[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/19775480/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/20140629/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  4  5 
42 28 26 31  4 
 1  2  3  4  5 
42 28 26 31  4 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
20 21 25 19 30 16 
 1  2  3  4  5  6 
20 21 25 19 30 16 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
29 14 34 28 61 
 1  2  3  4  5 
29 14 34 28 61 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
27 36 12 20 33 18 20 
 1  2  3  4  5  6  7 
27 36 12 20 33 18 20 
[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] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 169 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "84"                  
freq.contrast "84"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 169 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                 
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, 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 21  4
  subtype2 19  2
  subtype3 15  4
subtype1 subtype2 subtype3 
      25       21       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 
       39.48        13.55        36.03         8.02        20.05         1.02 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3885 TCGA-AG-3887 
       34.03        12.03         7.99         0.99        17.95        36.95 
TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.01        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A025 TCGA-AG-A02G 
       37.02        36.03         9.07        12.00        49.97        38.96 
TCGA-AG-A02X 
       41.00 

$subtype2
TCGA-AF-2691 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       43.04        34.49        12.00        32.02         7.07        36.03 
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-3611 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       13.94        19.99        29.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3902 
        1.02        13.02        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 
   20.05    19.04    19.99 
[1] "1.0 - 50.0 (20.1)" "1.0 - 50.0 (19.0)" "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"
D1V6, binary
          cls
clus        0  1
  subtype1 21  4
  subtype2 20  2
  subtype3 16  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2   20    2
  subtype3   16    6
   clus
vv  subtype1 subtype2 subtype3
  0       21       20       16
  1        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 14  6
  subtype2 15  3
  subtype3 13  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    6
  subtype2   15    3
  subtype3   13    1
     clus
vv    subtype1 subtype2 subtype3
  NO        14       15       13
  YES        6        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 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"
          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 11  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       12       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 
       39.48        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-3611 
       43.04        34.49        12.00        46.03         2.01        13.94 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A02X 
       19.04        17.95        36.95        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        20.05        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 
       36.03        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 
   39.48    46.03    36.03    48.03    38.04    50.04    38.96    51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   24.02    25.53    13.55    17.03    30.49    11.51    19.99    49.97 
[1] "8.0 - 39.5 (24.0)" "2.0 - 46.0 (25.5)" "1.0 - 36.0 (13.6)"
[4] "1.9 - 48.0 (17.0)" "1.0 - 38.0 (30.5)" "1.0 - 50.0 (11.5)"
[7] "1.0 - 39.0 (20.0)" "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"
D2V6, binary
          cls
clus        0  1
  subtype1  5  1
  subtype2 13  0
  subtype3 12  1
  subtype4  7  2
  subtype5  6  2
  subtype6  7  2
  subtype7  5  3
  subtype8  2  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2   13    0
  subtype3   12    1
  subtype4    7    2
  subtype5    6    2
  subtype6    7    2
  subtype7    5    3
  subtype8    2    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0        5       13       12        7        6        7        5        2
  1        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 4 2
  subtype2 7 4
  subtype3 7 2
  subtype4 6 0
  subtype5 6 1
  subtype6 5 1
  subtype7 6 0
  subtype8 1 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    7    4
  subtype3    7    2
  subtype4    6    0
  subtype5    6    1
  subtype6    5    1
  subtype7    6    0
  subtype8    1    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         4        7        7        6        6        5        6        1
  YES        2        4        2        0        1        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  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"
          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  8
  subtype2 29  3
  subtype3 26  4
  subtype4 28  7
subtype1 subtype2 subtype3 subtype4 
      63       32       30       35 
subtype1 subtype2 subtype3 subtype4 
       8        3        4        7 
$subtype1
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        39.48        17.23        43.04        13.55        34.49 
TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       16.83        12.00         8.02        20.05         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        37.02         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-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01W TCGA-AG-A020 
        3.98        20.98        13.94        37.02        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       51.98        49.97        61.97         1.45        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05        33.17         6.97         4.73        12.39 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1H8 
       15.02        13.97        19.99         5.95         5.29        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 
       20.55        19.96        20.91        18.28        17.69         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
        0.53         1.12        55.76 

$subtype2
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3609 TCGA-AG-3611 
       19.10        37.74        14.50        15.39        19.99        13.94 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
       20.98        29.98        17.95        35.01         1.02        28.04 
TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 
       14.04        46.03         6.02        25.97        23.01        36.03 
TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A032 TCGA-CI-6623 TCGA-DC-6156 TCGA-DY-A1DE 
       12.00        38.96        38.04         9.37        15.02       129.27 
TCGA-DY-A1DF TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       24.13        16.41        11.97        31.30         0.39         0.66 
TCGA-F5-6863 TCGA-G5-6233 
        0.76        18.28 

