[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"        "-oTREAD-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/READ-TP/11541704/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/11589276/READ-TP.mergedcluster.txt"

nPatients in clinical file=171, in cluster file=169, common to both=169
[1]  12 169
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
25 22 22 
 1  2  3 
25 22 22 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
 6 13 13  9  8  9  8  3 
 1  2  3  4  5  6  7  8 
 6 13 13  9  8  9  8  3 
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
66 32 31 36 
 1  2  3  4 
66 32 31 36 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
29 39 30 
 1  2  3 
29 39 30 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
33 43 54 
 1  2  3 
33 43 54 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
25 25 30  6 30 14 
 1  2  3  4  5  6 
25 25 30  6 30 14 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
34 30 33 66 
 1  2  3  4 
34 30 33 66 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
56 35 41 31 
 1  2  3  4 
56 35 41 31 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
18 42 17 10 56 
 1  2  3  4  5 
18 42 17 10 56 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
24 63 56 
 1  2  3 
24 63 56 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
 9 14 15 13 
 1  2  3  4 
 9 14 15 13 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
10 13 18  5  5 
 1  2  3  4  5 
10 13 18  5  5 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 169 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         734          546          524         1309          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-4110 TCGA-AF-5654 
         387         1148           NA         1146          441          257 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
         468          609          316         2635         2007          360 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
          NA          365          974          244          215           31 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
          61           NA           31         1400           NA           NA 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 
        1035           NA         1522          366          184           NA 
TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
          NA           30          485          608           NA          608 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
          NA          243           30          912           31         1003 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
          30           30           NA          608           31           NA 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3891 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1124          518          548          396         1065          426 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
          31         1461           NA          974          608          853 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 
        1096          427           31          518           NA           NA 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          30          638          424          183          790          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
        1126          485         1096          276           31          365 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
         943         2130         1947          334           NA         1520 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
          NA           NA         1885         1247         1157         3562 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
          15           44            6           21           22          140 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
          55          310          184          184           NA          212 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
         285          144          425         1826          243          334 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
         335          457          395          365          425          457 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        1095          216          914          394          397          306 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
         161         3846         1258         1741         3932          734 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
        1566          992           15           73          625          607 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
         636          517          556          482          538          497 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
         496          499          262          350          328          415 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
         531          364          257           NA         1141          952 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
         452           12           31           20           21           16 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
          34           23           14           NA         1696           NA 
TCGA-G5-6641 
         804 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=118,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=10,	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] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 169 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=49, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  30 115  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  30 115  14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  30 115  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  30 115  14 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
86 45 35 
[1] "table(vv)"
vv
N0 N1 N2 
86 45 35 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
86 45 35 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
86 45 35 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=18, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 20  4
  subtype2 17  2
  subtype3 15  4
subtype1 subtype2 subtype3 
      24       19       19 
subtype1 subtype2 subtype3 
       4        2        4 
$subtype1
TCGA-AF-2689 TCGA-AF-2692 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 
       17.95        13.55        36.03         8.02         2.01         1.02 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3887 TCGA-AG-3894 
       34.03        12.03         7.99         0.99        36.95        14.01 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X 
       36.03         9.07        12.00        49.97        38.96        41.00 

$subtype2
TCGA-AF-2691 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       43.04        12.72        12.00        32.02         7.07         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       46.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 
       19.99        29.98         0.99        19.99         1.02        13.02 
TCGA-AG-3902 
       32.02 

$subtype3
TCGA-AF-3913 TCGA-AG-3584 TCGA-AG-3609 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       10.39        24.00        19.99        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A026 
       17.03        15.95         1.02        31.00        51.98         1.94 
TCGA-AG-A032 
       38.04 

subtype1 subtype2 subtype3 
    0.99     0.99     1.02 
subtype1 subtype2 subtype3 
   49.97    50.04    51.98 
subtype1 subtype2 subtype3 
   15.98    13.02    19.99 
[1] "1.0 - 50.0 (16.0)" "1.0 - 50.0 (13.0)" "1.0 - 52.0 (20.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8        1         7         2          3          0        4
  subtype2       7        1         8         0          2          2        2
  subtype3       3        1         5         0          5          2        6
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        7        3
  STAGE II          1        1        1
  STAGE IIA         7        8        5
  STAGE III         2        0        0
  STAGE IIIB        3        2        5
  STAGE IIIC        0        2        2
  STAGE IV          4        2        6
[1] 7 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  3  6 16  0
  subtype2  2  5 15  0
  subtype3  0  4 14  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        2        0
  T2        6        5        4
  T3       16       15       14
  T4        0        0        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 16  5  4
  subtype2 16  4  2
  subtype3 10  6  6
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       16       16       10
  N1        5        4        6
  N2        4        2        6
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1 21  4
  subtype2 20  2
  subtype3 16  6
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       21       20       16
  M1        4        2        6
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 12 13
  subtype2  9 13
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   13
  subtype2    9   13
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12        9       10
  MALE         13       13       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1 19  3
  subtype2 18  3
  subtype3 21  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    3
  subtype2   18    3
  subtype3   21    1
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                19       18       21
  RECTAL MUCINOUS ADENOCARCINOMA        3        3        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1  0 25
  subtype2  1 21
  subtype3  0 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   25
  subtype2    1   21
  subtype3    0   22
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        0
  YES       25       21       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 22  0  3
  subtype2 19  0  2
  subtype3 16  1  5
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       22       19       16
  R1        0        0        1
  R2        3        2        5
[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"
D1V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     2
  subtype2                         0     2
  subtype3                         1     0
D1V12, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        2        1 
character(0)

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1  4  2
  subtype2  8  1
  subtype3 13  0
  subtype4  5  2
  subtype5  7  1
  subtype6  7  1
  subtype7  6  2
  subtype8  2  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       6        9       13        7        8        8        8        3 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        1        0        2        1        1        2        1 
$subtype1
TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3593 TCGA-AG-3726 TCGA-AG-3894 
       17.95        36.03         8.02        34.03         7.99        14.01 

$subtype2
TCGA-AF-2691 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3887 
       43.04        12.72        12.00        46.03         2.01        36.95 
TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A02X 
       13.02        32.02        41.00 

$subtype3
TCGA-AF-2692 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       13.55        12.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L 
       12.00 

$subtype4
TCGA-AF-3913 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       10.39        48.03        28.04        36.03        14.04        17.03 
TCGA-AG-A026 
        1.94 

$subtype5
TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3728 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
       32.02        24.00        29.98        35.01         1.02        19.99 
TCGA-AG-A01N TCGA-AG-A032 
       31.00        38.04 

$subtype6
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        7.07         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3878 TCGA-AG-A011 
        0.99        37.02 

$subtype7
TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
        1.02        19.99        19.99        19.99         1.02        17.03 
TCGA-AG-4007 TCGA-AG-A02G 
        1.02        38.96 

