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       20        4       16
  YES       34       32       33       52
[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"
D3V10, continuous
D3V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         8
  subtype2                                0     1                         7
  subtype3                                0     0                         1
  subtype4                                0     2                         3
          vv
clus       WHITE
  subtype1    44
  subtype2    43
  subtype3    35
  subtype4    60
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   0        1        0        2
  BLACK OR AFRICAN AMERICAN               8        7        1        3
  WHITE                                  44       43       35       60
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
          cls
clus        0  1
  subtype1  5 47
  subtype2  2 46
  subtype3  2 35
  subtype4  4 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   47
  subtype2    2   46
  subtype3    2   35
  subtype4    4   62
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        2        4
  NOT HISPANIC OR LATINO       47       46       35       62
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 35 27
  subtype2 31 36
  subtype3 26 14
subtype1 subtype2 subtype3 
      62       67       40 
subtype1 subtype2 subtype3 
      27       36       14 
$subtype1
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6870 
         462          248          722          725          623          451 
TCGA-BA-6873 TCGA-BB-4217 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4733 
         113          187          721         1230          392          642 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 
        1250         1330         1007         1980         1681         1977 
TCGA-CN-5366 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5329 
        1966          933          628           45           98         1422 
TCGA-CQ-5331 TCGA-CQ-6219 TCGA-CQ-7068 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 
        1399         1974         1309          522         1950          546 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5979 
        1958          519          406          701         1840         1315 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6961 
        1665         1899         1952         3835         1969         1959 
TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7248 
        3837         1936         1959         1987         1979         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
        1976         1099         1974         1957         1937         1972 
TCGA-CV-7432 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 
        1937         1981          828          773          701          491 
TCGA-DQ-7592 TCGA-IQ-7630 
         299          485 

$subtype2
TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
         276         1747           63         1157          142         1151 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 
         993          395          625          811         1268          173 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 
        1081         1966         1975          630          629          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         629          432          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5325 
         611          394          432          429           46          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6222 
        1660         1393          317          129         1000         1407 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5436 
         985         1959         1959         1955         3295          584 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6433 
        1978         2886         2437         1478          215          641 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6943 TCGA-CV-6954 TCGA-CV-7095 
        1970         1948         1969         1948         1957         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7410 TCGA-CV-7418 
        1970         1939         1945         1952         1948         1955 
TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7446 TCGA-CV-7568 TCGA-D6-6827 
        1947         1984         1959         1958         1961          568 
TCGA-DQ-7591 
         622 

$subtype3
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6872 TCGA-CN-4722 
        1288         1762          520          644          384          799 
TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5365 
         817          758         1960         1988         1045         1980 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6021 TCGA-CN-6994 TCGA-CQ-5323 TCGA-CQ-5324 
         683          290         1970          735         1466         1207 
TCGA-CQ-6218 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6941 
        1253         1179         1007         2327         2641         1959 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1966         1969         1959         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7428 TCGA-CV-7434 TCGA-CX-7085 TCGA-CX-7086 
         797         1960         1973         1958          321          237 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-IQ-7632 
         292           77          154          441 

subtype1 subtype2 subtype3 
      45       46       77 
subtype1 subtype2 subtype3 
    3837     3295     2641 
subtype1 subtype2 subtype3 
    1312     1151     1137 
[1] "45.0 - 3837.0 (1312.0)" "46.0 - 3295.0 (1151.0)" "77.0 - 2641.0 (1137.0)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       3       18        12        41         1
  subtype2       2       11         7        57         2
  subtype3       4       10        12        19         1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3        2        4
  STAGE II        18       11       10
  STAGE III       12        7       12
  STAGE IVA       41       57       19
  STAGE IVB        1        2        1
[1] 5 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       T0+T1 T2 T3 T4
  subtype1     5 26 12 33
  subtype2     4 19 27 31
  subtype3     4 14 14 15
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        5        4        4
  T2          26       19       14
  T3          12       27       14
  T4          33       31       15
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 29  9 26  1
  subtype2 15  5 45  2
  subtype3 28  7  8  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       29       15       28
  N1        9        5        7
  N2       26       45        8
  N3        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"
          vv
clus       M0
  subtype1  9
  subtype2  8
  subtype3  5
[1] "NOT AVAILABLE: table dimension [3x1]"
D4V7, binary
          cls
clus        0  1
  subtype1 22 56
  subtype2 21 64
  subtype3 19 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   56
  subtype2   21   64
  subtype3   19   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       21       19
  MALE         56       64       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    78
  subtype2                                    85
  subtype3                                    49
[1] "NOT AVAILABLE: table dimension [3x1]"
D4V9, binary
          cls
clus        0  1
  subtype1 22 56
  subtype2 28 57
  subtype3 11 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   56
  subtype2   28   57
  subtype3   11   38
     clus
vv    subtype1 subtype2 subtype3
  NO        22       28       11
  YES       56       57       38
[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"
D4V10, continuous
D4V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                        10
  subtype2                                0     2                         6
  subtype3                                0     1                         3
          vv
clus       WHITE
  subtype1    64
  subtype2    74
  subtype3    44
D4V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   0        2        1
  BLACK OR AFRICAN AMERICAN              10        6        3
  WHITE                                  64       74       44
[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"
D4V13, binary
          cls
clus        0  1
  subtype1  7 69
  subtype2  4 75
  subtype3  2 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   69
  subtype2    4   75
  subtype3    2   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        4        2
  NOT HISPANIC OR LATINO       69       75       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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 122  43
  subtype2  75  40
  subtype3  85  30
subtype1 subtype2 subtype3 
     165      115      115 
subtype1 subtype2 subtype3 
      43       40       30 
$subtype1
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6868 
         462         1983          276         1762          520          190 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         644           63          236          895          855          622 
TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 
         850          623          187         2878          140          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         310          536          687          638         1153          428 
TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4738 
         624          721         1230          993         1250         1960 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5374 
        1330         1268         1045         1081         1681          290 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
         630          629         1970         1110          318          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         735          429          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V1 TCGA-CN-A6V3 
         645          225          526          348          223          298 
TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
        1466          317         1000         1959          707          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         998          391          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1777         1521         1050         1125 
TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7364 
        1969          311          345          354          234         1435 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 
        1245         1960          105         1979           30          997 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 
        1951          392          908          156          181          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5443 TCGA-CV-5978 
        1472         1955          522         1950         1958          215 
TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6960 
         641         1969         1952         1959         3835         1969 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1959         1939         1952         1095          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1976         1099         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1947         1972         1981         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
        1954         1970          714          701           77          154 
TCGA-D6-6827 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7589 
         568          435          424          338          516          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 
        1131          658           92          206           25           44 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61G TCGA-KU-A66S TCGA-KU-A6H7 
          10         1057          122          360          224          378 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-QK-A64Z 
         254          910         1559         1120          578          553 
TCGA-QK-A6V9 TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         567         1326         1663         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
        1043         1894         1497 

