[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/10005940/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/10668120/HNSC-TP.mergedcluster.txt"

nPatients in clinical file=423, in cluster file=528, common to both=423
[1]  10 423
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
149  83 151  34 
  1   2   3   4 
149  83 151  34 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
68 58 81 78 58 63 17 
 1  2  3  4  5  6  7 
68 58 81 78 58 63 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 
159 122 127 
  1   2   3 
159 122 127 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 42 141 123 102 
  1   2   3   4 
 42 141 123 102 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
120 169 132 
  1   2   3 
120 169 132 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
175  99 147 
  1   2   3 
175  99 147 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
128 137 119 
  1   2   3 
128 137 119 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 73 109  58  95  49 
  1   2   3   4   5 
 73 109  58  95  49 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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 423 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415           NA          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          113          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BB-4217 TCGA-BB-4223 
         216           NA          182           NA          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        2161          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         993          642          758          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
          NA         1330          811         1268           NA          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
         512          173           NA         1081          194           NA 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
          NA           NA           NA           NA           NA           NA 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          290          630          424          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98           NA 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202          424          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         119           NA          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         447          225          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
         367           NA         1466         1207          654           NA 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 
         129          870           NA           NA         1000         1407 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1057          985           NA           NA           NA          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968           NA          613           NA          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
          NA         1050         1125           NA          514           NA 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479           NA         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245           NA          105           NA          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
          30          972           NA         1036           NA          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
          NA          997         1430           NA          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         4241 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         3930         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        3270         2886         2327         2784         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        1315         1665          641         1899           NA           NA 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
          NA           NA         3835           NA           NA           NA 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         3381           NA           NA           NA           NA 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
          NA         3497         1724           NA         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
         954          797           NA           NA           NA           NA 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
          NA           NA           NA         1099           NA           NA 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
          NA           NA           NA         4335           NA           NA 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
          NA           NA           NA          851           NA           NA 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
          NA          750           NA          717          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         237          828           NA          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548           NA          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
          14           13           NA            6           NA          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
          25           NA           NA           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
         360          412           NA          440           NA          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
          56          111          112          254          910           NA 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
        1652          721           NA         1120           NA          578 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
        1917           NA           NA           NA           NA           NA 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
         400          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-UF-A7JV 
         225           64           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=150,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=270,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	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=49,	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=82,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	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=18,	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 423 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 40 111  86 133 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 40 111  86 133 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 40 111  86 133 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 40 111  86 133 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
137  56 133   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
137  56 133   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
137  56 133   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
137  56 133   7 
PATHOLOGY.M.STAGE, nv=2, 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=82, 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  78  42
  subtype2  52  21
  subtype3 105  27
  subtype4  22   8
subtype1 subtype2 subtype3 subtype4 
     120       73      132       30 
subtype1 subtype2 subtype3 subtype4 
      42       21       27        8 
$subtype1
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6868 
         462          283          415          248         1636          190 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-4224 
         451          384          113          236          182          278 
TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4726 
         133         1153          436            5          721          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 
         452          392          369          395          240         1988 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6024 
        1977         1966         1966          424          433          224 
TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5332 
         611          429          447          367         1422          317 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4CB 
         985         1959         1959         1007          509          545 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 
         358         1971         1969          379          350         1956 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7383 
        1191         1440         1960          759         1036         1954 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
         907         1955          522         1438          584         1978 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
        2886         2437          406         2641         1478         1315 
TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7090 
        1665         1969         1952         1969         1969         3837 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 
        1970         1970         1945         1724          954          797 
TCGA-CV-7248 TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7086 
        1967         1937         1981          750          717          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 
         828          292          701          491          154          128 
TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         112         1778         1081          548         1965          575 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W 
         299          564          490           92          585           14 
TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8635 TCGA-IQ-7630 
         133          403            2            5           25          485 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         360          440          210           34           56         1652 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
        1954         1968          400          553          228           64 

$subtype2
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A6D8 
        1983          276          520          644           63          513 
TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4725 
        2878          536          687          428          624          485 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6012 
         462          993         1330         1081          630          629 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A498 
        1970          424          318          394          119          443 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-A4C9 
         225          526          348         1466         1000          613 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6477 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 
         608         2562          514          234         1435         1245 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7398 TCGA-CR-7399 
         105         1979           30          392          156          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5978 
         911         1472         1950         3295          546          215 
TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 
        1970         1959         1957         1959         1939         1987 
TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1095         1099         1974         1955         1957         1947 
TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A461 TCGA-CX-7082 TCGA-D6-8568 TCGA-DQ-5629 
        1972         1959         1954          317          106          516 
TCGA-DQ-7595 TCGA-F7-A623 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A6HZ 
         324            6           37           55           44          111 
TCGA-IQ-A61O 
         360 

$subtype3
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-A4IF 
         722         1288         1762          725          623          895 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         216          187          140          558          310          423 
TCGA-BB-7866 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4733 
         638         1955            4          799          613          642 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1960          811         1268          512          173         1980 
TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 
        1980         1975          413          290          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A63V TCGA-CN-A63Y 
          45          432           98          202          484          175 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1207          654         1660         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7068 
         870         1057          815         1461         1378         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 
         901          877         1963          391          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-6484 TCGA-CR-6492 TCGA-CR-7376 
         362          311          345          354          479          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 
        1968          796          997         1430         1951          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-CV-5443 TCGA-CV-5971 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 
        1958          701         1899         1948         3835         1948 
TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 
        1959         1936         1959         1979         1444         1960 
TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q 
        1948         1937         1973         1984          851         1945 
TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-DQ-5630 TCGA-DQ-7590 
         321           77          568          104         1030          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A61V 
         622          369          368          340          658          384 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-7754 TCGA-HD-8634 
          13          407           58          414           25           24 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          11           49           10           33         1057          122 
TCGA-IQ-7632 TCGA-KU-A66S TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         441          224          111          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II 
        1120          578         1917          357          245          225 

$subtype4
TCGA-BA-5559 TCGA-BA-A6DA TCGA-CN-5355 TCGA-CN-6996 TCGA-CN-6998 TCGA-CQ-5330 
        1747          351          488          432           46          896 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CR-6467 TCGA-CR-7373 
         968         1960          548          393         1777          889 
TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6952 TCGA-CV-7254 
        2327          519         1840          641         1966         1976 
TCGA-CV-7434 TCGA-CV-A6JD TCGA-D6-6516 TCGA-F7-A50G TCGA-F7-A61S TCGA-IQ-A61E 
        1958         1970          773           15            3          588 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67G TCGA-QK-A6IG 
         412          351           14          392          112          218 