$subtype3
TCGA-AF-3913 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3592 TCGA-AG-3593 
       10.39        86.63        11.84         7.07        34.03        34.03 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3909 TCGA-AG-4001 
       15.95        19.99         0.99        19.99        19.99        36.03 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A026 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.07        31.00         1.94         7.17        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DG 
        5.03         8.98        27.95         5.03       126.44        51.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-F5-6811 TCGA-G5-6572 
        2.40        15.85        16.34        16.31        32.19        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        36.03 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3732 
       24.00        34.03         2.01         6.05         0.99        32.98 
TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01J 
       19.04        36.95        32.02         1.02        15.95         1.02 
TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CL-5917 
       64.01        41.00        38.56         0.69         0.72        78.12 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 
       10.98         4.01        41.36        57.24         0.49        17.00 
TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
       11.51        28.57         0.69        12.46        26.43 

subtype1 subtype2 subtype3 subtype4 
    0.53     0.39     0.99     0.49 
subtype1 subtype2 subtype3 subtype4 
   70.03   129.27   126.44    78.12 
subtype1 subtype2 subtype3 subtype4 
  15.020   18.690   16.325   20.020 
[1] "0.5 - 70.0 (15.0)"  "0.4 - 129.3 (18.7)" "1.0 - 126.4 (16.3)"
[4] "0.5 - 78.1 (20.0)" 
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          3          6        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        3
  STAGE IIIC        4        4        0        6
  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"
D3V6, binary
          cls
clus        0  1
  subtype1 52  9
  subtype2 24  4
  subtype3 24  5
  subtype4 26  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    9
  subtype2   24    4
  subtype3   24    5
  subtype4   26    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       52       24       24       26
  1        9        4        5        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"
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 40  5
  subtype2 17  7
  subtype3 18  3
  subtype4 18  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    5
  subtype2   17    7
  subtype3   18    3
  subtype4   18    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        40       17       18       18
  YES        5        7        3        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 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"
          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 26  3
  subtype2 33  5
  subtype3 26  4
subtype1 subtype2 subtype3 
      29       38       30 
subtype1 subtype2 subtype3 
       3        5        4 
$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        46.03        64.01 
TCGA-AH-6549 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-5869 
       17.49        26.43         6.05         4.73        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD 
        8.98        15.02        27.95        10.98       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 
       49.51        28.57         0.39        12.46        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        38.56         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        12.39        78.12        21.01        11.01        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EI-6506 
       19.99         5.95         4.01        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-3591 TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3742 
       15.39        34.03        34.03        20.98        37.02         0.99 
TCGA-AG-4021 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A036 
        3.98        70.03        10.98         1.94        61.97       117.11 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-6683 TCGA-DT-5265 
        0.69         0.72        33.17         7.17         5.03         5.29 
TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       24.13         2.40        20.91        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-7004 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        8.61        11.51         8.45        32.19         0.53        18.28 

subtype1 subtype2 subtype3 
    0.39     0.66     0.53 
subtype1 subtype2 subtype3 
  129.27    78.12   117.11 
subtype1 subtype2 subtype3 
  24.130   15.175   15.850 
[1] "0.4 - 129.3 (24.1)" "0.7 - 78.1 (15.2)"  "0.5 - 117.1 (15.8)"
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          4          3        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        4        6        4
  STAGE IIIC        3        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"
D4V6, binary
          cls
clus        0  1
  subtype1 19  7
  subtype2 28  2
  subtype3 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    7
  subtype2   28    2
  subtype3   23    3
   clus
vv  subtype1 subtype2 subtype3
  0       19       28       23
  1        7        2        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 14  3
  subtype2 21  4
  subtype3 16  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    3
  subtype2   21    4
  subtype3   16    3
     clus
vv    subtype1 subtype2 subtype3
  NO        14       21       16
  YES        3        4        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, 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"
          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 32  9
  subtype2 22  5
  subtype3 19  5
  subtype4 27  3
  subtype5  4  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      41       27       24       30        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9        5        5        3        0 
$subtype1
TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 
       39.48        16.83        15.39        10.39         8.02        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3598 
       24.00         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A00Y 
        0.99        20.98         0.99         1.02        13.94        23.01 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02G TCGA-AH-6897 TCGA-DC-4745 
       36.03         9.07        51.98        38.96        26.43        21.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.03        13.97        27.95        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
       32.61         0.49         2.40        20.91        18.28        17.69 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6810 TCGA-G5-6641 
        8.61        10.78        13.64         0.39        26.43 