$subtype8
TCGA-AG-3586 TCGA-AG-A023 TCGA-AG-A025 
        1.02        51.98        49.97 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    7.99     2.01     0.99     1.94     1.02     0.99     1.02     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   36.03    46.03    36.03    48.03    38.04    50.04    38.96    51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   15.98    32.02    13.55    17.03    30.49     6.56    18.51    49.97 
[1] "8.0 - 36.0 (16.0)" "2.0 - 46.0 (32.0)" "1.0 - 36.0 (13.6)"
[4] "1.9 - 48.0 (17.0)" "1.0 - 38.0 (30.5)" "1.0 - 50.0 (6.6)" 
[7] "1.0 - 39.0 (18.5)" "1.0 - 52.0 (50.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       2        1         2         0          0          0        1
  subtype2       4        1         6         0          2          0        0
  subtype3       5        0         4         1          2          0        1
  subtype4       0        1         4         0          1          1        2
  subtype5       1        0         1         0          4          0        2
  subtype6       2        0         3         0          0          2        2
  subtype7       3        0         0         0          1          1        3
  subtype8       1        0         0         1          0          0        1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           2        4        5        0        1        2        3
  STAGE II          1        1        0        1        0        0        0
  STAGE IIA         2        6        4        4        1        3        0
  STAGE III         0        0        1        0        0        0        0
  STAGE IIIB        0        2        2        1        4        0        1
  STAGE IIIC        0        0        0        1        0        2        1
  STAGE IV          1        0        1        2        2        2        3
            clus
vv           subtype8
  STAGE I           1
  STAGE II          0
  STAGE IIA         0
  STAGE III         1
  STAGE IIIB        0
  STAGE IIIC        0
  STAGE IV          1
[1] 7 8
[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  1  4  0
  subtype2  2  2  9  0
  subtype3  1  4  8  0
  subtype4  0  0  7  2
  subtype5  0  2  6  0
  subtype6  0  2  7  0
  subtype7  0  4  3  1
  subtype8  1  0  1  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        1        2        1        0        0        0        0        1
  T2        1        2        4        0        2        2        4        0
  T3        4        9        8        7        6        7        3        1
  T4        0        0        0        2        0        0        1        1
[1] 4 8
[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
  subtype1  5  0  1
  subtype2 11  2  0
  subtype3  9  3  1
  subtype4  5  2  2
  subtype5  3  4  1
  subtype6  5  1  3
  subtype7  3  3  2
  subtype8  1  0  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        5       11        9        5        3        5        3        1
  N1        0        2        3        2        4        1        3        0
  N2        1        0        1        2        1        3        2        2
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1  5  1
  subtype2 13  0
  subtype3 12  1
  subtype4  7  2
  subtype5  6  2
  subtype6  7  2
  subtype7  5  3
  subtype8  2  1
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  M0        5       13       12        7        6        7        5        2
  M1        1        0        1        2        2        2        3        1
[1] 2 8
[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 4 2
  subtype2 5 8
  subtype3 6 7
  subtype4 3 6
  subtype5 4 4
  subtype6 3 6
  subtype7 3 5
  subtype8 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    5    8
  subtype3    6    7
  subtype4    3    6
  subtype5    4    4
  subtype6    3    6
  subtype7    3    5
  subtype8    3    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        4        5        6        3        4        3        3
  MALE          2        8        7        6        4        6        5
        clus
vv       subtype8
  FEMALE        3
  MALE          0
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1  6  0
  subtype2  8  4
  subtype3 10  1
  subtype4  9  0
  subtype5  7  1
  subtype6  8  1
  subtype7  8  0
  subtype8  2  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    0
  subtype2    8    4
  subtype3   10    1
  subtype4    9    0
  subtype5    7    1
  subtype6    8    1
  subtype7    8    0
  subtype8    2    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                 6        8       10        9        7
  RECTAL MUCINOUS ADENOCARCINOMA        0        4        1        0        1
                                clus
vv                               subtype6 subtype7 subtype8
  RECTAL ADENOCARCINOMA                 8        8        2
  RECTAL MUCINOUS ADENOCARCINOMA        1        0        0
[1] 2 8
[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  0  6
  subtype2  1 12
  subtype3  0 13
  subtype4  0  9
  subtype5  0  8
  subtype6  0  9
  subtype7  0  8
  subtype8  0  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    1   12
  subtype3    0   13
  subtype4    0    9
  subtype5    0    8
  subtype6    0    9
  subtype7    0    8
  subtype8    0    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         0        1        0        0        0        0        0        0
  YES        6       12       13        9        8        9        8        3
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  6  0  0
  subtype2 12  0  0
  subtype3 12  0  1
  subtype4  7  1  1
  subtype5  6  0  2
  subtype6  7  0  2
  subtype7  5  0  3
  subtype8  2  0  1
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0        6       12       12        7        6        7        5        2
  R1        0        0        0        1        0        0        0        0
  R2        0        0        1        1        2        2        3        1
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     1
  subtype2                         0     2
  subtype3                         0     1
  subtype4                         1     0
  subtype5                         0     0
  subtype6                         0     0
  subtype7                         0     0
  subtype8                         0     0
D2V12, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        2        1        1 
character(0)

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 55  7
  subtype2 26  3
  subtype3 25  4
  subtype4 25  8
subtype1 subtype2 subtype3 subtype4 
      62       29       29       33 
subtype1 subtype2 subtype3 subtype4 
       7        3        4        8 
$subtype1
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        13.55        12.72 
TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.45        12.00         8.02         2.01         1.02        46.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 
       50.04        12.03         7.99         0.99         1.02         0.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4008 
        1.02        17.03        13.02        14.01        48.03        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
       20.98        13.94        37.02        70.03        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       49.97        61.97         1.45         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 
        6.05         6.05         6.97         4.73        13.97        15.02 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6506 
       13.97        30.05        12.95         5.29        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 
       19.96        20.91        18.28        17.69         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 
       13.64        17.46         8.45         9.96        37.51         0.53 
TCGA-F5-6861 TCGA-G5-6235 
        1.12        55.76 

$subtype2
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3609 TCGA-AG-3728 
       19.10        37.74        14.50        15.39        19.99        29.98 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A00C 
       35.01         1.02        28.04        14.04         0.99         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A032 
       25.97        23.01        36.03        12.00        38.96        38.04 
TCGA-CI-6623 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6881 TCGA-EI-7002 
        9.37        15.02       129.27        24.13        16.41        11.97 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 
       31.30         0.39         0.66         0.76        18.28 

$subtype3
TCGA-AF-3913 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3593 TCGA-AG-3608 
       10.39        86.63        11.84         7.07        34.03        15.95 
TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A016 
       19.99         0.99        19.99        19.99        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A026 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
       31.00         1.94         7.99        10.98        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DG TCGA-EF-5831 
       12.00        36.00        10.06       126.44        51.48         2.40 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-F5-6811 TCGA-G5-6572 
       15.85        16.34        16.31         1.02        47.08 

$subtype4
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       20.02        10.39        65.98        36.03        32.02         1.02 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3887 
       24.00         2.01         6.05         0.99        32.98        36.95 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A02X 
       32.02         1.02        15.95         1.02        64.01        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CL-5917 TCGA-DC-6158 TCGA-DC-6682 
        0.49         0.69         0.72        60.03         7.10        13.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6883 TCGA-F5-6702 
       41.36        57.24         0.49        17.00        11.51        14.86 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
        0.69         0.46        26.43 