$subtype2
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BA-A6DG 
         283          248         1747          113          216         1976 
TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 
         436         1955         1157         1151          642          395 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5366 
         625          811         1007          173         1977         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
        1966         1975          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CQ-5325 
         432          202          224          611          432          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 
        1422         1393          341         1974         1407          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1959         1179          509         1950         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 
        1963          303         1971          514          379         1191 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
         759          972         1968          796         1954         1430 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 
         913          946          216         1077         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
         584         1978         2437          519          406          701 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6961 TCGA-CV-7095 
        1478         1315         1970         1948         1959         1970 
TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7435 
        1970         1945         1444          954         1974         1959 
TCGA-CV-A45R TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CX-7082 
        5480         1722         1977          670          110          317 
TCGA-CX-7085 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM 
         321          491          106          128          539          232 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 
        1778         1081         1030          548          299          490 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 
         384           14           13          414            5           55 
TCGA-HD-8635 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A6H8 
          25          588          412          440          360          168 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-UF-A7JD 
        1726         1954         1917          400          357          735 
TCGA-UF-A7JS 
         413 

$subtype3
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         415          722         1288          725          623         1636 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ 
         451          384          918          351          182          314 
TCGA-BB-4224 TCGA-BB-7863 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
         278          423            5            4          799          142 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5365 
         392          817          758         1988         1980         1980 
TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6020 TCGA-CN-6998 TCGA-CN-A641 TCGA-CQ-5324 
         683          933           98           46          367         1207 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 
        1660         1399          129         1253         1057         1750 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CE TCGA-CR-6471 
        1007         1309         1274          877          785         1966 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7379 
         350          479         1956         1440          889         1036 
TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
         907          898          930          546         2886         2327 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6943 TCGA-CV-6945 
        2641         1840         1665         1899         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7180 
        1966         1957         3837         1959         1936         1987 
TCGA-CV-7183 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1979         1937         1973         1937         1984         1958 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
         851         1945         1075          906         1959          646 
TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-A4ZB 
         685          237          828          773          292          376 
TCGA-D6-A6EK TCGA-D6-A6ES TCGA-DQ-7588 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         483          389         1965           15          585            3 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 
           6          407           58          133            2           37 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 
          24           11           49           33          485          441 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         552           14           34          392           56          111 
TCGA-MZ-A7D7 TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-UF-A7JC 
         240         1968          228          225          387          484 
TCGA-UF-A7JJ 
         214 

subtype1 subtype2 subtype3 
      10        5        2 
subtype1 subtype2 subtype3 
    3835     5480     3837 
subtype1 subtype2 subtype3 
     799      759      758 
[1] "10.0 - 3835.0 (799.0)" "5.0 - 5480.0 (759.0)"  "2.0 - 3837.0 (758.0)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       3       25        29        84         5
  subtype2      14       23        18        67         3
  subtype3       7       25        24        72         3
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3       14        7
  STAGE II        25       23       25
  STAGE III       29       18       24
  STAGE IVA       84       67       72
  STAGE IVB        5        3        3
[1] 5 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       T0+T1 T2 T3 T4
  subtype1    15 41 34 61
  subtype2    18 44 27 37
  subtype3    11 36 30 55
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       15       18       11
  T2          41       44       36
  T3          34       27       30
  T4          61       37       55
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 59 21 51  4
  subtype2 43 17 57  2
  subtype3 59 20 38  1
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       59       43       59
  N1       21       17       20
  N2       51       57       38
  N3        4        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"
          vv
clus       M0 MX
  subtype1 56 24
  subtype2 48 11
  subtype3 49 15
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       56       48       49
  MX       24       11       15
[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"
D5V7, binary
          cls
clus         0   1
  subtype1  39 150
  subtype2  35  99
  subtype3  51  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39  150
  subtype2   35   99
  subtype3   51   91
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39       35       51
  MALE        150       99       91
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   181
  subtype2                                   133
  subtype3                                   142
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   8
  subtype2                                                   0
  subtype3                                                   0
D5V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            181      133
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                8        0
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            142
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                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"
D5V9, binary
          cls
clus         0   1
  subtype1  32 157
  subtype2  29 105
  subtype3  20 122
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  157
  subtype2   29  105
  subtype3   20  122
     clus
vv    subtype1 subtype2 subtype3
  NO        32       29       20
  YES      157      105      122
[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"
D5V10, continuous
D5V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        17
  subtype2                                1     4                         7
  subtype3                                0     5                        10
          vv
clus       WHITE
  subtype1   164
  subtype2   114
  subtype3   124
D5V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   2        4        5
  BLACK OR AFRICAN AMERICAN              17        7       10
  WHITE                                 164      114      124
[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"
D5V13, binary
          cls
clus         0   1
  subtype1   8 161
  subtype2  10 117
  subtype3   5 132
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  161
  subtype2   10  117
  subtype3    5  132
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8       10        5
  NOT HISPANIC OR LATINO      161      117      132
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 36  9
  subtype2 87 46
  subtype3 84 29
  subtype4 75 29
subtype1 subtype2 subtype3 subtype4 
      45      133      113      104 
subtype1 subtype2 subtype3 subtype4 
       9       46       29       29 
$subtype1
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DL 
         462          520          644          895          182          623 
TCGA-BB-7864 TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4739 
         687         1153         1230          817          993         1330 
TCGA-CN-5356 TCGA-CN-6988 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
        1045          318          225          526          348          367 
TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5432 
         707          358         1435          156          911         1950 
TCGA-CV-5441 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7242 TCGA-CV-7245 
        2886         1959         1957         1969         1095          797 
TCGA-CV-7250 TCGA-CV-7428 TCGA-CV-7440 TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-6823 
        1960         1973         1981         1954          237          701 
TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-KU-A66S 
         435          338          324         1131          384          224 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JF 
        1663         1252         1497 