subtype1 subtype2 subtype3 subtype4 
       2        6        4        3 
subtype1 subtype2 subtype3 subtype4 
    3837     3295     3835     2327 
subtype1 subtype2 subtype3 subtype4 
   558.5    613.0    723.5    568.0 
[1] "2.0 - 3837.0 (558.5)" "6.0 - 3295.0 (613.0)" "4.0 - 3835.0 (723.5)"
[4] "3.0 - 2327.0 (568.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       9       18        23        77         5
  subtype2       3       11        13        41         1
  subtype3       9       28        27        60         2
  subtype4       3        6         8        14         1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          9        3        9        3
  STAGE II        18       11       28        6
  STAGE III       23       13       27        8
  STAGE IVA       77       41       60       14
  STAGE IVB        5        1        2        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       T1 T2 T3 T4
  subtype1 14 36 27 56
  subtype2  5 21 21 23
  subtype3 17 43 26 43
  subtype4  4  8 11  9
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       14        5       17        4
  T2       36       21       43        8
  T3       27       21       26       11
  T4       56       23       43        9
[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 40 19 59  3
  subtype2 24  9 28  1
  subtype3 59 21 33  2
  subtype4 13  7  9  1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       40       24       59       13
  N1       19        9       21        7
  N2       59       28       33        9
  N3        3        1        2        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"
D1V6, binary
          cls
clus        0  1
  subtype1 33 17
  subtype2 15  7
  subtype3 46 20
  subtype4 14  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   17
  subtype2   15    7
  subtype3   46   20
  subtype4   14    4
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       33       15       46       14
  MX       17        7       20        4
[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"
D1V7, binary
          cls
clus         0   1
  subtype1  35 114
  subtype2  19  64
  subtype3  54  97
  subtype4  13  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  114
  subtype2   19   64
  subtype3   54   97
  subtype4   13   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       19       54       13
  MALE        114       64       97       21
[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                                   149
  subtype2                                    80
  subtype3                                   147
  subtype4                                    34
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
  subtype4                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   2
  subtype3                                                   4
  subtype4                                                   0
D1V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            149       80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        2
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            147       34
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                4        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  35 114
  subtype2  13  70
  subtype3  28 123
  subtype4   3  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  114
  subtype2   13   70
  subtype3   28  123
  subtype4    3   31
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        35       13       28        3
  YES      114       70      123       31
[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     4                        14
  subtype2                                0     1                        10
  subtype3                                0     4                         8
  subtype4                                0     1                         1
          vv
clus       WHITE
  subtype1   123
  subtype2    71
  subtype3   136
  subtype4    31
D1V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   4        1        4        1
  BLACK OR AFRICAN AMERICAN              14       10        8        1
  WHITE                                 123       71      136       31
[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  10 134
  subtype2   3  75
  subtype3   3 141
  subtype4   2  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  134
  subtype2    3   75
  subtype3    3  141
  subtype4    2   31
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           10        3        3        2
  NOT HISPANIC OR LATINO      134       75      141       31
[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 41 19
  subtype2 39 11
  subtype3 47 19
  subtype4 42 23
  subtype5 47  8
  subtype6 36 13
  subtype7  8  8
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      60       50       66       65       55       49       16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      19       11       19       23        8       13        8 
$subtype1
TCGA-BA-5557 TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 
         623          216          187          436         1955            4 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 
         613          642         1960          173         1980         1966 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5331 
         594          629          202          432          654         1399 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CA 
        1974         1407         1959          815          968         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6492 
         545          303         1971         1969          379          479 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7391 
         972         1968          796         1954         1951          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CV-5971 TCGA-CV-6943 
         946          908          898          216          701         1948 
TCGA-CV-6961 TCGA-CV-7238 TCGA-CV-7410 TCGA-CV-7433 TCGA-CV-7568 TCGA-CX-7085 
        1959         1444         1948         1984         1961          321 
TCGA-D6-6824 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5630 TCGA-F7-8489 TCGA-F7-A620 
          77          106          112         1030          658           13 
TCGA-H7-A6C4 TCGA-HD-8634 TCGA-IQ-7632 TCGA-MT-A51W TCGA-P3-A6T8 TCGA-QK-A652 
         414           24          441           14          400          357 

$subtype2
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-7864 
         462          520          644          895          182          687 
TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 
        1153          452          462          993          240         1330 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6988 TCGA-CN-A63T TCGA-CN-A63U 
         811          512         1081          318          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CR-5247 
         484          348          367         1959          613          358 
TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6941 
        1435          759          156          911         2886         1959 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        1957         1969         1959         1095          797         1960 
TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-6823 
        1973         1959         1981         1954          237          701 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8224 
         324          564          384          403           37           55 
TCGA-IQ-7631 TCGA-KU-A66S 
         122          224 

$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 
         485          395         1988         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-6020 TCGA-CN-6998 TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6223 
         413           98           46         1422          870         1057 
TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4CE TCGA-CR-6477 
         985         1378         1007          901          393          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-A6JE TCGA-CV-A6JN 
        1945         1987         1979          954          750          717 
TCGA-D6-6517 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7592 
         292          128         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          210           34 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6II 
        1652         1954          578          553          228          225 

$subtype4
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 
         415          276          190          451          236          513 
TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4735 
         351          536          428          624          721          369 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         630          424          629          432         1970          424 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CQ-5332 
         224          611          394          119          429          317 
TCGA-CQ-6221 TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 
        1000          391          608          105         1979           30 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         392          907         1955         1950         3295         1438 
TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-7101 TCGA-CV-7235 
        1978          215         1969         1969         1939         1724 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1967         1976         1099         1955         1957         1947 
TCGA-CV-7430 TCGA-CV-7446 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6827 
        1972         1958          317          828          773          568 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7589 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 
         104          516          575           92           14            6 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61H TCGA-P3-A6T4 
          25          111          360          412         1968 

$subtype5
TCGA-BA-4077 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6871 TCGA-BB-4223 TCGA-BB-4225 
        1983         1762         1747           63         2878          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-CN-4741 TCGA-CN-5374 TCGA-CN-6013 
         558          310          638         1268          290          433 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CR-5243 TCGA-CR-5248 
         443          447          175         1466         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 
        1125          362          311          345          234         1245 
TCGA-CR-7385 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 
         997          181         1472          522         2327         1958 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-7100 TCGA-CV-7406 TCGA-DQ-7590 TCGA-DQ-7591 
         641         1970         1959         1974          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 
         369          368          340           25           44           10 
TCGA-HL-7533 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
        1057          112          254          910          721         1120 
TCGA-QK-A6IF 
         245 

$subtype6
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BB-7863 TCGA-C9-A47Z 
         722         1288          725         1636          423            5 
TCGA-CN-4722 TCGA-CN-4734 TCGA-CN-5363 TCGA-CN-6018 TCGA-CQ-5324 TCGA-CQ-5327 
         799          758         1977           45         1207         1660 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
         896          341          129         1461         1309          877 
TCGA-CQ-A4CD TCGA-CR-6484 TCGA-CR-7373 TCGA-CR-7386 TCGA-CR-7395 TCGA-CV-5444 
         548          354          889         1430          930         2437 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-7097 
         519         1840         1899         3835         1966         1970 
TCGA-CV-7099 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD 
        1936         1937         1958          851         1945         1970 
TCGA-D6-6825 TCGA-D6-6826 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-A4C1 
         491          154          407           58            2           11 
TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A6T2 
          49           33          588          392          111         1917 
TCGA-QK-A6IG 
         218 