subtype1 subtype2 subtype3 subtype4 
    0.53     0.39     0.99     0.46 
subtype1 subtype2 subtype3 subtype4 
   70.03   129.27   126.44    65.98 
subtype1 subtype2 subtype3 subtype4 
  13.595   18.280   15.850   14.860 
[1] "0.5 - 70.0 (13.6)"  "0.4 - 129.3 (18.3)" "1.0 - 126.4 (15.8)"
[4] "0.5 - 66.0 (14.9)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1      17        4        12         1         0         4          6
  subtype2       4        1         7         0         1         1          1
  subtype3       5        1        12         0         0         0          0
  subtype4       4        2         9         1         1         0          2
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          6          4        7         4
  subtype2          8          4        3         2
  subtype3          7          0        3         2
  subtype4          2          7        5         1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          17        4        5        4
  STAGE II          4        1        1        2
  STAGE IIA        12        7       12        9
  STAGE IIB         1        0        0        1
  STAGE IIC         0        1        0        1
  STAGE III         4        1        0        0
  STAGE IIIA        6        1        0        2
  STAGE IIIB        6        8        7        2
  STAGE IIIC        4        4        0        7
  STAGE IV          7        3        3        5
  STAGE IVA         4        2        2        1
[1] 11  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  5 16 41  4
  subtype2  2  3 24  3
  subtype3  1  5 22  2
  subtype4  1  5 25  5
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5        2        1        1
  T2       16        3        5        5
  T3       41       24       22       25
  T4        4        3        2        5
[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
  subtype1 37 18 11
  subtype2 12 10 10
  subtype3 19  9  2
  subtype4 17  8 10
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       37       12       19       17
  N1       18       10        9        8
  N2       11       10        2       10
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 52  8   1  4
  subtype2 24  3   1  4
  subtype3 24  5   0  1
  subtype4 26  6   0  4
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        52       24       24       26
  M1         8        3        5        6
  M1A        1        1        0        0
  MX         4        4        1        4
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 33 33
  subtype2 13 19
  subtype3 17 14
  subtype4 13 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   33
  subtype2   13   19
  subtype3   17   14
  subtype4   13   23
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       33       13       17       13
  MALE         33       19       14       23
[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"
D3V8, binary
          cls
clus        0  1
  subtype1 54  9
  subtype2 30  0
  subtype3 31  0
  subtype4 31  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54    9
  subtype2   30    0
  subtype3   31    0
  subtype4   31    4
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                54       30       31       31
  RECTAL MUCINOUS ADENOCARCINOMA        9        0        0        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"
D3V9, binary
          cls
clus        0  1
  subtype1  3 63
  subtype2  2 30
  subtype3  0 31
  subtype4  1 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   63
  subtype2    2   30
  subtype3    0   31
  subtype4    1   35
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        2        0        1
  YES       63       30       31       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 52  1  4  1
  subtype2 25  0  1  0
  subtype3 23  1  2  1
  subtype4 23  0  5  2
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       52       25       23       23
  R1        1        0        1        0
  R2        4        1        2        5
  RX        1        0        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    36
  subtype2     0                         0    15
  subtype3     0                         5    13
  subtype4     0                         1    17
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        5        1
  WHITE                           36       15       13       17
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 25  4
  subtype2 33  5
  subtype3 23  3
subtype1 subtype2 subtype3 
      29       38       26 
subtype1 subtype2 subtype3 
       4        5        3 
$subtype1
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-4022 TCGA-AG-A01Y 
       24.13        37.74        86.63        65.98         0.99        64.01 
TCGA-AH-6549 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-5869 
        0.20         4.60         6.05         4.73        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD 
       12.00        15.02        36.00         7.10       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6885 TCGA-EI-7002 
      129.27        51.48         0.49        16.34        13.64        11.97 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6864 TCGA-G5-6641 
       37.51        14.86         0.39         0.46        26.43 

$subtype2
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       17.23        19.10        14.50        20.02        10.39        11.84 
TCGA-AG-3732 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 
       32.98         0.49         1.45         1.81        10.19         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 
        9.37        13.97        60.03        10.98        11.01        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EI-6506 
       30.05        12.95        13.05        41.36        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-6917 
       19.96        17.00        15.85        16.41        10.78        17.46 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        9.96        31.30         0.66         0.69         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

$subtype3
TCGA-AF-6136 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 
       15.39         1.02         0.99        70.03        10.98         1.94 
TCGA-AG-A02N TCGA-AG-A036 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CL-5918 
       61.97       117.11         0.69         0.72         6.05         7.99 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 
       10.06         5.29        24.13         2.40        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-7004 TCGA-F5-6811 
       17.69        16.31         8.61        11.51         8.45         1.02 
TCGA-F5-6814 TCGA-G5-6233 
        0.53        18.28 

subtype1 subtype2 subtype3 
    0.20     0.49     0.53 
subtype1 subtype2 subtype3 
  129.27    60.03   117.11 
subtype1 subtype2 subtype3 
  15.020   13.970    9.335 
[1] "0.2 - 129.3 (15.0)" "0.5 - 60.0 (14.0)"  "0.5 - 117.1 (9.3)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       5        2         5         1         0         0          1
  subtype2       5        0         7         1         0         1          8
  subtype3       1        4         8         0         2         3          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          4        3         4
  subtype2          6          5        1         2
  subtype3          4          2        2         3
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           5        5        1
  STAGE II          2        0        4
  STAGE IIA         5        7        8
  STAGE IIB         1        1        0
  STAGE IIC         0        0        2
  STAGE III         0        1        3
  STAGE IIIA        1        8        0
  STAGE IIIB        3        6        4
  STAGE IIIC        4        5        2
  STAGE IV          3        1        2
  STAGE IVA         4        2        3
[1] 11  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  2  4 20  3
  subtype2  1  7 24  6
  subtype3  1  2 25  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        1        1
  T2        4        7        2
  T3       20       24       25
  T4        3        6        2
[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
  subtype1 13  8  7
  subtype2 15 15  8
  subtype3 15  7  7
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       13       15       15
  N1        8       15        7
  N2        7        8        7
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 19  6   1  3
  subtype2 28  1   1  7
  subtype3 23  3   0  4
D4V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        19       28       23
  M1         6        1        3
  M1A        1        1        0
  MX         3        7        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 12 17
  subtype2 16 23
  subtype3 16 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   17
  subtype2   16   23
  subtype3   16   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       16       16
  MALE         17       23       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"
D4V8, binary
          cls
clus        0  1
  subtype1 28  1
  subtype2 36  1
  subtype3 26  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    1
  subtype2   36    1
  subtype3   26    4
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                28       36       26
  RECTAL MUCINOUS ADENOCARCINOMA        1        1        4
[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"
D4V9, binary
          cls
clus        0  1
  subtype1  2 27
  subtype2  2 37
  subtype3  1 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   27
  subtype2    2   37
  subtype3    1   29
     clus
vv    subtype1 subtype2 subtype3
  NO         2        2        1
  YES       27       37       29
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 20  0  0  2
  subtype2 26  1  0  1
  subtype3 20  1  2  2
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       20       26       20
  R1        0        1        1
  R2        0        0        2
  RX        2        1        2
[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"
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         4    23
  subtype2     0                         1    36
  subtype3     1                         0    18
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN        4        1        0
  WHITE                           23       36       18
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 20  8
  subtype2 37  4
  subtype3 41 10
subtype1 subtype2 subtype3 
      28       41       51 
subtype1 subtype2 subtype3 
       8        4       10 
$subtype1
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 
       17.95        17.23        12.72        36.03         7.07         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3742 
        2.01        12.03         6.05        19.99         1.02         0.99 
TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-DC-5337 TCGA-DC-6156 
        0.99        36.03         1.02        17.03        15.02        15.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 
       12.95        10.06         5.29         9.96        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        0.66         0.69         0.76        47.08 

$subtype2
TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3882 TCGA-AG-3891 TCGA-AG-3893 
       10.39        37.68        20.02        19.99        18.02        35.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 
       48.03        32.02        14.04         0.99        25.97        15.95 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02N TCGA-AG-A02X 
        1.02        31.00        70.03        64.01        61.97        41.00 
TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 
      117.11         1.45         0.69         0.72        10.19         7.99 
TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EI-6506 
       11.01         7.10        30.05        13.05        41.36        20.55 
TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6465 
       19.96        15.85        16.34        16.41        17.46        37.51 
TCGA-F5-6571 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
       31.30         1.12         0.46        18.28        55.76 