$subtype2
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-4224 
         283          248          113          216         1976          278 
TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 
         436         1955            5            4         1157         1151 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
         642          395          625          811         1988         1007 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
         173         1081         1977         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         683          628          594          629           45          432 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CQ-5325 
         202          224          611          432           46          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 
        1660         1422         1393          341         1974         1407 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
         985         1959         1179         1007          509         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 
        1353         1960         1963          303         1971          514 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
         379         1956         1191          759          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        1036          796         1954         1430          913          946 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         908          216         1077         3295         1438          584 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
        1978         2437          519          406          701         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6943 
        1840         1315         1665         1970         1948         1948 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7238 
        1966         1959         1970         1970         1945         1444 
TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7435 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A464 
         954         1974         1959         1945         5480         1722 
TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6825 
        1977          670          110          317          321          491 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          539          232         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A61W TCGA-F7-A620 
        1030          548          299          490           14           13 
TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-IQ-A61E 
         414            5           55           44           25          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A51X TCGA-P3-A5QA TCGA-P3-A6SX 
         412          440          168           34         1726         1954 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II TCGA-UF-A7J9 TCGA-UF-A7JD 
        1917          400          357          225         1043          735 
TCGA-UF-A7JS 
         413 

$subtype3
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         415          722         1288          725          623         1636 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DJ 
         190          451          384          918          351          314 
TCGA-BB-7863 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4734 
         423          799          721          142          392          758 
TCGA-CN-4738 TCGA-CN-5365 TCGA-CN-6011 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49A 
        1960         1980          933          735          443          391 
TCGA-CN-A6V3 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 
         298         1399          129         1253         1057         1750 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1309         1274          877          893          998          785 
TCGA-CQ-A4CG TCGA-CR-6471 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 
         391         1966         1969          354          350          479 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7389 TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5439 
        1440          889          392          898          930          546 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-7090 
        2327         2641         1899         3835         1969         3837 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7410 TCGA-CV-7427 
        1959         1936         1987         1979         1948         1937 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A6JD 
        1937         1984         1958          851         1960         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 
        1075          906         1959          646          714          685 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A4ZB 
         828          773          292           77          154          376 
TCGA-D6-A6EK TCGA-D6-A6ES TCGA-DQ-7588 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         483          389         1965          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
         585            3            6          407           58          133 
TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
           2           37           24           11           49           33 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A 
         485          441          360          552           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A6IH 
          56          111          578         1968          553          228 
TCGA-QK-A6IJ TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ 
         387         1326         1894          484          214 

$subtype4
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-7269 
        1983          276         1762         1747           63          236 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         855          622          850          187         2878          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 
         558          310          536          638          428          624 
TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 
        1250         1268         1980         1681          290          630 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
         629           98         1970         1110          394          429 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 
         535          904          645          223         1466         1207 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         317         1000         1959          950         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1777         1521         1050         1125 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
         311          345          234         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7399 
        1979           30          997         1951          907          181 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5443 TCGA-CV-5978 TCGA-CV-6433 
        1472         1955          522         1958          215          641 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7248 
        1969         1952         1959         1939         1952         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 
        1976         1099         1955         1957         1947         1972 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-D6-6827 TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 
        1940         1946          568          424          516          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-H7-A76A 
         775          622          369          368          340          206 
TCGA-HD-7754 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61O TCGA-KU-A6H7 
          25           10         1057          122          360          378 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6V9 
         254          240          910         1559         1120          567 
TCGA-UF-A71B TCGA-UF-A71E 
        1319         1278 