$subtype7
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-5355 TCGA-CN-5361 TCGA-CQ-7067 TCGA-CQ-A4C7 
         142          392          488          194          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           64 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       4       37        3        6       10        2       56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1984     2886     3837     3295     2878     3835     1970 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   679.5    628.5    581.0    536.0    721.0    851.0    528.5 
[1] "4.0 - 1984.0 (679.5)"  "37.0 - 2886.0 (628.5)" "3.0 - 3837.0 (581.0)" 
[4] "6.0 - 3295.0 (536.0)"  "10.0 - 2878.0 (721.0)" "2.0 - 3835.0 (851.0)" 
[7] "56.0 - 1970.0 (528.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       8       11        12        33         0
  subtype2       2       10        11        29         1
  subtype3       6       13        16        35         2
  subtype4       2        8        11        43         2
  subtype5       2        5        10        17         1
  subtype6       3       14         8        31         3
  subtype7       1        3         3         9         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          8        2        6        2        2        3        1
  STAGE II        11       10       13        8        5       14        3
  STAGE III       12       11       16       11       10        8        3
  STAGE IVA       33       29       35       43       17       31        9
  STAGE IVB        0        1        2        2        1        3        0
[1] 5 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       T1 T2 T3 T4
  subtype1 13 21 11 20
  subtype2  4 14 14 21
  subtype3  8 24 22 19
  subtype4  4 17 15 31
  subtype5  7 13  9  8
  subtype6  3 17 12 27
  subtype7  1  5  3  7
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       13        4        8        4        7        3        1
  T2       21       14       24       17       13       17        5
  T3       11       14       22       15        9       12        3
  T4       20       21       19       31        8       27        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 25 11 25  0
  subtype2 26  7 16  1
  subtype3 26  8 29  1
  subtype4 17  9 32  2
  subtype5 12  8 12  1
  subtype6 27  9 12  2
  subtype7  4  4  7  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       25       26       26       17       12       27        4
  N1       11        7        8        9        8        9        4
  N2       25       16       29       32       12       12        7
  N3        0        1        1        2        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"
D2V6, binary
          cls
clus        0  1
  subtype1 30  5
  subtype2 11  9
  subtype3 23  9
  subtype4 12  7
  subtype5 12  9
  subtype6 14  9
  subtype7  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    5
  subtype2   11    9
  subtype3   23    9
  subtype4   12    7
  subtype5   12    9
  subtype6   14    9
  subtype7    7    0
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       30       11       23       12       12       14        7
  MX        5        9        9        7        9        9        0
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 24 44
  subtype2 10 48
  subtype3 29 52
  subtype4 18 60
  subtype5  7 51
  subtype6 32 31
  subtype7  3 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   44
  subtype2   10   48
  subtype3   29   52
  subtype4   18   60
  subtype5    7   51
  subtype6   32   31
  subtype7    3   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       24       10       29       18        7       32        3
  MALE         44       48       52       60       51       31       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                                    68
  subtype2                                    57
  subtype3                                    80
  subtype4                                    77
  subtype5                                    54
  subtype6                                    63
  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                                                   1
  subtype3                                                   0
  subtype4                                                   1
  subtype5                                                   4
  subtype6                                                   0
  subtype7                                                   0
D2V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             68       57
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        1
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             80       77
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        1
                                                             clus
vv                                                            subtype5 subtype6
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             54       63
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                4        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 53
  subtype2 10 48
  subtype3 14 67
  subtype4 19 59
  subtype5 13 45
  subtype6  7 56
  subtype7  3 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   53
  subtype2   10   48
  subtype3   14   67
  subtype4   19   59
  subtype5   13   45
  subtype6    7   56
  subtype7    3   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        15       10       14       19       13        7        3
  YES       53       48       67       59       45       56       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                                0     4                         2
  subtype2                                0     0                         8
  subtype3                                1     1                         4
  subtype4                                0     2                        10
  subtype5                                0     0                         3
  subtype6                                0     3                         4
  subtype7                                0     0                         2
          vv
clus       WHITE
  subtype1    59
  subtype2    48
  subtype3    71
  subtype4    65
  subtype5    55
  subtype6    55
  subtype7    14
D2V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   4        0        1        2        0
  BLACK OR AFRICAN AMERICAN               2        8        4       10        3
  WHITE                                  59       48       71       65       55
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   3        0
  BLACK OR AFRICAN AMERICAN               4        2
  WHITE                                  55       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  1 64
  subtype2  2 51
  subtype3  6 73
  subtype4  4 71
  subtype5  2 52
  subtype6  2 60
  subtype7  1 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   64
  subtype2    2   51
  subtype3    6   73
  subtype4    4   71
  subtype5    2   52
  subtype6    2   60
  subtype7    1   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        6        4        2        2
  NOT HISPANIC OR LATINO       64       51       73       71       52       60
                        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 29 16
  subtype3 16 14
  subtype4 28 24
subtype1 subtype2 subtype3 subtype4 
      42       45       30       52 
subtype1 subtype2 subtype3 subtype4 
      21       16       14       24 
$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          485          142          452          613          392 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 
         642          369         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          462         1268          488          512 
TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6024 
         194          290          630          433          424          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          424         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          240          811         1988 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
         173         1081         1966         1975          413          629 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 
         594          629          432          202          119          432 
TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
          46          654         1660          896          129          870 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5436 
        1000          985         1959          815         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         1724 
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 
   723.5   1095.0   1752.5    925.0 
[1] "45.0 - 3837.0 (723.5)"   "63.0 - 3295.0 (1095.0)" 
[3] "113.0 - 2327.0 (1752.5)" "46.0 - 2641.0 (925.0)"  
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       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
  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"
D3V6, binary
          cls
clus       0
  subtype1 9
  subtype2 6
  subtype3 1
  subtype4 6
[1] "NOT AVAILABLE: table only has an event [0]"
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 32 35
  subtype3 27 13
subtype1 subtype2 subtype3 
      62       67       40 
subtype1 subtype2 subtype3 
      27       35       13 
$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          452          392          642 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 
         369         1330          488         1980          194         1977 
TCGA-CN-5366 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5329 
        1966          424          433           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          485          142          613 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 
         993          395          240          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          424          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          896          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         1724         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 
         462          758         1960         1988          512         1980 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6021 TCGA-CN-6994 TCGA-CQ-5323 TCGA-CQ-5324 
         413          290         1970          119         1466         1207 
TCGA-CQ-6218 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6941 
         870          815         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 
  1204.0    993.0    980.5 
[1] "45.0 - 3837.0 (1204.0)" "46.0 - 3295.0 (993.0)"  "77.0 - 2641.0 (980.5)" 
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       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
  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"
D4V6, binary
          cls
clus       0
  subtype1 9
  subtype2 8
  subtype3 5
[1] "NOT AVAILABLE: table only has an event [0]"
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 103  36
  subtype2  68  36
  subtype3  78  27
subtype1 subtype2 subtype3 
     139      104      105 
subtype1 subtype2 subtype3 
      36       36       27 
$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-A6D8 TCGA-BB-4217 
         644           63          236          895          513          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
        2878          140          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4727 
         638         1153          428          624          721          452 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5356 
         993          369         1960         1330         1268          512 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6021 
        1081          194          290          630          629         1970 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 
         424          318          394          119          429          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5332 
         447          225          526          348         1466          317 
TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
        1000         1959          613          545          548          391 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6481 
        1777         1521         1050         1125         1969          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         345          354          234         1435         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
         105         1979           30          997         1951          392 
TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         908          156          181          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5443 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6935 
         522         1950         1958          215          641         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6960 TCGA-CV-7100 TCGA-CV-7101 
        1952         1959         3835         1969         1959         1939 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1724         1095          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 
        1099         1948         1955         1957         1947         1972 
TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JD TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
        1981         1954         1970          701           77          154 
TCGA-D6-6827 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
         568          516          575          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I 
         368          324          340          564          658           92 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61G 
          25           44           10         1057          122          360 
TCGA-KU-A66S TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         224          254          910          721         1120          578 
TCGA-QK-A64Z 
         553 