$subtype3
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 
        8.45        15.39        10.39        32.02         8.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 
       24.00         1.02        46.03        34.03        50.04         0.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99         0.99         1.02        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 
       23.01        37.02        36.03         9.07        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-4745 
        1.94        38.96         0.49         0.20         4.60        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       12.99        13.97        36.00       126.44        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
       24.13        51.48        32.61         0.49         2.40        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 
       17.00        18.28        17.69        16.31         8.61        10.78 
TCGA-EI-6885 TCGA-F5-6810 TCGA-G5-6641 
       13.64         0.39        26.43 

subtype1 subtype2 subtype3 
    0.66     0.46     0.20 
subtype1 subtype2 subtype3 
   47.08   117.11   129.27 
subtype1 subtype2 subtype3 
   10.01    18.28    15.39 
[1] "0.7 - 47.1 (10.0)"  "0.5 - 117.1 (18.3)" "0.2 - 129.3 (15.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       5        2         7         0         0         0          0
  subtype2       7        4        11         0         1         2          4
  subtype3       9        1        13         1         0         4          4
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          6        5         3
  subtype2          7          2        3         0
  subtype3          8          2        8         2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           5        7        9
  STAGE II          2        4        1
  STAGE IIA         7       11       13
  STAGE IIB         0        0        1
  STAGE IIC         0        1        0
  STAGE III         0        2        4
  STAGE IIIA        0        4        4
  STAGE IIIB        4        7        8
  STAGE IIIC        6        2        2
  STAGE IV          5        3        8
  STAGE IVA         3        0        2
[1] 11  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  2  3 21  6
  subtype2  0  9 34  0
  subtype3  3 11 36  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        0        3
  T2        3        9       11
  T3       21       34       36
  T4        6        0        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 14  7 11
  subtype2 25 11  6
  subtype3 25 19  9
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       14       25       25
  N1        7       11       19
  N2       11        6        9
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 24  6   2  0
  subtype2 34  3   0  5
  subtype3 40  9   0  5
D5V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        24       34       40
  M1         6        3        9
  M1A        2        0        0
  MX         0        5        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 14 19
  subtype2 16 27
  subtype3 30 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   19
  subtype2   16   27
  subtype3   30   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       16       30
  MALE         19       27       24
[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"
D5V8, binary
          cls
clus        0  1
  subtype1 28  3
  subtype2 42  1
  subtype3 47  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    3
  subtype2   42    1
  subtype3   47    6
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                28       42       47
  RECTAL MUCINOUS ADENOCARCINOMA        3        1        6
[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"
D5V9, binary
          cls
clus        0  1
  subtype1  1 32
  subtype2  2 41
  subtype3  2 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    2   41
  subtype3    2   52
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        2
  YES       32       41       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 24  0  5  1
  subtype2 36  1  1  1
  subtype3 37  1  6  1
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       24       36       37
  R1        0        1        1
  R2        5        1        6
  RX        1        1        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"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    14
  subtype2     0                         1    25
  subtype3     0                         2    26
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        0
  BLACK OR AFRICAN AMERICAN        0        1        2
  WHITE                           14       25       26
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 14  6
  subtype2 19  4
  subtype3 22  6
  subtype4  5  1
  subtype5 26  3
  subtype6 12  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      20       23       28        6       29       14 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        4        6        1        3        2 
$subtype1
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 
       17.95        10.39        36.03         1.02        24.00        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
        2.01        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 
        0.99         1.02         0.99         0.99         1.02        36.03 
TCGA-AG-4007 TCGA-AG-4008 
        1.02        17.03 

$subtype2
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3893 
       17.23        12.72        37.68        20.02         7.07        35.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A02X TCGA-AG-A036 TCGA-DC-5337 TCGA-DC-6156 
       37.02        15.95        41.00       117.11        15.02        15.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6571 
       12.95        10.06         5.29        17.46         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
       14.86         1.12         0.76        55.76        47.08 

$subtype3
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.45        15.39        10.39         2.01         1.02        46.03 
TCGA-AG-3598 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 
       50.04        13.94         6.02        23.01        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02        10.98        51.98         1.94        38.96        61.97 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-5869 TCGA-DY-A1H8 TCGA-EI-6510 
        0.49         0.20         4.60        12.99        32.61        18.28 
TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6811 TCGA-G5-6641 
       17.69        13.64         1.02        26.43 

$subtype4
TCGA-AG-3578 TCGA-AG-3580 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-F5-6864 
       32.02         8.02        24.13        20.91        17.00         0.46 

$subtype5
TCGA-AG-3882 TCGA-AG-3891 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4022 
       19.99        18.02        48.03        32.02        14.04         0.99 
TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AH-6547 
       20.98        25.97        31.00        70.03        64.01         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6158 
        0.69         0.72        10.19         7.99        11.01         7.10 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 
       30.05        13.05        41.36        20.55        19.96        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-F5-6465 TCGA-G5-6233 
       16.34        16.41         8.61        37.51        18.28 