subtype1 subtype2 subtype3 subtype4 
     156        4        2       10 
subtype1 subtype2 subtype3 subtype4 
    2886     5480     3837     2878 
subtype1 subtype2 subtype3 subtype4 
   817.0    908.0    685.0    879.5 
[1] "156.0 - 2886.0 (817.0)" "4.0 - 5480.0 (908.0)"   "2.0 - 3837.0 (685.0)"  
[4] "10.0 - 2878.0 (879.5)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       0        7        10        24         1
  subtype2      15       25        25        79         3
  subtype3       6       25        20        73         4
  subtype4       3       16        16        47         3
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0       15        6        3
  STAGE II         7       25       25       16
  STAGE III       10       25       20       16
  STAGE IVA       24       79       73       47
  STAGE IVB        1        3        4        3
[1] 5 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       T0+T1 T2 T3 T4
  subtype1     2 10 11 20
  subtype2    23 47 36 42
  subtype3     9 34 22 64
  subtype4    10 30 22 27
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        2       23        9       10
  T2          10       47       34       30
  T3          11       36       22       22
  T4          20       42       64       27
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 23  5 12  1
  subtype2 50 21 66  2
  subtype3 65 18 32  1
  subtype4 23 14 36  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       23       50       65       23
  N1        5       21       18       14
  N2       12       66       32       36
  N3        1        2        1        3
[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"
          vv
clus       M0 MX
  subtype1 13  6
  subtype2 58 11
  subtype3 53 18
  subtype4 29 15
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       13       58       53       29
  MX        6       11       18       15
[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"
D6V7, binary
          cls
clus         0   1
  subtype1   7  41
  subtype2  46 110
  subtype3  51  92
  subtype4  21  97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   41
  subtype2   46  110
  subtype3   51   92
  subtype4   21   97
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       46       51       21
  MALE         41      110       92       97
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    47
  subtype2                                   155
  subtype3                                   143
  subtype4                                   111
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           0
  subtype4                                                           1
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   1
  subtype2                                                   1
  subtype3                                                   0
  subtype4                                                   6
D6V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             47      155
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        1
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            143      111
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        6
[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"
D6V9, binary
          cls
clus         0   1
  subtype1   6  42
  subtype2  34 122
  subtype3  15 128
  subtype4  26  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   42
  subtype2   34  122
  subtype3   15  128
  subtype4   26   92
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       34       15       26
  YES       42      122      128       92
[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"
D6V10, continuous
D6V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         7
  subtype2                                1     8                         8
  subtype3                                1     2                         9
  subtype4                                0     1                        10
          vv
clus       WHITE
  subtype1    39
  subtype2   131
  subtype3   126
  subtype4   106
D6V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   0        8        2        1
  BLACK OR AFRICAN AMERICAN               7        8        9       10
  WHITE                                  39      131      126      106
[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"
D6V13, binary
          cls
clus         0   1
  subtype1   1  41
  subtype2  10 138
  subtype3   7 126
  subtype4   5 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2   10  138
  subtype3    7  126
  subtype4    5  105
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1       10        7        5
  NOT HISPANIC OR LATINO       41      138      126      105
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 127  46
  subtype2  98  24
  subtype3  78  45
subtype1 subtype2 subtype3 
     173      122      123 
subtype1 subtype2 subtype3 
      46       24       45 
$subtype1
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 
         102          415         1983          276          520          451 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 
          63          622          850          623          142         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         140          133          558          310          536          687 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4731 
        1153          428          624          799          721          993 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5359 
        1250         1960         1330         1268         1045         1980 
TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 
        1081          290          630          629          628           45 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A49A 
        1110          318          394          735          429          391 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         645          484          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7068 
        1207          317         1253         1057         1959         1309 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 
        1274         1950          707          998          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
        1966         1050          362          311          345          234 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1440         1245         1960          105         1979 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7398 TCGA-CR-7399 
          30          997         1951          392          156          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
         911         1472         1955          522         1950         1438 
TCGA-CV-5443 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1958          215          641         1969         1952         1959 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7242 
        1969         1959         1936         1959         1939         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7446 
        1955         1947         1972         1958         1959         1958 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1960         1940         1946         1954         1970         1075 
TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-D6-6517 TCGA-D6-6826 
         714          685         1950          317          292          154 
TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 
         568          376          424          389          338          516 
TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I 
         622          324          340         1131          490           92 
TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A633 
         407          403          206           25           37           49 
TCGA-HD-A634 TCGA-IQ-7631 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-MT-A67G 
          10          122          360          224          378          112 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T4 
         240          910         1559         1120          578         1968 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA 
         553          245          228          567          198          135 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          157          168         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
        1252         1278         1043         1894         1497 

$subtype2
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
         462          248          722         1288         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A4IF 
         623         1636          190          644          384          895 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BB-4217 
         855          918          351          182          314          187 
TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 
         278          423          638          436            5            4 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-5361 TCGA-CN-5365 
         142         1230          392          817         1681         1980 
TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         683          933         1970           46          443          535 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5331 
         904          225          526          348          367         1399 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4C6 
         129         1000         1750         1560          877         1353 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-6473 TCGA-CR-6478 
         893          785          391          303         1125         1969 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7390 
         354          350          479         1956          889          907 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5973 
         898          930          546         2886         2327         2641 
TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6954 TCGA-CV-7235 TCGA-CV-7410 TCGA-CV-7427 
        1840         1899         1957         1952         1948         1937 
TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
        1937         1981          851          906         1959          646 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A6EK 
         237          828          773          701          539          483 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
         435          368          548         1965          575          369 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
         658           15          585            3          384           13 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 
           6           58          133            2            5           24 
TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
          11           33         1057          485          441          588 
TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         360          351          552           14          392           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         111          254         1726          218          225          387 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

$subtype3
TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-8596 
        1747          113          236          216         1976         1955 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 
        1157         1151          642          395          625          811 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
        1988         1007          173         1977         1966         1966 
TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
        1975          594          629          432           98          202 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         224          611          432          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 
        1393          341         1974         1407          985         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CR-6474 
        1179         1007          509         1960         1963         1971 
TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
         514          379         1191          759          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        1036          796         1954         1430          913          946 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
         908          216         1077         3295          584         1978 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 
        2437          519          406          701         1478         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1665         1970         1948         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 
        1966         1959         3837         1970         1970         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7422 TCGA-CV-7428 
        1987         1979         1444          954         1957         1973 
TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A464 TCGA-CV-A468 
        1984         1961         1945         5480         1722         1977 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
         670          110          606          321           77          491 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         106          128          232         1778         1081         1030 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A61W TCGA-H7-A6C4 TCGA-HD-8224 
         775          299          368           14          414           55 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 
          44           25          111          412          440          168 
TCGA-MT-A51X TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A8Z9 
          34         1954         1917          400          357          149 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
         484          735          665 