$subtype2
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BB-7872 
         283          248         1747          113          216          436 
TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        1955          485          613          642          395          240 
TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
         811          488          173         1977         1966         1966 
TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
        1975          433          594          629           45          432 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5329 
         202          224          611          432          654         1422 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 
         896          341         1974         1407          985         1959 
TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CH 
         815          509          968         1960         1963          303 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 
        1971          514          379         1191          759          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        1968          796         1954         1430          913          946 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
         216         1077         3295         1438          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-6441 TCGA-CV-6934 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 
        1970         1948         1959         1970         1970         1945 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7435 TCGA-CX-7082 TCGA-CX-7085 
        1444          954         1974         1959          317          321 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 
         491          106          128          112         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A61V TCGA-F7-A61W 
        1030          548          299          490          384           14 
TCGA-F7-A620 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-IQ-A61E 
          13          414            5           55           25          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 
         412          440          360         1652         1954         1917 
TCGA-P3-A6T8 TCGA-QK-A652 
         400          357 

$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-A6DA TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7863 
         451          384          351          182          278          423 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
           5            4          799          142          392          462 
TCGA-CN-4734 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5373 TCGA-CN-6011 
         758         1988         1980         1980          413          424 
TCGA-CN-6020 TCGA-CN-6998 TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 
          98           46          367         1207         1660         1399 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
         129          870         1057         1461         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CE TCGA-CR-6471 TCGA-CR-6491 TCGA-CR-6492 
         901          877          393         1966          350          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7394 
        1956         1440          889         1036          907          898 
TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 
         930          546         2886         2327         2641         1840 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1665         1899         1948         1969         1966         1957 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7427 
        3837         1959         1936         1987         1979         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1973         1937         1984         1958          851         1945 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         750          717          237          828          773          292 
TCGA-D6-A4ZB TCGA-DQ-7588 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 
         104         1965           15          585            3            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8634 
         407           58          133            2           37           24 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-KU-A66T 
          11           49           33          485          441          210 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T4 
          14           34          392           56          111         1968 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

subtype1 subtype2 subtype3 
      10        5        2 
subtype1 subtype2 subtype3 
    3835     3295     3837 
subtype1 subtype2 subtype3 
     630      648      725 
[1] "10.0 - 3835.0 (630.0)" "5.0 - 3295.0 (648.0)"  "2.0 - 3837.0 (725.0)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       3       18        28        69         4
  subtype2      14       20        17        61         2
  subtype3       7       23        23        60         3
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3       14        7
  STAGE II        18       20       23
  STAGE III       28       17       23
  STAGE IVA       69       61       60
  STAGE IVB        4        2        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       T1 T2 T3 T4
  subtype1 11 33 32 49
  subtype2 18 39 26 32
  subtype3 10 33 26 48
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       11       18       10
  T2       33       39       33
  T3       32       26       26
  T4       49       32       48
[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 43 19 44  4
  subtype2 39 15 52  2
  subtype3 50 19 33  1
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       39       50
  N1       19       15       19
  N2       44       52       33
  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"
D5V6, binary
          cls
clus        0  1
  subtype1 33 18
  subtype2 36 11
  subtype3 35 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   18
  subtype2   36   11
  subtype3   35   14
    clus
vv   subtype1 subtype2 subtype3
  M0       33       36       35
  MX       18       11       14
[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  35 124
  subtype2  33  89
  subtype3  48  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  124
  subtype2   33   89
  subtype3   48   79
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       33       48
  MALE        124       89       79
[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                                   153
  subtype2                                   121
  subtype3                                   127
          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                                                   6
  subtype2                                                   0
  subtype3                                                   0
D5V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            153      121
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6        0
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            127
  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  32 127
  subtype2  29  93
  subtype3  20 107
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  127
  subtype2   29   93
  subtype3   20  107
     clus
vv    subtype1 subtype2 subtype3
  NO        32       29       20
  YES      127       93      107
[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                                0     2                        16
  subtype2                                1     4                         7
  subtype3                                0     4                        10
          vv
clus       WHITE
  subtype1   137
  subtype2   104
  subtype3   111
D5V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   2        4        4
  BLACK OR AFRICAN AMERICAN              16        7       10
  WHITE                                 137      104      111
[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   6 142
  subtype2   8 110
  subtype3   3 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  142
  subtype2    8  110
  subtype3    3  121
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        8        3
  NOT HISPANIC OR LATINO      142      110      121
[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 31  8
  subtype2 79 42
  subtype3 74 24
  subtype4 65 25
subtype1 subtype2 subtype3 subtype4 
      39      121       98       90 
subtype1 subtype2 subtype3 subtype4 
       8       42       24       25 
$subtype1
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-7864 
         462          520          644          895          182          687 
TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4739 TCGA-CN-5356 
        1153          452          462          993         1330          512 
TCGA-CN-6988 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-A4C9 
         318          225          526          348          367          613 
TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5441 
         358         1435          156          911         1950         2886 
TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        1959         1957         1969         1095          797         1960 
TCGA-CV-7428 TCGA-CV-7440 TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-6823 TCGA-DQ-7595 
        1973         1981         1954          237          701          324 
TCGA-F7-7848 TCGA-F7-A61V TCGA-KU-A66S 
         564          384          224 

$subtype2
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BB-4224 TCGA-BB-7872 
         283          248          113          216          278          436 
TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 
        1955            5            4          485          613          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
         395          240          811         1988          488          173 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1081         1977         1966         1966         1975          413 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
         433          594          629           45          432          202 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5327 
         224          611          432           46          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 
        1422          896          341         1974         1407          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1959          815         1007          509          968         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 
        1963          303         1971          514          379         1956 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1191          759          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 
        1954         1430          913          946          908          216 
TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 
        1077         3295         1438          584         1978         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         519          406          701         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 
        1665         1970         1948         1948         1966         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 
        1970         1970         1945         1444          954         1974 
TCGA-CV-7435 TCGA-CV-A45Q TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6825 TCGA-D6-8568 
        1959         1945          317          321          491          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         128          112         1778         1081         1030          548 
TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C4 TCGA-HD-7753 
         299          490           14           13          414            5 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
          55           44           25          588          412          440 
TCGA-MT-A51X TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 
          34         1652         1954         1917          400          357 
TCGA-QK-A6II 
         225 

$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-A6DA TCGA-BB-7863 TCGA-CN-4722 
         190          451          384          351          423          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4734 TCGA-CN-4738 TCGA-CN-5365 
         721          142          392          758         1960         1980 
TCGA-CN-6011 TCGA-CN-6994 TCGA-CN-A498 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 
         424          119          443         1399          129          870 
TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB 
        1057         1461         1309          901          877          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6471 TCGA-CR-6478 TCGA-CR-6484 
         548          393          391         1966         1969          354 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7389 TCGA-CR-7394 
         350          479         1440          889          392          898 
TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6942 
         930          546         2327         2641         1899         3835 
TCGA-CV-6945 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 
        1969         3837         1959         1936         1987         1979 
TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1948         1937         1937         1984         1958          851 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1970          750          717          828          773          292 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-DQ-7588 TCGA-F7-8489 TCGA-F7-A50G 
          77          154          104         1965          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
          92          585            3            6          407           58 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
         133            2           37           24           11           49 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A51W 
          33          485          441          360          210           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A64Z 
         392           56          111          578         1968          553 
TCGA-QK-A6IH TCGA-QK-A6IJ 
         228           64 