$subtype6
TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       10.98        13.97        36.00       126.44        57.24       129.27 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6884 TCGA-F5-6810 
       51.48         0.49         2.40        16.31        10.78         0.39 
TCGA-F5-6812 TCGA-F5-6813 
        0.66         0.69 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.99     0.76     0.20     0.46     0.69     0.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   36.03   117.11    61.97    32.02    70.03   129.27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   8.220   15.950   13.315   18.955   18.020   12.475 
[1] "1.0 - 36.0 (8.2)"   "0.8 - 117.1 (15.9)" "0.2 - 62.0 (13.3)" 
[4] "0.5 - 32.0 (19.0)"  "0.7 - 70.0 (18.0)"  "0.4 - 129.3 (12.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       4        1         4         0         0         2          0
  subtype2       4        1         4         0         0         1          3
  subtype3       5        2         6         0         0         2          2
  subtype4       1        0         1         0         0         0          0
  subtype5       6        3        10         0         1         1          1
  subtype6       1        0         6         1         0         0          2
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          3        8         0
  subtype2          6          2        0         3
  subtype3          4          0        6         1
  subtype4          1          3        0         0
  subtype5          3          1        2         0
  subtype6          2          1        0         1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           4        4        5        1        6        1
  STAGE II          1        1        2        0        3        0
  STAGE IIA         4        4        6        1       10        6
  STAGE IIB         0        0        0        0        0        1
  STAGE IIC         0        0        0        0        1        0
  STAGE III         2        1        2        0        1        0
  STAGE IIIA        0        3        2        0        1        2
  STAGE IIIB        3        6        4        1        3        2
  STAGE IIIC        3        2        0        3        1        1
  STAGE IV          8        0        6        0        2        0
  STAGE IVA         0        3        1        0        0        1
[1] 11  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  3 19  2
  subtype2  1  4 16  3
  subtype3  2  7 18  3
  subtype4  1  0  5  0
  subtype5  0  7 23  0
  subtype6  0  2 10  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        1        2        1        0        0
  T2        3        4        7        0        7        2
  T3       19       16       18        5       23       10
  T4        2        3        3        0        0        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  9  8  8
  subtype2 10  8  6
  subtype3 14 10  5
  subtype4  2  1  3
  subtype5 21  5  3
  subtype6  8  5  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        9       10       14        2       21        8
  N1        8        8       10        1        5        5
  N2        8        6        5        3        3        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1 17  8   0  0
  subtype2 20  1   2  1
  subtype3 19  6   0  5
  subtype4  6  0   0  0
  subtype5 23  2   0  4
  subtype6 13  1   0  0
D6V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0        17       20       19        6       23       13
  M1         8        1        6        0        2        1
  M1A        0        2        0        0        0        0
  MX         0        1        5        0        4        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 14 11
  subtype2  8 17
  subtype3 17 13
  subtype4  4  2
  subtype5 11 19
  subtype6  6  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   11
  subtype2    8   17
  subtype3   17   13
  subtype4    4    2
  subtype5   11   19
  subtype6    6    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       14        8       17        4       11        6
  MALE         11       17       13        2       19        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 23  1
  subtype2 21  3
  subtype3 25  4
  subtype4  5  1
  subtype5 29  1
  subtype6 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    1
  subtype2   21    3
  subtype3   25    4
  subtype4    5    1
  subtype5   29    1
  subtype6   14    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                23       21       25        5       29
  RECTAL MUCINOUS ADENOCARCINOMA        1        3        4        1        1
                                clus
vv                               subtype6
  RECTAL ADENOCARCINOMA                14
  RECTAL MUCINOUS ADENOCARCINOMA        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1  0 25
  subtype2  2 23
  subtype3  2 28
  subtype4  0  6
  subtype5  1 29
  subtype6  0 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   25
  subtype2    2   23
  subtype3    2   28
  subtype4    0    6
  subtype5    1   29
  subtype6    0   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         0        2        2        0        1        0
  YES       25       23       28        6       29       14
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 18  0  7  0
  subtype2 21  1  0  1
  subtype3 19  1  4  1
  subtype4  5  0  0  0
  subtype5 24  0  1  1
  subtype6 10  0  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       18       21       19        5       24       10
  R1        0        1        1        0        0        0
  R2        7        0        4        0        1        0
  RX        0        1        1        0        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1     1
  subtype2     1                         0    16
  subtype3     0                         1    12
  subtype4     0                         0     4
  subtype5     0                         0    19
  subtype6     0                         1    13
D6V12, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2       17       13        4       19       14 
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype5" "subtype3" "subtype5" "subtype5"
[13] "subtype3" "subtype5" "subtype5" "subtype5" "subtype6" "subtype5"
[19] "subtype2" "subtype3" "subtype6" "subtype2" "subtype6" "subtype5"
[25] "subtype5" "subtype2" "subtype5" "subtype2" "subtype2" "subtype6"
[31] "subtype5" "subtype6" "subtype6" "subtype4" "subtype6" "subtype3"
[37] "subtype6" "subtype6" "subtype5" "subtype5" "subtype4" "subtype4"
[43] "subtype3" "subtype5" "subtype3" "subtype5" "subtype6" "subtype5"
[49] "subtype5" "subtype6" "subtype3" "subtype2" "subtype2" "subtype5"
[55] "subtype2" "subtype2" "subtype6" "subtype3" "subtype6" "subtype6"
[61] "subtype2" "subtype2" "subtype4" "subtype5" "subtype2" "subtype2"
[67] "subtype3"
                           clus
vv                          subtype2 subtype3 subtype4 subtype5 subtype6
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        1        0        0        1
  WHITE                           16       12        4       19       13
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 27  5
  subtype2 25  2
  subtype3 25  7
  subtype4 53  7
subtype1 subtype2 subtype3 subtype4 
      32       27       32       60 
subtype1 subtype2 subtype3 subtype4 
       5        2        7        7 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-4022 
       24.13        17.23        37.74        20.02         1.02         0.99 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-4745 TCGA-DC-6156 TCGA-DC-6158 
        0.69         0.72        10.19        10.98        15.02         7.10 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6507 
       12.95         5.29       129.27        24.13         2.40        19.96 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 
        1.12         0.46 

$subtype2
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 
       19.10        14.50        15.39        10.39         7.07         2.01 
TCGA-AG-3599 TCGA-AG-3732 TCGA-AG-3902 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 
       12.03        32.98        32.02         0.49         1.45         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-6160 TCGA-EI-6506 
        6.05         6.05         6.97         4.73        30.05        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       20.91        18.28        17.69        16.41         8.61        10.78 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$subtype3
TCGA-AF-5654 TCGA-AG-3609 TCGA-AG-3742 TCGA-AG-A02G TCGA-AH-6549 TCGA-AH-6897 
        8.45        19.99         0.99        38.96         0.20         4.60 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        9.37        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       12.99        12.00        13.97        36.00        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
       17.00        15.85        16.34        16.31        11.51        11.97 
TCGA-F5-6863 TCGA-G5-6572 
        0.76        47.08 

$subtype4
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02         8.02         1.02        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        61.97        41.00        38.04       117.11 

subtype1 subtype2 subtype3 subtype4 
    0.39     0.49     0.20     0.99 
subtype1 subtype2 subtype3 subtype4 
  129.27    55.76   126.44   117.11 
subtype1 subtype2 subtype3 subtype4 
  10.075   14.500   13.970   18.510 
[1] "0.4 - 129.3 (10.1)" "0.5 - 55.8 (14.5)"  "0.2 - 126.4 (14.0)"
[4] "1.0 - 117.1 (18.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        2         9         0         0         0          3
  subtype2       6        0         4         1         1         2          3
  subtype3       7        0         6         1         1         0          3
  subtype4      16        6        19         0         0         4          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          8        3         4
  subtype2          5          0        3         3
  subtype3          6          3        2         2
  subtype4          9          3        9         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        6        7       16
  STAGE II          2        0        0        6
  STAGE IIA         9        4        6       19
  STAGE IIB         0        1        1        0
  STAGE IIC         0        1        1        0
  STAGE III         0        2        0        4
  STAGE IIIA        3        3        3        0
  STAGE IIIB        3        5        6        9
  STAGE IIIC        8        0        3        3
  STAGE IV          3        3        2        9
  STAGE IVA         4        3        2        0
[1] 11  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  0  3 27  4
  subtype2  1  7 19  3
  subtype3  3  7 19  3
  subtype4  5 12 45  4
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        1        3        5
  T2        3        7        7       12
  T3       27       19       19       45
  T4        4        3        3        4
[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
  subtype1 13  8 12
  subtype2 13 12  5
  subtype3 15 11  5
  subtype4 42 14 10
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       13       13       15       42
  N1        8       12       11       14
  N2       12        5        5       10
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 25  4   2  2
  subtype2 17  4   0  9
  subtype3 25  4   0  3
  subtype4 57  9   0  0
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        25       17       25       57
  M1         4        4        4        9
  M1A        2        0        0        0
  MX         2        9        3        0
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 16 18
  subtype2 11 19
  subtype3 15 18
  subtype4 31 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   18
  subtype2   11   19
  subtype3   15   18
  subtype4   31   35
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       16       11       15       31
  MALE         18       19       18       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 31  3
  subtype2 23  4
  subtype3 33  0
  subtype4 57  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    3
  subtype2   23    4
  subtype3   33    0
  subtype4   57    6
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                31       23       33       57
  RECTAL MUCINOUS ADENOCARCINOMA        3        4        0        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1  3 31
  subtype2  2 28
  subtype3  0 33
  subtype4  1 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   31
  subtype2    2   28
  subtype3    0   33
  subtype4    1   65
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        2        0        1
  YES       31       28       33       65
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 26  0  2  1
  subtype2 18  1  1  0
  subtype3 21  0  1  3
  subtype4 56  1  8  0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       26       18       21       56
  R1        0        1        0        1
  R2        2        1        1        8
  RX        1        0        3        0
[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"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    29
  subtype2     0                         0    23
  subtype3     0                         2    26
  subtype4     0                         1     3
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        2        1
  WHITE                           29       23       26        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 43 11
  subtype2 31  1
  subtype3 33  4
  subtype4 23  5
subtype1 subtype2 subtype3 subtype4 
      54       32       37       28 
subtype1 subtype2 subtype3 subtype4 
      11        1        4        5 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3742 
       24.13        17.23        37.74         8.45        20.02         0.99 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 
        0.20         0.69         0.72         4.60        10.19         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        36.00         7.10        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 
       51.48        32.61         0.49         2.40        19.96        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
       15.85        16.34        16.31        11.51        13.64        17.46 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         9.96        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.66         0.69         0.53         0.76         0.46        47.08 