subtype1 subtype2 subtype3 
      10        2       14 
subtype1 subtype2 subtype3 
    2878     2886     5480 
subtype1 subtype2 subtype3 
     735      547      985 
[1] "10.0 - 2878.0 (735.0)" "2.0 - 2886.0 (547.0)"  "14.0 - 5480.0 (985.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       6       27        25       105         7         1
  subtype2       9       23        25        63         2         0
  subtype3      11       25        23        72         3         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          6        9       11
  STAGE II        27       23       25
  STAGE III       25       25       23
  STAGE IVA      105       63       72
  STAGE IVB        7        2        3
  STAGE IVC        1        0        0
[1] 6 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       T0+T1 T2 T3 T4
  subtype1    14 43 39 77
  subtype2    15 38 28 45
  subtype3    18 48 27 42
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       14       15       18
  T2          43       38       48
  T3          39       28       27
  T4          77       45       42
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 74 19 63  5
  subtype2 54 21 36  2
  subtype3 41 23 57  1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       74       54       41
  N1       19       21       23
  N2       63       36       57
  N3        5        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"
          vv
clus       M0 M1 MX
  subtype1 63  1 27
  subtype2 58  0 21
  subtype3 46  0 10
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       63       58       46
  M1        1        0        0
  MX       27       21       10
[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"
D7V7, binary
          cls
clus         0   1
  subtype1  45 160
  subtype2  43  99
  subtype3  46  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45  160
  subtype2   43   99
  subtype3   46   99
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       43       46
  MALE        160       99       99
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   195
  subtype2                                   142
  subtype3                                   144
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           1
  subtype2                                                           0
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   9
  subtype2                                                   0
  subtype3                                                   1
D7V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            195      142
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                9        0
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            144
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                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"
D7V9, binary
          cls
clus         0   1
  subtype1  32 173
  subtype2  17 125
  subtype3  31 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  173
  subtype2   17  125
  subtype3   31  114
     clus
vv    subtype1 subtype2 subtype3
  NO        32       17       31
  YES      173      125      114
[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"
D7V10, continuous
D7V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        25
  subtype2                                0     7                        10
  subtype3                                1     3                         8
          vv
clus       WHITE
  subtype1   175
  subtype2   120
  subtype3   125
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   1        7        3
  BLACK OR AFRICAN AMERICAN              25       10        8
  WHITE                                 175      120      125
[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"
D7V13, binary
          cls
clus         0   1
  subtype1   7 179
  subtype2   7 127
  subtype3  10 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  179
  subtype2    7  127
  subtype3   10  129
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        7       10
  NOT HISPANIC OR LATINO      179      127      129
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 107  51
  subtype2  79  29
  subtype3 117  35
subtype1 subtype2 subtype3 
     158      108      152 
subtype1 subtype2 subtype3 
      51       29       35 
$subtype1
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
         102          248         1747          384          113          895 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z 
         216         1976          142          436         1955            5 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
           4         1157         1151          642          395          625 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
         811         1988         1007          173         1081         1977 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 
        1966         1966         1975          683          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 
         629          432          202          224          611          432 
TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63V TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
          46          391          484          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 
        1393          341          129         1974         1407          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
        1959         1179         1560         1007          509         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6474 
        1353         1960         1963          785          303         1971 
TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
         514          379         1191          759          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        1036          796         1954         1430          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 
         908          898          216         1077         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1438          584         1978         2437          519          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
         701         1478         1840         1315         1665         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 
        1948         1969         1948         1969         1966         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7243 
        1970         1970         1945         1987         1444          954 
TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CV-A45R 
        1974         1957         1984         1961         1945         5480 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7082 
        1722         1977          670          110          606          317 
TCGA-CX-7085 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM 
         321          491          106          128          539          232 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 
        1778         1081         1030          548          299          368 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 
         384           14           13          414            5           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
          44           24           25          111          485          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
         412          440          351          168           34          392 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG 
        1726         1954         1917          400          357          218 
TCGA-QK-A6II TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
         225          149          157         1043          484          735 
TCGA-UF-A7JH TCGA-UF-A7JS 
         665          413 

$subtype2
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 
         415         1288          520          725         1636          451 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-4227 TCGA-BB-7863 
         236          850          182          623          133          423 
TCGA-BB-7870 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4738 
        1153          799          721          392          817         1960 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-6010 TCGA-CN-6011 
        1330         1045         1681         1980          630          933 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A63T 
          45           98          318          394          735          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5332 TCGA-CQ-6221 
         526          348          367          298          317         1000 
TCGA-CQ-6223 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-6478 
        1057         1274          877          707          998         1969 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7388 
         345          354         1435          105           30         1951 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5439 
         907          156          181          911          522          546 
TCGA-CV-5441 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7101 
        2886          215         1959         1957         1959         1939 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1952         1095          797         1967         1960         1099 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A461 
        1955         1947         1959         1981         1958         1954 
TCGA-CV-A6JE TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-CX-7086 TCGA-D6-6826 TCGA-D6-6827 
        1075          646         1950          237          154          568 
TCGA-D6-A4ZB TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7595 
         376          389          338          516         1965          324 
TCGA-F7-8298 TCGA-H7-A6C5 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-7631 TCGA-IQ-7632 
         490          403           11           49          122          441 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A6T0 
         360          224          552           56          240          578 
TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3K 
         553          228          387          198          135          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JJ 
        1326         1663         1319         1252         1894          214 

$subtype3
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5557 
         462         1983          276          722         1762          623 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         190          644           63          855          622          918 
TCGA-BA-A6DA TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         351          314          187         2878          278          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         558          310          536          687          638          428 
TCGA-BB-8601 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4741 
         624          142         1230          993         1250         1268 
TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6997 
        1980          290          629         1970         1110          429 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A6V1 
         443          535          904          645          175          223 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6228 TCGA-CQ-7063 
        1466         1207         1399         1253         1959         1750 
TCGA-CQ-7068 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
        1309          893          391          950         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-6491 
        1050         1125          362          311          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
         479         1956         1440         1245         1960         1979 
TCGA-CR-7373 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5430 
         889          997          392          930         1472         1955 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 
        2327         1958         2641          641         1899         1952 
TCGA-CV-6942 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 
        3835         1969         3837         1936         1959         1979 
TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1976         1948         1937         1973         1972         1937 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JD 
        1958          851         1960         1940         1946         1970 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6516 
         906         1959          714          685          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         292          701           77          483          435          424 
TCGA-D6-A6EQ TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 
         368          575          775          622          369          340 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
        1131          658           15           92          585            3 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
           6          407           58          133          206            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61G 
          25           37           10           33         1057          360 
TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         378           14          111          112          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8ZA 
        1559         1120         1968          245          567          135 
TCGA-UF-A71E TCGA-UF-A7JF 
        1278         1497 