$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-A6D8 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         513          187         2878          140          558          310 
TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4735 TCGA-CN-4741 
         536          638          428          624          369         1268 
TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6020 
        1980          194          290          630          629           98 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A49B TCGA-CQ-5323 
        1970          424          394          429          447         1466 
TCGA-CQ-5324 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-A4CI TCGA-CR-5243 
        1207          317         1000         1959          608         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 
        1663         1152          799         1777         1521         1050 
TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7369 
        1125          311          345          234         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 
         105         1979           30          997         1951          907 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5443 TCGA-CV-5978 
         181         1472         1955          522         1958          215 
TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7235 
         641         1969         1952         1959         1939         1724 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1967         1976         1099         1955         1957         1947 
TCGA-CV-7430 TCGA-D6-6827 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1972          568          516          575          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-HD-7754 TCGA-HD-A634 TCGA-HL-7533 
         369          368          340           25           10         1057 
TCGA-IQ-7631 TCGA-IQ-A61O TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         122          360          254          910          721         1120 

subtype1 subtype2 subtype3 subtype4 
     156        4        2       10 
subtype1 subtype2 subtype3 subtype4 
    2886     3295     3837     2878 
subtype1 subtype2 subtype3 subtype4 
   644.0    759.0    565.5    681.0 
[1] "156.0 - 2886.0 (644.0)" "4.0 - 3295.0 (759.0)"   "2.0 - 3837.0 (565.5)"  
[4] "10.0 - 2878.0 (681.0)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       0        6        10        20         1
  subtype2      15       21        23        72         2
  subtype3       6       23        20        57         3
  subtype4       3       11        15        41         3
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0       15        6        3
  STAGE II         6       21       23       11
  STAGE III       10       23       20       15
  STAGE IVA       20       72       57       41
  STAGE IVB        1        2        3        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       T1 T2 T3 T4
  subtype1  1  9 11 16
  subtype2 22 42 34 36
  subtype3  9 30 19 52
  subtype4  7 24 20 25
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1       22        9        7
  T2        9       42       30       24
  T3       11       34       19       20
  T4       16       36       52       25
[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 18  5 11  1
  subtype2 43 19 61  2
  subtype3 54 16 26  1
  subtype4 17 13 31  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       18       43       54       17
  N1        5       19       16       13
  N2       11       61       26       31
  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"
D6V6, binary
          cls
clus        0  1
  subtype1  7  6
  subtype2 43 11
  subtype3 34 17
  subtype4 20  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    6
  subtype2   43   11
  subtype3   34   17
  subtype4   20    9
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        7       43       34       20
  MX        6       11       17        9
[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  6 36
  subtype2 43 98
  subtype3 48 75
  subtype4 19 83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   36
  subtype2   43   98
  subtype3   48   75
  subtype4   19   83
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       43       48       19
  MALE         36       98       75       83
[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                                    41
  subtype2                                   140
  subtype3                                   123
  subtype4                                    97
          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                                                   4
D6V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             41      140
  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                            123       97
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        4
[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  36
  subtype2  34 107
  subtype3  15 108
  subtype4  26  76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   36
  subtype2   34  107
  subtype3   15  108
  subtype4   26   76
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       34       15       26
  YES       36      107      108       76
[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                                0     1                         8
  subtype4                                0     1                        10
          vv
clus       WHITE
  subtype1    34
  subtype2   118
  subtype3   110
  subtype4    90
D6V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   0        8        1        1
  BLACK OR AFRICAN AMERICAN               7        8        8       10
  WHITE                                  34      118      110       90
[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  38
  subtype2   7 130
  subtype3   5 112
  subtype4   4  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   38
  subtype2    7  130
  subtype3    5  112
  subtype4    4   93
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        7        5        4
  NOT HISPANIC OR LATINO       38      130      112       93
[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  89  17
  subtype2 101  41
  subtype3  69  42
subtype1 subtype2 subtype3 
     106      142      111 
subtype1 subtype2 subtype3 
      17       41       42 
$subtype1
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 
         462          415          248          722         1288          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DA 
         623         1636          190          644          895          351 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7866 TCGA-C9-A47Z 
         182          187          278          423          638            5 
TCGA-C9-A480 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-5361 
           4          142          452          392          462          194 
TCGA-CN-5365 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
        1980          413          424           46          443          447 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5331 TCGA-CQ-5334 
         225          526          348          367         1399          129 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
        1000         1461         1378          877          968          545 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-6478 TCGA-CR-6491 TCGA-CR-6492 
         393          391          303         1969          350          479 
TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7390 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 
        1956          889          907          930          546         2886 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-7235 TCGA-CV-7410 
        2327         2641         1840         1899         1724         1948 
TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A6JN TCGA-CX-7086 
        1937         1937         1981          851          717          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-DQ-5631 TCGA-DQ-7588 
         828          773          701          112          548         1965 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         575          369          658           15          585            3 
TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
         384           13            6           58          133            2 
TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
           5           24           11           49          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L 
        1057          485          441          588          360          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
         210           14          392           56          111          254 
TCGA-P3-A5QA TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
        1652          218          225           64 

$subtype2
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6871 
        1983          276         1762          520          451           63 
TCGA-BA-A6D8 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         513         2878          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4722 
         536          687         1153          428          624          799 
TCGA-CN-4723 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
         721          993          369         1960         1330         1268 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
         512         1980         1081          290          630          629 
TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
         433           45         1970          424          318          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         119          429          484          175         1466         1207 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7068 TCGA-CQ-7069 
         317          870         1057         1959         1309          901 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         613          548          608         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         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1125          362          311          345          354          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-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 
        1957         1969         3837         1959         1936         1959 
TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1939         1095          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7434 
        1099         1974         1955         1947         1972         1958 
TCGA-CV-7435 TCGA-CV-7446 TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 
        1959         1958         1954         1970          750          317 
TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7591 
         292          154          568          104          516          622 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-H7-7774 
         324          340          564          490           92          407 
TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-7631 TCGA-IQ-A61O 
         403           25           37           10          122          360 
TCGA-KU-A66S TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         224          112          910          721         1120          578 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH 
        1968          553          245          228 