$subtype2
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-3732 
       19.10        14.50        15.39        10.39         1.02        32.98 
TCGA-AG-3902 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 
       32.02         0.99         0.49         1.45         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6160 
        6.05         6.97         4.73        13.97        10.98        30.05 
TCGA-DC-6681 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       12.95        20.55        20.91        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6861 TCGA-G5-6233 
        8.61        10.78         8.45        37.51         1.12        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype3
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       43.04        13.55        12.72        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        2.01        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        6.05         0.99        15.95         0.99        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       35.01         1.02        19.99        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       13.94         6.02        37.02        36.03         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       31.00        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 
       38.04 

$subtype4
TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       10.39        36.03         8.02         1.02        46.03        34.03 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3882 
       19.99        19.99         7.99         0.99        29.98        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 
        1.02        17.03        14.01        48.03        28.04        36.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W 
        1.02        25.97        23.01        15.95         9.07        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 
       64.01         1.94        38.96       117.11 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.49     0.99     0.99 
subtype1 subtype2 subtype3 subtype4 
  129.27    55.76    61.97   117.11 
subtype1 subtype2 subtype3 subtype4 
   13.02    13.46    14.04    19.99 
[1] "0.2 - 129.3 (13.0)" "0.5 - 55.8 (13.5)"  "1.0 - 62.0 (14.0)" 
[4] "1.0 - 117.1 (20.0)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       8        1        14         1         1         0          4
  subtype2       4        1         5         1         1         2          5
  subtype3      11        2        12         0         0         2          0
  subtype4       7        4         7         0         0         2          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          7         10        3         4
  subtype2          6          0        3         5
  subtype3          6          2        6         0
  subtype4          4          2        5         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           8        4       11        7
  STAGE II          1        1        2        4
  STAGE IIA        14        5       12        7
  STAGE IIB         1        1        0        0
  STAGE IIC         1        1        0        0
  STAGE III         0        2        2        2
  STAGE IIIA        4        5        0        0
  STAGE IIIB        7        6        6        4
  STAGE IIIC       10        0        2        2
  STAGE IV          3        3        6        5
  STAGE IVA         4        5        0        0
[1] 11  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  9 37  6
  subtype2  1  5 25  4
  subtype3  4  8 28  1
  subtype4  1  7 20  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        1        4        1
  T2        9        5        8        7
  T3       37       25       28       20
  T4        6        4        1        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 25 14 14
  subtype2 14 15  6
  subtype3 26  8  7
  subtype4 18  8  5
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       25       14       26       18
  N1       14       15        8        8
  N2       14        6        7        5
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 42  6   1  5
  subtype2 21  4   1  9
  subtype3 35  6   0  0
  subtype4 26  5   0  0
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        42       21       35       26
  M1         6        4        6        5
  M1A        1        1        0        0
  MX         5        9        0        0
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 22 34
  subtype2 18 17
  subtype3 20 21
  subtype4 13 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   34
  subtype2   18   17
  subtype3   20   21
  subtype4   13   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       22       18       20       13
  MALE         34       17       21       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 55  1
  subtype2 29  4
  subtype3 29  8
  subtype4 31  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    1
  subtype2   29    4
  subtype3   29    8
  subtype4   31    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                55       29       29       31
  RECTAL MUCINOUS ADENOCARCINOMA        1        4        8        0
[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"
D8V9, binary
          cls
clus        0  1
  subtype1  3 53
  subtype2  2 33
  subtype3  1 40
  subtype4  0 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   53
  subtype2    2   33
  subtype3    1   40
  subtype4    0   31
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        2        1        0
  YES       53       33       40       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"
          vv
clus       R0 R1 R2 RX
  subtype1 39  0  1  4
  subtype2 22  1  1  0
  subtype3 35  0  5  0
  subtype4 25  1  5  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       39       22       35       25
  R1        0        1        0        1
  R2        1        1        5        5
  RX        4        0        0        0
[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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    50
  subtype2     0                         0    28
  subtype3     0                         0     3
  subtype4     0                         1     0
D8V12, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      53       28        3        1 
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[79] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        0
  BLACK OR AFRICAN AMERICAN        2        0        0
  WHITE                           50       28        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 11  6
  subtype2 32  6
  subtype3 15  1
  subtype4  9  1
  subtype5 43  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       38       16       10       50 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        6        1        1        7 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AH-6644 
       24.13        17.23        37.74        10.39        14.50         0.72 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 
       12.95         5.29        57.24       129.27        16.31         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
       31.30        14.86         0.66         0.69        47.08 

$subtype2
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-4022 
       19.10        15.39        20.02        10.39         1.02         0.99 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.49         1.45         0.69        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.73        13.97        60.03        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97         7.10        30.05        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6509 
       41.36        24.13        51.48        32.61        20.55        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-F5-6811 TCGA-G5-6233 
       18.28        15.85        17.69        16.34         1.02        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype3
TCGA-AF-5654 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-A00C TCGA-AG-A025 
        8.45        32.98         0.99        35.01         6.02        49.97 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA 
        6.05         7.99        15.02        15.02        36.00       126.44 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-F5-6465 
        0.49         2.40        20.91        37.51 

$subtype4
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-4001 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
        2.01        46.03        36.03        12.00        31.00        64.01 
TCGA-AG-A036 TCGA-AH-6549 TCGA-EI-6507 TCGA-F5-6810 
      117.11         0.20        19.96         0.39 