subtype1 subtype2 subtype3 
       4       11        2 
subtype1 subtype2 subtype3 
    5480     2886     3837 
subtype1 subtype2 subtype3 
   772.0    600.5    774.0 
[1] "4.0 - 5480.0 (772.0)"  "11.0 - 2886.0 (600.5)" "2.0 - 3837.0 (774.0)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      18       31        30        92         5         0
  subtype2       3       18        18        69         5         1
  subtype3       5       26        25        79         2         0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         18        3        5
  STAGE II        31       18       26
  STAGE III       30       18       25
  STAGE IVA       92       69       79
  STAGE IVB        5        5        2
  STAGE IVC        0        1        0
[1] 6 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       T0+T1 T2 T3 T4
  subtype1    26 56 41 54
  subtype2     5 29 25 57
  subtype3    16 44 28 53
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       26        5       16
  T2          56       29       44
  T3          41       25       28
  T4          54       57       53
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 64 25 72  3
  subtype2 58 12 34  4
  subtype3 47 26 50  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       64       58       47
  N1       25       12       26
  N2       72       34       50
  N3        3        4        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"
          vv
clus       M0 M1 MX
  subtype1 72  0 19
  subtype2 41  1 14
  subtype3 54  0 25
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       72       41       54
  M1        0        1        0
  MX       19       14       25
[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"
D8V7, binary
          cls
clus         0   1
  subtype1  56 133
  subtype2  44  87
  subtype3  34 138
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  133
  subtype2   44   87
  subtype3   34  138
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       44       34
  MALE        133       87      138
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   187
  subtype2                                   128
  subtype3                                   166
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   2
  subtype2                                                   2
  subtype3                                                   6
D8V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            187      128
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        2
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            166
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6
[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"
D8V9, binary
          cls
clus         0   1
  subtype1  35 154
  subtype2  14 117
  subtype3  31 141
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  154
  subtype2   14  117
  subtype3   31  141
     clus
vv    subtype1 subtype2 subtype3
  NO        35       14       31
  YES      154      117      141
[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"
D8V10, continuous
D8V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        12
  subtype2                                0     2                        17
  subtype3                                1     1                        14
          vv
clus       WHITE
  subtype1   159
  subtype2   109
  subtype3   152
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   8        2        1
  BLACK OR AFRICAN AMERICAN              12       17       14
  WHITE                                 159      109      152
[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"
D8V13, binary
          cls
clus         0   1
  subtype1  12 166
  subtype2   4 118
  subtype3   8 151
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  166
  subtype2    4  118
  subtype3    8  151
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12        4        8
  NOT HISPANIC OR LATINO      166      118      151
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 39 21
  subtype2 85 17
  subtype3 66 14
  subtype4 62 34
  subtype5 26 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      60      102       80       96       39 
subtype1 subtype2 subtype3 subtype4 subtype5 
      21       17       14       34       13 
$subtype1
TCGA-4P-AA8J TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 
         102          428         1955          594           45          432 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A49A TCGA-CN-A63V TCGA-CQ-5330 TCGA-CQ-5333 
         202          224          391          484         1393          341 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CA 
        1974         1407          985          509         1950         1963 
TCGA-CR-7397 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
         216         3295          584         1978         2437          519 
TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6945 TCGA-CV-6961 
         701          215         1970         1948         1969         1959 
TCGA-CV-7102 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1945         1444          954         1974         1948         1957 
TCGA-CV-7568 TCGA-CV-A464 TCGA-CV-A6JU TCGA-D6-6824 TCGA-D6-8568 TCGA-D6-A6EP 
        1961         1722          110           77          106          424 
TCGA-DQ-5630 TCGA-DQ-7594 TCGA-F7-8298 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
        1030          368          490           55           44           25 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-KU-A6H8 TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A8Z9 
         122          412          168         1954          400          149 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
         135          168         1043          735          665          214 

$subtype2
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DA 
         248         1288          725          895          918          351 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-7872 TCGA-C9-A47Z 
         182         1976          314          623          436            5 
TCGA-C9-A480 TCGA-CN-4742 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T 
           4         1988          443          535          904          225 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5331 TCGA-CQ-7064 TCGA-CQ-7065 
         348          175          367         1399         1560         1007 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         877         1353         1960          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
         391          303          514          379          479         1956 
TCGA-CV-5441 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-7427 TCGA-CV-A45O TCGA-CV-A45Q 
        2886         1478         1840         1937          851         1945 
TCGA-CV-A45R TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5480         1970         1075          906         1959          670 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-A4Z9 
         646          714          606          685         1950          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7588 
         376          483          232          368          548         1965 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         299           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
          14           13            6          407           58          414 
TCGA-HD-7753 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
           5           11           49          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L 
         485          441          588          360          440          351 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         360          552           14           34          392           56 
TCGA-MT-A67F TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 
         111         1726         1917         1968          553          357 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-UF-A7JC TCGA-UF-A7JS 
         218          228          225          387          484          413 

$subtype3
TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
         520          644           63          855          622          850 
TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 
         142          536          687          638         1153          624 
TCGA-CN-4739 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
        1330          629         1970         1110          318          394 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A6V3 TCGA-CQ-5332 TCGA-CQ-6228 TCGA-CQ-A4C9 
         645          526          298          317         1959          707 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562          358         1152          799         1777 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-7364 TCGA-CR-7374 TCGA-CR-7388 
        1050         1125          362         1435           30         1951 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 
         156          181          911         1955         1950         1438 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6960 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7418 
        2327         2641         1969         1095         1960         1955 
TCGA-CV-7424 TCGA-CV-7446 TCGA-CV-A461 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 
        1947         1958         1954          317          237          568 
TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7590 
         435          389          338          516          575          775 
TCGA-DQ-7591 TCGA-DQ-7595 TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A634 
         622          324          403           25           37           10 
TCGA-KU-A66S TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-QK-A8Z7 TCGA-QK-A8ZA 
         224          240         1559          578          198          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         157         1326         1663         1319         1252         1278 
TCGA-UF-A7JA TCGA-UF-A7JF 
        1894         1497 