$subtype3
TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BB-7872 
        1747          384          113          236          216          436 
TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        1955          485          613          642          395          240 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5366 
         811         1988          488          173         1977         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
        1966         1975          594          629          432           98 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5327 
         202          224          611          432          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 
        1422          896          341         1974         1407          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1959          815         1007          509         1960         1963 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 
        1971          514          379         1191          759          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 
        1968         1036          796         1954         1430          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 
         946          908          898          216         1077         3295 
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-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 
        1478         1315         1665         1970         1948         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 
        1948         1969         1966         1959         1970         1970 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7422 
        1945         1987         1979         1444          954         1957 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CX-7085 TCGA-D6-6824 
        1973         1984         1961         1945          321           77 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         491          106          128         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-IQ-A61H TCGA-IQ-A61J TCGA-MT-A51X TCGA-P3-A6SX 
          44           25          412          440           34         1954 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 
        1917          400          357 

subtype1 subtype2 subtype3 
       2       10       14 
subtype1 subtype2 subtype3 
    2886     3837     3835 
subtype1 subtype2 subtype3 
     442      721      913 
[1] "2.0 - 2886.0 (442.0)"  "10.0 - 3837.0 (721.0)" "14.0 - 3835.0 (913.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       8       19        26        49         2
  subtype2       5       21        24        83         5
  subtype3      11       23        20        65         2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          8        5       11
  STAGE II        19       21       23
  STAGE III       26       24       20
  STAGE IVA       49       83       65
  STAGE IVB        2        5        2
[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       T1 T2 T3 T4
  subtype1 12 33 26 35
  subtype2 10 35 34 61
  subtype3 18 42 25 37
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       12       10       18
  T2       33       35       42
  T3       26       34       25
  T4       35       61       37
[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 44 20 31  2
  subtype2 54 16 51  4
  subtype3 37 20 51  1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       44       54       37
  N1       20       16       20
  N2       31       51       51
  N3        2        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"
D7V6, binary
          cls
clus        0  1
  subtype1 43 21
  subtype2 32 19
  subtype3 33  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   21
  subtype2   32   19
  subtype3   33    8
    clus
vv   subtype1 subtype2 subtype3
  M0       43       32       33
  MX       21       19        8
[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"
D7V7, binary
          cls
clus         0   1
  subtype1  39  81
  subtype2  43 126
  subtype3  41  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   81
  subtype2   43  126
  subtype3   41   91
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39       43       41
  MALE         81      126       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                                   120
  subtype2                                   163
  subtype3                                   131
          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                                                   0
  subtype2                                                   5
  subtype3                                                   1
D7V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            120      163
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        5
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            131
  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  15 105
  subtype2  33 136
  subtype3  32 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15  105
  subtype2   33  136
  subtype3   32  100
     clus
vv    subtype1 subtype2 subtype3
  NO        15       33       32
  YES      105      136      100
[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                                0     4                         9
  subtype2                                0     2                        17
  subtype3                                1     4                         6
          vv
clus       WHITE
  subtype1   103
  subtype2   148
  subtype3   115
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   4        2        4
  BLACK OR AFRICAN AMERICAN               9       17        6
  WHITE                                 103      148      115
[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   5 110
  subtype2   5 154
  subtype3   8 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  110
  subtype2    5  154
  subtype3    8  121
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        5        8
  NOT HISPANIC OR LATINO      110      154      121
[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  99  49
  subtype2  58  25
  subtype3 102  26
subtype1 subtype2 subtype3 
     148       83      128 
subtype1 subtype2 subtype3 
      49       25       26 
$subtype1
TCGA-BA-5149 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         248          623         1747          384          113          236 
TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z 
         895          216          182          436         1955            5 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 
           4          485          142          613          642          395 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
         240          811         1988          488          173         1081 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 
        1977         1966         1966         1975          413          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 
         594          629          432           98          202          224 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63V TCGA-CQ-5325 TCGA-CQ-5327 
         611          432           46          484          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6222 
        1422          896          341          129         1974         1407 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959          815         1378         1007          509 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6474 
         968         1960         1963          393          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-7390 TCGA-CR-7391 
        1036          796         1954         1430          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 
         946          908          898          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-6945 TCGA-CV-6952 
        1970         1948         1969         1948         1969         1966 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 
        1959         1970         1970         1945         1987         1444 
TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45Q 
         954         1974         1957         1984         1961         1945 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         317          321          491          106          128          112 
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-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         490           15          585          384           14           13 
TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
         414            5           55           44           24           25 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         111          485          588          412          440          351 
TCGA-IQ-A61O TCGA-MT-A51X TCGA-MT-A67A TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 
         360           34          392         1652         1954         1917 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II 
         400          357          218          225 

$subtype2
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A6D8 
         415         1288          520         1636          451          513 
TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4729 
         133          423         1153          799          721          392 
TCGA-CN-4730 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5361 TCGA-CN-5365 
         462         1960         1330          512          194         1980 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
         630          424           45          318          394          119 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6221 
         225          526          348          367          317         1000 
TCGA-CQ-6223 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-6478 
        1057          901          877          613          548         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-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 
         156          181          911          522          546         2886 
TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 
         215         1959         1957         1959         1939         1724 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7418 
        1095          797         1967         1960         1099         1955 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A461 TCGA-CV-A6JE 
        1947         1959         1981         1958         1954          750 
TCGA-CX-7086 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7595 
         237          154          568          516         1965          324 
TCGA-H7-A6C5 TCGA-HD-A633 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A66T 
         403           49          122          441          224          210 
TCGA-MT-A67D TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
          56          578          553          228           64 

$subtype3
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         462         1983          276          722         1762          725 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A6DA TCGA-BB-4217 TCGA-BB-4223 
         190          644           63          351          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         278          140          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 
         638          428          624          452          993          369 
TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 
        1268         1980          290          629         1970          424 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         429          443          447          175         1466         1207 
TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4CB 
        1399          870         1959         1461         1309          545 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          608         2562          358         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-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         362          311          234          350          479         1956 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7385 
        1440         1245         1960         1979          889          997 
TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5443 
         392          930         1472         1955         2327         1958 
TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6960 
        2641          641         1899         1952         3835         1969 
TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7254 TCGA-CV-7410 
        3837         1936         1959         1979         1976         1948 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45O 
        1937         1973         1972         1937         1958          851 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
        1970          717          828          773          292          701 
TCGA-D6-6824 TCGA-D6-A4ZB TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
          77          104          575          775          622          369 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 
         340          564          658           92            3            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         407           58          133            2           25           37 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61G TCGA-MT-A51W 
          11           10           33         1057          360           14 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         1120 
TCGA-P3-A6T4 TCGA-QK-A6IF 
        1968          245 