$subtype2
TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-A014 TCGA-AG-A02X 
       17.23        20.02        32.02         7.07        15.95        41.00 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 
      117.11        38.56         1.45        15.02         5.95         5.03 
TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6571 
       24.13        20.55        17.00        16.31         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       28.57        32.19         0.66         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

$subtype3
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3594 
       34.49        10.39        11.84        36.03        36.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3742 
       12.03         6.05        19.99        19.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3891 TCGA-AG-4001 TCGA-AG-4005 
        0.99        19.04        17.95        18.02        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-DC-5337 TCGA-DT-5265 
        1.02        17.03         3.98        46.03        15.02         5.29 

$subtype4
TCGA-AF-3914 TCGA-AG-3882 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A00C 
       37.68        19.99        48.03        32.02        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
       25.97        31.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02N TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 
       61.97         0.69         0.72        10.19         7.17        11.01 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-EI-6507 
       10.98        19.99         4.01       126.44        41.36        19.96 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6813 
       15.85        16.34        16.41        17.46        49.51         0.69 

$subtype5
TCGA-AG-3893 TCGA-AG-A011 TCGA-AG-A01J TCGA-AH-6549 
       35.01        37.02         1.02        17.49 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     0.66     0.99     0.69     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27   117.11    46.03   126.44    37.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  20.050   17.230   16.025   18.710   26.250 
[1] "0.4 - 129.3 (20.1)" "0.7 - 117.1 (17.2)" "1.0 - 46.0 (16.0)" 
[4] "0.7 - 126.4 (18.7)" "1.0 - 37.0 (26.2)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       8        0         9         1         0         3          4
  subtype2       3        0         6         0         1         1          2
  subtype3       5        3         6         0         0         0          0
  subtype4       5        4         9         0         0         2          2
  subtype5       0        0         2         0         0         0          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          6          0        9         2
  subtype2          5          4        0         3
  subtype3          3          3        6         0
  subtype4          5          2        1         0
  subtype5          1          0        0         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           8        3        5        5        0
  STAGE II          0        0        3        4        0
  STAGE IIA         9        6        6        9        2
  STAGE IIB         1        0        0        0        0
  STAGE IIC         0        1        0        0        0
  STAGE III         3        1        0        2        0
  STAGE IIIA        4        2        0        2        0
  STAGE IIIB        6        5        3        5        1
  STAGE IIIC        0        4        3        2        0
  STAGE IV          9        0        6        1        0
  STAGE IVA         2        3        0        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  3 10 26  3
  subtype2  0  4 20  3
  subtype3  2  3 19  2
  subtype4  0  6 23  2
  subtype5  0  0  4  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3        0        2        0        0
  T2       10        4        3        6        0
  T3       26       20       19       23        4
  T4        3        3        2        2        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"
          vv
clus       N0 N1 N2
  subtype1 19 15  8
  subtype2 11  7  9
  subtype3 14  6  6
  subtype4 19  8  3
  subtype5  2  1  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       19       11       14       19        2
  N1       15        7        6        8        1
  N2        8        9        6        3        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 29  9
  subtype2 21  4
  subtype3 20  6
  subtype4 26  1
  subtype5  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    9
  subtype2   21    4
  subtype3   20    6
  subtype4   26    1
  subtype5    3    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       29       21       20       26        3
  1        9        4        6        1        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"
D5V7, binary
          cls
clus        0  1
  subtype1 24 18
  subtype2 14 14
  subtype3 12 14
  subtype4 10 21
  subtype5  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   18
  subtype2   14   14
  subtype3   12   14
  subtype4   10   21
  subtype5    1    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       14       12       10        1
  MALE         18       14       14       21        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"
D5V8, binary
          cls
clus        0  1
  subtype1 23  5
  subtype2 17  1
  subtype3 16  5
  subtype4 13  5
  subtype5  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    5
  subtype2   17    1
  subtype3   16    5
  subtype4   13    5
  subtype5    3    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        23       17       16       13        3
  YES        5        1        5        5        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"
D5V9, binary
          cls
clus        0  1
  subtype1 37  4
  subtype2 26  2
  subtype3 21  3
  subtype4 30  1
  subtype5  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    4
  subtype2   26    2
  subtype3   21    3
  subtype4   30    1
  subtype5    4    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                37       26       21       30        4
  RECTAL MUCINOUS ADENOCARCINOMA        4        2        3        1        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"
          vv
clus       R0 R1 R2 RX
  subtype1 30  0  6  0
  subtype2 22  1  0  0
  subtype3 19  0  5  1
  subtype4 24  1  1  1
  subtype5  3  0  0  1
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       30       22       19       24        3
  R1        0        1        0        1        0
  R2        6        0        5        1        0
  RX        0        0        1        1        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"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    21
  subtype2     0                         0    22
  subtype3     1                         2     2
  subtype4     0                         0    19
  subtype5     0                         0     1
D5V12, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       22        5       19        1 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype4" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[13] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
[19] "subtype1" "subtype4" "subtype3" "subtype1" "subtype1" "subtype2"
[25] "subtype1" "subtype4" "subtype4" "subtype2" "subtype4" "subtype2"
[31] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype4"
[43] "subtype1" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
[49] "subtype2" "subtype4" "subtype1" "subtype1" "subtype1" "subtype4"
[55] "subtype2" "subtype4" "subtype2" "subtype2" "subtype1" "subtype2"
[61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype2" "subtype2" "subtype1"
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        0
  BLACK OR AFRICAN AMERICAN        2        0        2        0
  WHITE                           21       22        2       19
[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(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 14  4
  subtype2 17  3
  subtype3 21  4
  subtype4 15  3
  subtype5 23  6
  subtype6 14  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       20       25       18       29       16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        3        4        3        6        2 
$subtype1
TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       39.48        36.03        24.00        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
        6.05         0.99        19.99        19.99        20.98         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       37.02         0.99         0.99        36.03         1.02        17.03 