$subtype4
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         623         1636          190          384          113          236 
TCGA-BB-4227 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6020 
         133         1975          630          933          628           98 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 
         735          432          429           46         1466         1207 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6229 
        1660         1422          129         1253         1057         1179 
TCGA-CQ-7063 TCGA-CQ-7069 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 
        1750         1274         1966         1971          354          234 
TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
         350         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          759          889          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         796         1954         1430          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7404 
         946          908          898          930         1077         1472 
TCGA-CV-5970 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 
         406         1315         1665         1899         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-7090 
        1959         3835         1948         1966         1957         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7428 
        1987         1979         1952          797         1099         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
         828          773          292          701          491          154 
TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-F7-7848 TCGA-H7-8502 TCGA-HD-7229 
         128         1778         1081         1131          133            2 

$subtype5
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-7861 TCGA-CN-4733 
        1747          451          216          187          310          642 
TCGA-CN-4738 TCGA-CN-5358 TCGA-CN-6017 TCGA-CN-A6V1 TCGA-CQ-5325 TCGA-CQ-6221 
        1960          173          629          223          654         1000 
TCGA-CQ-7068 TCGA-CR-5248 TCGA-CR-6470 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7385 
        1309         1663         1521         1969          311          997 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-7248 TCGA-CV-A45Y 
         522          546         1958          641         1967         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A468 TCGA-CX-7085 TCGA-DQ-7593 TCGA-DQ-7596 
        1940         1946         1977          321          369          340 
TCGA-F7-8489 TCGA-H7-A76A TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         658          206          378          112          254          910 
TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A6V9 
        1120          245          567 

subtype1 subtype2 subtype3 subtype4 subtype5 
      25        3       10        2      112 
subtype1 subtype2 subtype3 subtype4 subtype5 
    3295     5480     2641     3837     1977 
subtype1 subtype2 subtype3 subtype4 subtype5 
   551.5    481.0    666.0   1185.0    641.0 
[1] "25.0 - 3295.0 (551.5)"  "3.0 - 5480.0 (481.0)"   "10.0 - 2641.0 (666.0)" 
[4] "2.0 - 3837.0 (1185.0)"  "112.0 - 1977.0 (641.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       2       13         9        43         3         0
  subtype2       6       20        24        55         2         0
  subtype3       2        7        14        43         3         1
  subtype4      11       20        18        58         1         0
  subtype5       3       11         3        15         1         0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          2        6        2       11        3
  STAGE II        13       20        7       20       11
  STAGE III        9       24       14       18        3
  STAGE IVA       43       55       43       58       15
  STAGE IVB        3        2        3        1        1
  STAGE IVC        0        0        1        0        0
[1] 6 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       T0+T1 T2 T3 T4
  subtype1     4 21 13 32
  subtype2    11 36 25 37
  subtype3     5 17 21 28
  subtype4    13 31 21 43
  subtype5    11 12  5  7
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        4       11        5       13       11
  T2          21       36       17       31       12
  T3          13       25       21       21        5
  T4          32       37       28       43        7
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 28 10 27  1
  subtype2 45 20 34  1
  subtype3 26 11 28  3
  subtype4 41 17 36  0
  subtype5 14  2 15  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       28       45       26       41       14
  N1       10       20       11       17        2
  N2       27       34       28       36       15
  N3        1        1        3        0        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"
          vv
clus       M0 M1 MX
  subtype1 20  0  9
  subtype2 64  0 30
  subtype3 27  1 12
  subtype4 29  0  1
  subtype5 14  0  5
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       20       64       27       29       14
  M1        0        0        1        0        0
  MX        9       30       12        1        5
[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"
D9V7, binary
          cls
clus        0  1
  subtype1 20 52
  subtype2 43 80
  subtype3 17 74
  subtype4 32 84
  subtype5 11 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   52
  subtype2   43   80
  subtype3   17   74
  subtype4   32   84
  subtype5   11   34
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       20       43       17       32       11
  MALE         52       80       74       84       34
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    71
  subtype2                                   122
  subtype3                                    84
  subtype4                                   116
  subtype5                                    43
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
  subtype4                                                           0
  subtype5                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   1
  subtype2                                                   0
  subtype3                                                   7
  subtype4                                                   0
  subtype5                                                   2
D9V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             71      122
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        0
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             84      116
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                7        0
                                                             clus
vv                                                            subtype5
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             43
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2
[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"
D9V9, binary
          cls
clus         0   1
  subtype1   8  64
  subtype2   7 116
  subtype3  13  78
  subtype4  24  92
  subtype5   9  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   64
  subtype2    7  116
  subtype3   13   78
  subtype4   24   92
  subtype5    9   36
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         8        7       13       24        9
  YES       64      116       78       92       36
[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"
D9V10, continuous
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         9
  subtype2                                1     8                         4
  subtype3                                0     1                        13
  subtype4                                0     2                         8
  subtype5                                1     0                         6
          vv
clus       WHITE
  subtype1    59
  subtype2   107
  subtype3    75
  subtype4   100
  subtype5    37
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        1
  ASIAN                                   0        8        1        2        0
  BLACK OR AFRICAN AMERICAN               9        4       13        8        6
  WHITE                                  59      107       75      100       37
[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"
D9V13, binary
          cls
clus         0   1
  subtype1   3  62
  subtype2   7 109
  subtype3   3  77
  subtype4   7 105
  subtype5   3  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   62
  subtype2    7  109
  subtype3    3   77
  subtype4    7  105
  subtype5    3   39
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        7        3        7        3
  NOT HISPANIC OR LATINO       62      109       77      105       39
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  76  41
  subtype2 153  47
  subtype3  49  11
subtype1 subtype2 subtype3 
     117      200       60 
subtype1 subtype2 subtype3 
      41       47       11 
$subtype1
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BA-A8YP 
         102          248          384          113          216          142 
TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4733 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5370 
         436         1955          642         1988          173         1975 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
         594          629          432          202          224          318 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63V TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         432           46          484          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6229 
        1393          129         1974         1407          985         1179 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
        1560          509         1950          358         1971          514 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         379         1191          759          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         796         1954         1430          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 
         908          898          930          216         1077         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
        3295         1438          584         1978         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
         406          701         1478         1840         1315         1665 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 
        1970         1948         1969         1948         1966         1959 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        3837         1970         1970         1959         1945         1987 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 
        1952         1444          954         1974         1957         1984 
TCGA-CV-7435 TCGA-CV-7568 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JU TCGA-CV-A6K0 
        1959         1961         1722         1977          110          606 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 
         317          321          701          491          106          128 
TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7594 
         232         1778         1081         1030          548          368 
TCGA-F7-8298 TCGA-H7-8501 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A6HZ 
         490           58           55           44           25          111 
TCGA-IQ-A61H TCGA-KU-A6H8 TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A8Z9 TCGA-QK-AA3J 
         412          168         1954          400          149          157 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH 
        1043          735          665 