subtype1 subtype2 subtype3 
       4       30        2 
subtype1 subtype2 subtype3 
    3295     2886     3837 
subtype1 subtype2 subtype3 
   635.5    546.0    709.0 
[1] "4.0 - 3295.0 (635.5)"  "30.0 - 2886.0 (546.0)" "2.0 - 3837.0 (709.0)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1      17       28        34        82         2
  subtype2       2       13        14        49         5
  subtype3       5       22        22        66         2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         17        2        5
  STAGE II        28       13       22
  STAGE III       34       14       22
  STAGE IVA       82       49       66
  STAGE IVB        2        5        2
[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       T1 T2 T3 T4
  subtype1 25 53 42 44
  subtype2  3 20 19 42
  subtype3 12 37 24 47
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       25        3       12
  T2       53       20       37
  T3       42       19       24
  T4       44       42       47
[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 56 28 65  2
  subtype2 39  7 26  4
  subtype3 40 21 42  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       56       39       40
  N1       28        7       21
  N2       65       26       42
  N3        2        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"
D8V6, binary
          cls
clus        0  1
  subtype1 55 17
  subtype2 19 11
  subtype3 34 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55   17
  subtype2   19   11
  subtype3   34   20
    clus
vv   subtype1 subtype2 subtype3
  M0       55       19       34
  MX       17       11       20
[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"
D8V7, binary
          cls
clus         0   1
  subtype1  54 121
  subtype2  37  62
  subtype3  32 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54  121
  subtype2   37   62
  subtype3   32  115
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       54       37       32
  MALE        121       62      115
[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                                   173
  subtype2                                    98
  subtype3                                   143
          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                                                   1
  subtype2                                                   1
  subtype3                                                   4
D8V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            173       98
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        1
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            143
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                4
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1  38 137
  subtype2  12  87
  subtype3  30 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38  137
  subtype2   12   87
  subtype3   30  117
     clus
vv    subtype1 subtype2 subtype3
  NO        38       12       30
  YES      137       87      117
[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                         8
  subtype2                                0     2                        11
  subtype3                                0     0                        13
          vv
clus       WHITE
  subtype1   150
  subtype2    85
  subtype3   131
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   8        2        0
  BLACK OR AFRICAN AMERICAN               8       11       13
  WHITE                                 150       85      131
[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  11 159
  subtype2   3  93
  subtype3   4 133
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  159
  subtype2    3   93
  subtype3    4  133
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           11        3        4
  NOT HISPANIC OR LATINO      159       93      133
[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 94 13
  subtype2 87 35
  subtype3 56 39
subtype1 subtype2 subtype3 
     107      122       95 
subtype1 subtype2 subtype3 
      13       35       39 
$subtype1
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 TCGA-BA-A4IF 
         248         1288          725          623          644          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 
         513          351          182          423          687          436 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
           5            4           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         526          348          175          367         1207          654 
TCGA-CQ-5331 TCGA-CQ-6221 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1399         1000         1378         1007          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960          613         1963          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6492 TCGA-CR-6493 
         303          608          514         1969          479         1956 
TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        1950         2886         2327         2641         1478         1840 
TCGA-CV-6003 TCGA-CV-7427 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE 
        1665         1937          851         1945         1970          750 
TCGA-CV-A6JN TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5631 TCGA-DQ-7588 
         717          128          112          104          548         1965 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         622          299           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 
         384           14           13            6           58          414 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
         403            5           24           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
         111           33          485          441          588          360 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 
         910         1652         1917         1968          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          228          225           64 

$subtype2
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         520         1636         1747          190          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 
         384          113          187          133          310          536 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-6010 
         638         1153          624         1960         1330          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 
         424          629          433         1970          424          318 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 
         394          429         1466          317          870         1057 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
        1959         1461         1309         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-6484 TCGA-CR-6487 TCGA-CR-6491 
         362          311          345          354          234          350 
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-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         889           30          997         1951          392          907 
TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 
         913          908          898          930          156          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5439 
         911         1472         1955          522         1438          546 
TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1958          641         1899         1969         1952         1959 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7242 
        1966         1969         1959         1936         1939         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 
         797         1967         1960         1976         1099         1955 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 
        1947         1973         1972         1937         1959         1981 
TCGA-CV-7446 TCGA-CV-A461 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1958         1954          317          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5624 
         292          701          491          154          568         1778 
TCGA-DQ-5629 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         516          775          369          324          340          564 
TCGA-F7-8489 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
         658          407            2           25           37         1057 
TCGA-P3-A5QE TCGA-P3-A6SW 
         721         1120 

$subtype3
TCGA-BA-7269 TCGA-BA-A6DB TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4733 TCGA-CN-4742 
         236          216          428         1955          642         1988 
TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         173         1975          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
          98          202          224          611          119          432 
TCGA-CN-A63V TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 
         484         1660         1422          896          341          129 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 
        1974         1407          985         1959          815          509 
TCGA-CQ-7069 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6488 TCGA-CR-7365 
         901          545          358         1971          379         1191 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         759          972         1968         1036          796         1954 
TCGA-CR-7386 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5436 
        1430          946          216         1077         3295          584 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 
        1978         2437          519          406          701          215 
TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1315         1970         1948         3835         1948         1969 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        1957         1959         3837         1970         1970         1959 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1945         1987         1979         1724         1444          954 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7568 
        1974         1948         1957         1984         1958         1961 
TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 
         321           77          106         1081         1030          575 
TCGA-DQ-7594 TCGA-F7-8298 TCGA-H7-8502 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         368          490          133           55           44           25 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T8 
         122          412         1954          578          400 

subtype1 subtype2 subtype3 
       3        2       25 
subtype1 subtype2 subtype3 
    2886     2562     3837 
subtype1 subtype2 subtype3 
   436.0    902.5    946.0 
[1] "3.0 - 2886.0 (436.0)"  "2.0 - 2562.0 (902.5)"  "25.0 - 3837.0 (946.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       7       19        32        50         3
  subtype2       8       18        16        62         2
  subtype3       8       24        19        61         2
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          7        8        8
  STAGE II        19       18       24
  STAGE III       32       16       19
  STAGE IVA       50       62       61
  STAGE IVB        3        2        2
[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       T1 T2 T3 T4
  subtype1 14 37 30 32
  subtype2 12 23 27 45
  subtype3 12 40 23 39
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       14       12       12
  T2       37       23       40
  T3       30       27       23
  T4       32       45       39
[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 42 21 37  2
  subtype2 46 13 37  2
  subtype3 34 20 45  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       42       46       34
  N1       21       13       20
  N2       37       37       45
  N3        2        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"
D9V6, binary
          cls
clus        0  1
  subtype1 48 35
  subtype2 25  4
  subtype3 22  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   35
  subtype2   25    4
  subtype3   22    9
    clus
vv   subtype1 subtype2 subtype3
  M0       48       25       22
  MX       35        4        9
[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"
D9V7, binary
          cls
clus         0   1
  subtype1  46  82
  subtype2  31 106
  subtype3  37  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   82
  subtype2   31  106
  subtype3   37   82
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       46       31       37
  MALE         82      106       82
[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                                   124
  subtype2                                   135
  subtype3                                   118
          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                                                   3
  subtype2                                                   2
  subtype3                                                   1
D9V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            124      135
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                3        2
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            118
  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"
D9V9, binary
          cls
clus         0   1
  subtype1   9 119
  subtype2  30 107
  subtype3  23  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  119
  subtype2   30  107
  subtype3   23   96
     clus
vv    subtype1 subtype2 subtype3
  NO         9       30       23
  YES      119      107       96
[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"
D9V10, continuous
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                         7
  subtype2                                0     2                        16
  subtype3                                0     1                         7
          vv
clus       WHITE
  subtype1   108
  subtype2   117
  subtype3   106
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   7        2        1
  BLACK OR AFRICAN AMERICAN               7       16        7
  WHITE                                 108      117      106
[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"
D9V13, binary
          cls
clus         0   1
  subtype1   6 115
  subtype2   5 126
  subtype3   7 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  115
  subtype2    5  126
  subtype3    7  108
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        5        7
  NOT HISPANIC OR LATINO      115      126      108
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 40 12
  subtype2 63 31
  subtype3 49  6
  subtype4 49 30
  subtype5 36  8
subtype1 subtype2 subtype3 subtype4 subtype5 
      52       94       55       79       44 
subtype1 subtype2 subtype3 subtype4 subtype5 
      12       31        6       30        8 
$subtype1
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-A6DE 
         248         1288          623         1636          384          182 
TCGA-BB-7863 TCGA-CQ-5324 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
         423         1207         1422          129          870         1000 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-6471 
         901          877          545          548          391         1966 
TCGA-CR-7367 TCGA-CR-7390 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-7090 TCGA-CV-7099 
        1440          907         1899         3835         3837         1936 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 
        1959         1979         1724         1973         1937         1958 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-DQ-7588 
        1970          750          237          828          292         1965 
TCGA-F7-A61W TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
          14          133           37           11           49           33 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67D TCGA-P3-A6T0 
         441          360          360          210           56          578 
TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
        1917          553          228           64 