$subtype2
TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A02X 
       17.23        20.02         7.07        15.95         1.02        41.00 
TCGA-AG-A036 TCGA-AH-6547 TCGA-DC-5869 TCGA-DC-6681 TCGA-DC-6683 TCGA-EI-6506 
      117.11         1.45         5.03         5.95         5.03        20.55 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6861 TCGA-F5-6863 
        9.96        49.51        31.30        28.57         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6235 
       18.28        55.76 

$subtype3
TCGA-AF-3400 TCGA-AF-3914 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3893 TCGA-AG-A00H 
       34.49        37.68        32.02        46.03        35.01        25.97 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6156 TCGA-DC-6158 
       31.00        64.01         7.17        11.01        15.02        10.98 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
      126.44        41.36        24.13        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6864 
       15.85        16.34        16.41        17.46        32.19        12.46 
TCGA-G5-6572 
       47.08 

$subtype4
TCGA-AF-3913 TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3891 
       10.39        11.84        36.03        19.04        19.99        18.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AH-6643 
       48.03        32.02        14.04         3.98        46.03         0.69 
TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6682 TCGA-DT-5265 
        0.72        10.19        15.02        19.99         4.01         5.29 

$subtype5
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3591 
       16.83        10.39         8.02        20.05         1.02        34.03 
TCGA-AG-3598 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       50.04        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       36.03         9.07        70.03        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-6155 
       38.96        61.97        38.56        17.49        26.43        13.97 
TCGA-DY-A1H8 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       32.61        17.69         8.61        10.78        13.64 