$subtype5
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 
       17.95        43.04        13.55        12.72        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
       14.04         1.02        17.03        20.98        13.94        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       36.03         9.07        70.03        10.98         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X 
       61.97        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     0.49     0.49     0.20     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    60.03   126.44   117.11    70.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
   14.86    13.97    15.02    25.48    16.49 
[1] "0.7 - 129.3 (14.9)" "0.5 - 60.0 (14.0)"  "0.5 - 126.4 (15.0)"
[4] "0.2 - 117.1 (25.5)" "1.0 - 70.0 (16.5)" 
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       0        1         4         0         0         0          0
  subtype2       6        1         6         1         1         2          5
  subtype3       6        0         4         1         0         0          0
  subtype4       1        1         3         0         0         1          0
  subtype5      15        5        16         0         0         3          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          5        1         3
  subtype2          9          4        3         2
  subtype3          3          0        1         2
  subtype4          1          0        2         0
  subtype5          5          4        8         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        6        6        1       15
  STAGE II          1        1        0        1        5
  STAGE IIA         4        6        4        3       16
  STAGE IIB         0        1        1        0        0
  STAGE IIC         0        1        0        0        0
  STAGE III         0        2        0        1        3
  STAGE IIIA        0        5        0        0        0
  STAGE IIIB        2        9        3        1        5
  STAGE IIIC        5        4        0        0        4
  STAGE IV          1        3        1        2        8
  STAGE IVA         3        2        2        0        0
[1] 11  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  0  0 14  3
  subtype2  2  9 29  2
  subtype3  3  3  9  2
  subtype4  0  2  8  0
  subtype5  4 12 37  3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        2        3        0        4
  T2        0        9        3        2       12
  T3       14       29        9        8       37
  T4        3        2        2        0        3
[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
  subtype1  5  4  7
  subtype2 16 19  7
  subtype3 11  4  2
  subtype4  6  1  2
  subtype5 36 10 10
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        5       16       11        6       36
  N1        4       19        4        1       10
  N2        7        7        2        2       10
[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"
          vv
clus       M0 M1 M1A MX
  subtype1 11  2   1  3
  subtype2 28  4   0  9
  subtype3 13  2   1  1
  subtype4  7  2   0  1
  subtype5 48  8   0  0
D9V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        11       28       13        7       48
  M1         2        4        2        2        8
  M1A        1        0        1        0        0
  MX         3        9        1        1        0
[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"
D9V7, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 18 24
  subtype3 11  6
  subtype4  3  7
  subtype5 26 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   18   24
  subtype3   11    6
  subtype4    3    7
  subtype5   26   30
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        8       18       11        3       26
  MALE         10       24        6        7       30
[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"
D9V8, binary
          cls
clus        0  1
  subtype1 15  2
  subtype2 40  1
  subtype3 17  0
  subtype4  9  1
  subtype5 46  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    2
  subtype2   40    1
  subtype3   17    0
  subtype4    9    1
  subtype5   46    6
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                15       40       17        9       46
  RECTAL MUCINOUS ADENOCARCINOMA        2        1        0        1        6
[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"
D9V9, binary
          cls
clus        0  1
  subtype1  2 16
  subtype2  3 39
  subtype3  0 17
  subtype4  0 10
  subtype5  1 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   16
  subtype2    3   39
  subtype3    0   17
  subtype4    0   10
  subtype5    1   55
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        3        0        0        1
  YES       16       39       17       10       55
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 12  0  0  1
  subtype2 23  1  1  1
  subtype3 13  0  1  1
  subtype4  7  0  2  1
  subtype5 47  1  7  0
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       12       23       13        7       47
  R1        0        1        0        0        1
  R2        0        1        1        2        7
  RX        1        1        1        1        0
[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"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    15
  subtype2     0                         1    35
  subtype3     0                         1    10
  subtype4     0                         0     3
  subtype5     0                         0     4
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        1        1        1        0        0
  WHITE                           15       35       10        3        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 18  3
  subtype2 48 10
  subtype3 44  8
subtype1 subtype2 subtype3 
      21       58       52 
subtype1 subtype2 subtype3 
       3       10        8 
$subtype1
TCGA-AF-2687 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3731 TCGA-AG-3893 
       24.13        32.02         2.01        46.03         1.02        35.01 
TCGA-AG-4001 TCGA-AG-A01Y TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
       36.03        64.01       117.11         0.20         0.69         6.05 
TCGA-CI-6624 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6513 
        4.73        57.24       129.27         0.49        20.91        16.34 
TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6641 
       14.86         0.39        26.43 

$subtype2
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       17.23        19.10        37.74        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A00C 
       20.02        10.39        32.98         0.99         0.99         6.02 
TCGA-AG-A025 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6620 
       49.97         0.49         1.45         0.72        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        24.13        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        17.00        18.28        15.85        17.69 
TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       16.31         9.96        37.51        31.30         1.02         0.66 
TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69        18.28        55.76        47.08 

$subtype3
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
       14.04         1.02        17.03        20.98        13.94        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       36.03         9.07        12.00        31.00        70.03        10.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.94        38.96        61.97        41.00 

subtype1 subtype2 subtype3 
    0.20     0.49     0.99 
subtype1 subtype2 subtype3 
  129.27   126.44    70.03 
subtype1 subtype2 subtype3 
  20.910   14.760   14.995 
[1] "0.2 - 129.3 (20.9)" "0.5 - 126.4 (14.8)" "1.0 - 70.0 (15.0)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       2        1         5         1         0         1          1
  subtype2      11        2        14         1         1         2          4
  subtype3      15        5        14         0         0         3          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          5          2        4         1
  subtype2         10          7        1         6
  subtype3          5          4       10         0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2       11       15
  STAGE II          1        2        5
  STAGE IIA         5       14       14
  STAGE IIB         1        1        0
  STAGE IIC         0        1        0
  STAGE III         1        2        3
  STAGE IIIA        1        4        0
  STAGE IIIB        5       10        5
  STAGE IIIC        2        7        4
  STAGE IV          4        1       10
  STAGE IVA         1        6        0
[1] 11  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  1  2 19  2
  subtype2  4 11 41  6
  subtype3  4 13 37  2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        4        4
  T2        2       11       13
  T3       19       41       37
  T4        2        6        2
[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
  subtype1  9  9  5
  subtype2 30 18 13
  subtype3 35 11 10
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0        9       30       35
  N1        9       18       11
  N2        5       13       10
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1 17  5   0  2
  subtype2 44  3   2 12
  subtype3 46 10   0  0
D10V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        17       44       46
  M1         5        3       10
  M1A        0        2        0
  MX         2       12        0
[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"
D10V7, binary
          cls
clus        0  1
  subtype1  9 15
  subtype2 32 31
  subtype3 25 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   15
  subtype2   32   31
  subtype3   25   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       32       25
  MALE         15       31       31
[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"
D10V8, binary
          cls
clus        0  1
  subtype1 21  3
  subtype2 59  2
  subtype3 47  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    3
  subtype2   59    2
  subtype3   47    5
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                21       59       47
  RECTAL MUCINOUS ADENOCARCINOMA        3        2        5
[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"
D10V9, binary
          cls
clus        0  1
  subtype1  1 23
  subtype2  4 59
  subtype3  1 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    4   59
  subtype3    1   55
     clus
vv    subtype1 subtype2 subtype3
  NO         1        4        1
  YES       23       59       55
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 15  0  4  1
  subtype2 40  1  0  3
  subtype3 47  1  7  0
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       15       40       47
  R1        0        1        1
  R2        4        0        7
  RX        1        3        0
[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"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    13
  subtype2     1                         2    50
  subtype3     0                         1     4
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        0
  BLACK OR AFRICAN AMERICAN        0        2        1
  WHITE                           13       50        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"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1  8  1
  subtype2 10  3
  subtype3 11  3
  subtype4 10  2
subtype1 subtype2 subtype3 subtype4 
       9       13       14       12 
subtype1 subtype2 subtype3 subtype4 
       1        3        3        2 
$subtype1
TCGA-AF-2687 TCGA-AG-3731 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6156 
       24.13         1.02         6.05        15.02        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-F5-6811 
       36.00         7.10         1.02 

$subtype2
TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-DC-6681 TCGA-DY-A1DE TCGA-EI-6514 
       37.74        14.50         0.99        12.95       129.27        16.31 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         0.39         0.66 
TCGA-G5-6572 
       47.08 