$subtype2
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IG 
         190          644          451           63          236          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ 
         622          918          850          351          182          314 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         623          187          133          310          536          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4738 
         638         1153          428          624            5         1960 
TCGA-CN-4739 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 
        1330          630          933          629          628           45 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
          98         1970         1110          394          735          429 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          535          904          645          225          526 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6228 
        1207         1399          317         1253         1057         1959 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CG TCGA-CQ-A4CI 
        1750         1309          877          707          391          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1966         1050         1125         1969          362          311 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          234          350          479         1956         1435 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
        1440         1245         1960          105         1979          889 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7398 TCGA-CR-7399 
          30          997         1951          392          156          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 
         911         1472         1955          522          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
        2327         1958         2641          215          641         1899 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 
        1952         1959         3835         1957         1969         1959 
TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1936         1939         1979         1095          797         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1960         1099         1955         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O 
        1972         1937         1958         1981         1958          851 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JY TCGA-CX-7086 
        1960         1940         1946         1954          646          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
         828          773          292           77          154          568 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 
         376          483          435          389          338          516 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 
        1965          575          775          622          369          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 
         340         1131          658           92            3            6 
TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         407          403          206            2           25           37 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
          49           10         1057          122          441          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67F 
         224          552          378           14           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          240          910         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         578         1968          245          387          567          198 
TCGA-QK-A8ZA TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         135         1326         1663         1319         1252         1278 
TCGA-UF-A7JA TCGA-UF-A7JF 
        1894         1497 

$subtype3
TCGA-BA-A4IF TCGA-BA-A6DG TCGA-C9-A480 TCGA-CN-A49A TCGA-CQ-5333 TCGA-CQ-6221 
         895         1976            4          391          341         1000 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1007         1274         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CV-6945 TCGA-CV-7410 TCGA-CV-A45Q 
         998          785          303         1969         1948         1945 
TCGA-CV-A45R TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5480         1970         1075          906         1959          670 
TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A6EQ 
         714          685         1950          539          424          368 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         299           15          585          384           14           13 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7630 
         133          414            5           11           33          485 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-MT-A51X TCGA-MT-A67A 
         588          440          351          360           34          392 
TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
        1726         1917          553          357          218          228 
TCGA-QK-A6II TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
         225          135          168          484          214          413 

subtype1 subtype2 subtype3 
      25        2        4 
subtype1 subtype2 subtype3 
    3837     3835     5480 
subtype1 subtype2 subtype3 
   913.0    652.0    484.5 
[1] "25.0 - 3837.0 (913.0)" "2.0 - 3835.0 (652.0)"  "4.0 - 5480.0 (484.5)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      14       22        22        72         3         0
  subtype2       7       33        31       108         4         1
  subtype3       3       16        15        34         3         0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         14        7        3
  STAGE II        22       33       16
  STAGE III       22       31       15
  STAGE IVA       72      108       34
  STAGE IVB        3        4        3
  STAGE IVC        0        1        0
[1] 6 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       T0+T1 T2 T3 T4
  subtype1    18 41 31 43
  subtype2    19 52 37 80
  subtype3     7 24 17 24
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       18       19        7
  T2          41       52       24
  T3          31       37       17
  T4          43       80       24
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 47 21 54  1
  subtype2 78 29 62  4
  subtype3 29 10 24  1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       47       78       29
  N1       21       29       10
  N2       54       62       24
  N3        1        4        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"
          vv
clus       M0 M1 MX
  subtype1 42  0 10
  subtype2 70  1 30
  subtype3 42  0 17
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       42       70       42
  M1        0        1        0
  MX       10       30       17
[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"
D10V7, binary
          cls
clus         0   1
  subtype1  44  97
  subtype2  60 167
  subtype3  19  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   97
  subtype2   60  167
  subtype3   19   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       60       19
  MALE         97      167       60
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   139
  subtype2                                   219
  subtype3                                    78
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   2
  subtype2                                                   8
  subtype3                                                   0
D10V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            139      219
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        8
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             78
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                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"
D10V9, binary
          cls
clus         0   1
  subtype1  26 115
  subtype2  33 194
  subtype3   2  77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26  115
  subtype2   33  194
  subtype3    2   77
     clus
vv    subtype1 subtype2 subtype3
  NO        26       33        2
  YES      115      194       77
[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"
D10V10, continuous
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         9
  subtype2                                1     4                        26
  subtype3                                1     5                         5
          vv
clus       WHITE
  subtype1   124
  subtype2   191
  subtype3    63
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   2        4        5
  BLACK OR AFRICAN AMERICAN               9       26        5
  WHITE                                 124      191       63
[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"
D10V13, binary
          cls
clus         0   1
  subtype1   8 127
  subtype2  10 198
  subtype3   5  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  127
  subtype2   10  198
  subtype3    5   67
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8       10        5
  NOT HISPANIC OR LATINO      127      198       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"