$subtype2
TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BB-4227 
         520          644           63          236          513          133 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4738 
         536          687         1153          428          624         1960 
TCGA-CN-4739 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 
        1330          630          424          629           45           98 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
        1970          424          318          394          119          429 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6223 
         225          526          348          367          317         1057 
TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6470 TCGA-CR-6472 
        1959          613          608          358         1521         1050 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         345          354          234         1435         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7393 
         105         1979           30         1951          392          908 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         156          181          911         1472         1955          522 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 
         546         2886          215          641         1969         1952 
TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7242 
        1959         1957         1969         1959         1939         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 
         797         1967         1960         1976         1099         1955 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A461 
        1947         1972         1959         1981         1958         1954 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7589 
          77          154          568          104          516          575 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7754 
         324          564           92            6          403           25 
TCGA-HD-A634 TCGA-IQ-7631 TCGA-KU-A66S TCGA-P3-A6T4 
          10          122          224         1968 

$subtype3
TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A6DA TCGA-BB-4217 TCGA-BB-7861 
         725          190          451          351          187          310 
TCGA-BB-7866 TCGA-C9-A47Z TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CQ-5323 
         638            5          443          447          175         1466 
TCGA-CQ-5331 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
        1399         1461         1309         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
         799         1777         1125         1969          362          311 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7385 TCGA-CV-5442 
         350          479         1956          889          997         2327 
TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-A45O TCGA-CV-A6JN 
        1958         2641         1948         1937          851          717 
TCGA-D6-6516 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8489 
         773          775          622          369          340          658 
TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HL-7533 TCGA-MT-A51W 
           3          407           58            2         1057           14 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         1120 
TCGA-QK-A6IF 
         245 

$subtype4
TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BB-8596 TCGA-CN-4733 TCGA-CN-4742 
        1747          113          216         1955          642         1988 
TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         173         1975          433          594          629          432 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A63V TCGA-CQ-5327 
         202          224          611          432          484         1660 
TCGA-CQ-5330 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
         896         1974         1407          985         1959          815 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CR-6474 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 
        1378          509         1971          379         1191          759 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
         972         1968         1036          796         1954         1430 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 
         913          946          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-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6943 
         701         1315         1665         1970         1948         1948 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7180 
        1966         1959         1970         1970         1945         1987 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 TCGA-CX-7082 
        1444          954         1974         1957         1984          317 
TCGA-CX-7085 TCGA-D6-6825 TCGA-D6-8568 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         321          491          106         1778         1081         1030 
TCGA-DQ-7594 TCGA-F7-8298 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-P3-A6SX 
         368          490           55           44           25         1954 
TCGA-P3-A6T8 
         400 

$subtype5
TCGA-BA-A4IF TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5333 
         895          436            4           46          654          341 
TCGA-CQ-7065 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CH 
        1007          968         1960         1963          393          303 
TCGA-CR-6477 TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6945 
         514          898          930         1478         1840         1969 
TCGA-CV-7568 TCGA-CV-A45Q TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5631 
        1961         1945          701          128          112          548 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-A6C4 
         299           15          585          384           13          414 
TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H 
           5           24          111          485          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A51X TCGA-MT-A67A TCGA-P3-A5QA TCGA-QK-A652 
         440          351           34          392         1652          357 
TCGA-QK-A6IG TCGA-QK-A6II 
         218          225 

subtype1 subtype2 subtype3 subtype4 subtype5 
      11        6        2       25        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
    3837     2886     2641     3295     1969 
subtype1 subtype2 subtype3 subtype4 subtype5 
   686.5    591.5    717.0   1030.0    425.0 
[1] "11.0 - 3837.0 (686.5)"  "6.0 - 2886.0 (591.5)"   "2.0 - 2641.0 (717.0)"  
[4] "25.0 - 3295.0 (1030.0)" "4.0 - 1969.0 (425.0)"  
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       0       15        12        36         3
  subtype2       3       13        17        59         2
  subtype3       4        7        11        14         1
  subtype4      10       13        16        51         0
  subtype5       6       13        11        13         1
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        3        4       10        6
  STAGE II        15       13        7       13       13
  STAGE III       12       17       11       16       11
  STAGE IVA       36       59       14       51       13
  STAGE IVB        3        2        1        0        1
[1] 5 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       T1 T2 T3 T4
  subtype1  2 21 12 32
  subtype2  7 20 27 40
  subtype3  8 14  7 10
  subtype4 13 27 23 27
  subtype5  8 18 11  7
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        7        8       13        8
  T2       21       20       14       27       18
  T3       12       27        7       23       11
  T4       32       40       10       27        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 18  1
  subtype2 32 12 40  2
  subtype3 15 10  9  1
  subtype4 24 16 41  0
  subtype5 23  6 11  1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       28       32       15       24       23
  N1       10       12       10       16        6
  N2       18       40        9       41       11
  N3        1        2        1        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"
D10V6, binary
          cls
clus        0  1
  subtype1 18 13
  subtype2 19 11
  subtype3 13  9
  subtype4 22  5
  subtype5 23 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   13
  subtype2   19   11
  subtype3   13    9
  subtype4   22    5
  subtype5   23   10
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       18       19       13       22       23
  MX       13       11        9        5       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 24 49
  subtype2 25 84
  subtype3 19 39
  subtype4 32 63
  subtype5 14 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   49
  subtype2   25   84
  subtype3   19   39
  subtype4   32   63
  subtype5   14   35
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       25       19       32       14
  MALE         49       84       39       63       35
[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                                    72
  subtype2                                   107
  subtype3                                    55
  subtype4                                    94
  subtype5                                    49
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           1
  subtype2                                                           0
  subtype3                                                           0
  subtype4                                                           0
  subtype5                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   2
  subtype3                                                   3
  subtype4                                                   1
  subtype5                                                   0
D10V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             72      107
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        2
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             55       94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                3        1
                                                             clus
vv                                                            subtype5
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             49
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1  9 64
  subtype2 19 90
  subtype3  9 49
  subtype4 22 73
  subtype5  3 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   64
  subtype2   19   90
  subtype3    9   49
  subtype4   22   73
  subtype5    3   46
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       19        9       22        3
  YES       64       90       49       73       46
[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"
D10V10, continuous
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         5
  subtype2                                0     2                        14
  subtype3                                0     1                         7
  subtype4                                0     1                         3
  subtype5                                1     5                         1
          vv
clus       WHITE
  subtype1    64
  subtype2    91
  subtype3    50
  subtype4    87
  subtype5    39
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   1        2        1        1        5
  BLACK OR AFRICAN AMERICAN               5       14        7        3        1
  WHITE                                  64       91       50       87       39
[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"
D10V13, binary
          cls
clus        0  1
  subtype1  5 65
  subtype2  4 97
  subtype3  0 56
  subtype4  6 88
  subtype5  3 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   65
  subtype2    4   97
  subtype3    0   56
  subtype4    6   88
  subtype5    3   43
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        4        0        6        3
  NOT HISPANIC OR LATINO       65       97       56       88       43
[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"