$subtype3
TCGA-AF-6655 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-BM-6198 TCGA-CI-6619 
       20.02         0.49         1.45         0.20        10.19         6.05 
TCGA-CI-6624 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-G5-6233 
        4.73        13.05        10.06        41.36        32.61        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype4
TCGA-AF-6672 TCGA-AG-3732 TCGA-AH-6643 TCGA-CL-5918 TCGA-DC-4749 TCGA-DY-A1DD 
       10.39        32.98         0.69         7.99        11.01        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       51.48        20.55        19.96        17.00        15.85        16.34 

subtype1 subtype2 subtype3 subtype4 
    1.02     0.39     0.20     0.69 
subtype1 subtype2 subtype3 subtype4 
   36.00   129.27    55.76    57.24 
subtype1 subtype2 subtype3 subtype4 
   12.99    14.86    11.62    16.67 
[1] "1.0 - 36.0 (13.0)"  "0.4 - 129.3 (14.9)" "0.2 - 55.8 (11.6)" 
[4] "0.7 - 57.2 (16.7)" 
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  subtype1       3        0         1         0         0          0          1
  subtype2       0        1         6         0         0          0          0
  subtype3       1        0         2         1         1          3          3
  subtype4       2        0         3         0         1          0          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        1         2
  subtype2          2        1         3
  subtype3          0        1         0
  subtype4          2        1         1
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           3        0        1        2
  STAGE II          0        1        0        0
  STAGE IIA         1        6        2        3
  STAGE IIC         0        0        1        0
  STAGE III         0        0        1        1
  STAGE IIIA        0        0        3        0
  STAGE IIIB        1        0        3        3
  STAGE IIIC        1        2        0        2
  STAGE IV          1        1        1        1
  STAGE IVA         2        3        0        1
[1] 10  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  2  5  1
  subtype2  0  0 11  2
  subtype3  1  3 11  0
  subtype4  0  2 10  1
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        1        0
  T2        2        0        3        2
  T3        5       11       11       10
  T4        1        2        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  4  3  2
  subtype2  7  1  5
  subtype3  4  9  1
  subtype4  5  4  4
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        4        7        4        5
  N1        3        1        9        4
  N2        2        5        1        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"
          vv
clus       M0 M1 M1A MX
  subtype1  6  2   1  0
  subtype2  8  2   1  2
  subtype3  7  2   0  5
  subtype4 10  1   0  2
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0         6        8        7       10
  M1         2        2        2        1
  M1A        1        1        0        0
  MX         0        2        5        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1  3  6
  subtype2  8  6
  subtype3  4 11
  subtype4  5  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    8    6
  subtype3    4   11
  subtype4    5    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        8        4        5
  MALE          6        6       11        8
[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"
D11V8, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 13  0
  subtype3 14  1
  subtype4 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   13    0
  subtype3   14    1
  subtype4   13    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                 9       13       14       13
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        0
[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"
D11V9, binary
          cls
clus        0  1
  subtype1  1  8
  subtype2  1 13
  subtype3  1 14
  subtype4  1 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    8
  subtype2    1   13
  subtype3    1   14
  subtype4    1   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        1        1
  YES        8       13       14       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  6  0  1  0
  subtype2 10  0  1  0
  subtype3  6  1  0  1
  subtype4  9  0  0  1
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        6       10        6        9
  R1        0        0        1        0
  R2        1        1        0        0
  RX        0        0        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"
D11V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         2     6
  subtype2                         0    12
  subtype3                         0    15
  subtype4                         0    11
D11V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        2        0        0        0
  WHITE                            6       12       15       11
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1  8  1
  subtype2 11  2
  subtype3 12  4
  subtype4  4  1
  subtype5  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       13       16        5        5 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        2        4        1        1 
$subtype1
TCGA-AF-2687 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       24.13         1.02         0.20         6.05         6.05         4.73 
TCGA-DC-6682 TCGA-F5-6702 TCGA-F5-6810 
       13.05        14.86         0.39 

$subtype2
TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-3732 TCGA-AG-4022 TCGA-AH-6547 TCGA-DC-6681 
       37.74        14.50        32.98         0.99         1.45        12.95 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6571 
       10.06        57.24       129.27        16.31         9.96        31.30 
TCGA-F5-6812 
        0.66 

$subtype3
TCGA-AF-6655 TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-DC-4749 
       20.02        10.39         0.49         0.69        10.19        11.01 
TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 
       41.36        51.48        32.61        20.55        19.96        15.85 
TCGA-EI-6513 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       16.34        18.28        55.76        26.43 

$subtype4
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
        7.99        15.02        12.99        36.00         7.10 

$subtype5
TCGA-DC-6156 TCGA-EI-6509 TCGA-F5-6465 TCGA-F5-6811 TCGA-G5-6572 
       15.02        17.00        37.51         1.02        47.08 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.66     0.49     7.10     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   24.13   129.27    55.76    36.00    47.08 
subtype1 subtype2 subtype3 subtype4 subtype5 
    6.05    14.50    19.12    12.99    17.00 
[1] "0.2 - 24.1 (6.0)"   "0.7 - 129.3 (14.5)" "0.5 - 55.8 (19.1)" 
[4] "7.1 - 36.0 (13.0)"  "1.0 - 47.1 (17.0)" 
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  subtype1       1        0         2         0         0          0          0
  subtype2       1        1         4         0         0          0          2
  subtype3       1        0         3         1         2          3          4
  subtype4       3        0         1         0         0          0          1
  subtype5       0        0         2         0         0          0          0
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        3         2
  subtype2          2        0         2
  subtype3          1        1         1
  subtype4          0        0         0
  subtype5          1        0         1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        1        3        0
  STAGE II          0        1        0        0        0
  STAGE IIA         2        4        3        1        2
  STAGE IIC         0        0        1        0        0
  STAGE III         0        0        2        0        0
  STAGE IIIA        0        0        3        0        0
  STAGE IIIB        0        2        4        1        0
  STAGE IIIC        1        2        1        0        1
  STAGE IV          3        0        1        0        0
  STAGE IVA         2        2        1        0        1
[1] 10  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  0  1  9  0
  subtype2  0  1 10  2
  subtype3  1  3 13  1
  subtype4  1  2  2  0
  subtype5  0  0  3  1
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        1        1        0
  T2        1        1        3        2        0
  T3        9       10       13        2        3
  T4        0        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"
          vv
clus       N0 N1 N2
  subtype1  3  4  2
  subtype2  7  2  4
  subtype3  4 10  4
  subtype4  4  1  0
  subtype5  2  0  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        3        7        4        4        2
  N1        4        2       10        1        0
  N2        2        4        4        0        2
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1  4  5   0  1
  subtype2  9  0   1  3
  subtype3 11  2   0  4
  subtype4  4  0   0  1
  subtype5  3  0   1  0
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0         4        9       11        4        3
  M1         5        0        2        0        0
  M1A        0        1        0        0        1
  MX         1        3        4        1        0
[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"
D12V7, binary
          cls
clus        0  1
  subtype1  3  7
  subtype2  9  4
  subtype3  4 14
  subtype4  2  3
  subtype5  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    7
  subtype2    9    4
  subtype3    4   14
  subtype4    2    3
  subtype5    2    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        3        9        4        2        2
  MALE          7        4       14        3        3
[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"
D12V8, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 12  0
  subtype3 17  1
  subtype4  5  0
  subtype5  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   12    0
  subtype3   17    1
  subtype4    5    0
  subtype5    5    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                10       12       17        5        5
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        0        0
[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"
D12V9, binary
          cls
clus        0  1
  subtype1  1  9
  subtype2  1 12
  subtype3  2 16
  subtype4  0  5
  subtype5  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    1   12
  subtype3    2   16
  subtype4    0    5
  subtype5    0    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        1        2        0        0
  YES        9       12       16        5        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  4  0  2  1
  subtype2  9  0  0  0
  subtype3 11  1  0  0
  subtype4  4  0  0  1
  subtype5  3  0  0  0
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        4        9       11        4        3
  R1        0        0        1        0        0
  R2        2        0        0        0        0
  RX        1        0        0        1        0
[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"
D12V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     8
  subtype2                         0    11
  subtype3                         0    17
  subtype4                         2     3
  subtype5                         0     5
D12V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  BLACK OR AFRICAN AMERICAN        0        0        0        2        0
  WHITE                            8       11       17        3        5
[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"