$subtype6
TCGA-AF-6136 TCGA-AG-3885 TCGA-AG-3896 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DD 
       15.39        17.95         1.02        21.01        27.95        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 
      129.27        51.48         0.49         2.40        18.28        16.31 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.39         0.66         0.69        26.43 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.99     0.76     7.17     0.69     1.02     0.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   39.48   117.11   126.44    48.03    70.03   129.27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   18.51    16.59    24.13    14.53    17.69    17.13 
[1] "1.0 - 39.5 (18.5)"  "0.8 - 117.1 (16.6)" "7.2 - 126.4 (24.1)"
[4] "0.7 - 48.0 (14.5)"  "1.0 - 70.0 (17.7)"  "0.4 - 129.3 (17.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       3        1         4         0         0         2          0
  subtype2       3        0         4         0         1         1          2
  subtype3       3        1         8         0         0         0          2
  subtype4       4        2         5         0         0         1          0
  subtype5       6        3         6         0         0         2          3
  subtype6       2        0         5         1         0         0          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          3        5         0
  subtype2          5          2        0         2
  subtype3          6          2        1         1
  subtype4          1          1        4         0
  subtype5          2          0        6         0
  subtype6          4          1        0         2
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           3        3        3        4        6        2
  STAGE II          1        0        1        2        3        0
  STAGE IIA         4        4        8        5        6        5
  STAGE IIB         0        0        0        0        0        1
  STAGE IIC         0        1        0        0        0        0
  STAGE III         2        1        0        1        2        0
  STAGE IIIA        0        2        2        0        3        1
  STAGE IIIB        2        5        6        1        2        4
  STAGE IIIC        3        2        2        1        0        1
  STAGE IV          5        0        1        4        6        0
  STAGE IVA         0        2        1        0        0        2
[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  2 15  2
  subtype2  0  4 15  2
  subtype3  0  4 19  1
  subtype4  1  3 15  0
  subtype5  2  7 18  3
  subtype6  1  3 10  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        0        0        1        2        1
  T2        2        4        4        3        7        3
  T3       15       15       19       15       18       10
  T4        2        2        1        0        3        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  8  5  7
  subtype2  9  7  5
  subtype3 13  6  5
  subtype4 11  4  3
  subtype5 15  9  5
  subtype6  9  6  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        8        9       13       11       15        9
  N1        5        7        6        4        9        6
  N2        7        5        5        3        5        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"
D6V6, binary
          cls
clus        0  1
  subtype1 15  5
  subtype2 17  2
  subtype3 21  2
  subtype4 12  4
  subtype5 22  6
  subtype6 12  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    5
  subtype2   17    2
  subtype3   21    2
  subtype4   12    4
  subtype5   22    6
  subtype6   12    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       15       17       21       12       22       12
  1        5        2        2        4        6        1
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 11  9
  subtype2 12  9
  subtype3 10 15
  subtype4  6 13
  subtype5 14 16
  subtype6  8  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    9
  subtype2   12    9
  subtype3   10   15
  subtype4    6   13
  subtype5   14   16
  subtype6    8    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       11       12       10        6       14        8
  MALE          9        9       15       13       16        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 11  2
  subtype2 10  1
  subtype3 16  5
  subtype4 11  3
  subtype5 20  3
  subtype6  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    2
  subtype2   10    1
  subtype3   16    5
  subtype4   11    3
  subtype5   20    3
  subtype6    4    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        11       10       16       11       20        4
  YES        2        1        5        3        3        2
[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 18  1
  subtype2 20  1
  subtype3 23  2
  subtype4 17  1
  subtype5 25  4
  subtype6 15  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   20    1
  subtype3   23    2
  subtype4   17    1
  subtype5   25    4
  subtype6   15    1
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                18       20       23       17       25
  RECTAL MUCINOUS ADENOCARCINOMA        1        1        2        1        4
                                clus
vv                               subtype6
  RECTAL ADENOCARCINOMA                15
  RECTAL MUCINOUS ADENOCARCINOMA        1
[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 15  0  5  0
  subtype2 19  1  0  0
  subtype3 18  0  1  1
  subtype4 13  0  2  1
  subtype5 21  1  4  1
  subtype6 12  0  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       15       19       18       13       21       12
  R1        0        1        0        0        1        0
  R2        5        0        1        2        4        0
  RX        0        0        1        1        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                         0     1
  subtype2     0                         1    14
  subtype3     0                         0    19
  subtype4     1                         2     7
  subtype5     0                         0    11
  subtype6     0                         1    13
D6V12, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1       15       19       10       11       14 
 [1] "subtype2" "subtype3" "subtype4" "subtype3" "subtype5" "subtype6"
 [7] "subtype2" "subtype5" "subtype4" "subtype5" "subtype2" "subtype5"
[13] "subtype4" "subtype4" "subtype5" "subtype4" "subtype4" "subtype3"
[19] "subtype6" "subtype3" "subtype4" "subtype2" "subtype5" "subtype3"
[25] "subtype6" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
[31] "subtype4" "subtype3" "subtype3" "subtype6" "subtype6" "subtype3"
[37] "subtype6" "subtype5" "subtype6" "subtype6" "subtype2" "subtype3"
[43] "subtype3" "subtype3" "subtype6" "subtype3" "subtype5" "subtype3"
[49] "subtype6" "subtype3" "subtype5" "subtype5" "subtype5" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype6" "subtype3"
[61] "subtype6" "subtype6" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype3" "subtype6"
                           clus
vv                          subtype2 subtype3 subtype4 subtype5 subtype6
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        1        0        2        0        1
  WHITE                           14       19        7       11       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 24  4
  subtype2 13  0
  subtype3 31  3
  subtype4 23  5
  subtype5 49  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       13       34       28       58 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        0        3        5        9 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3731 
       24.13        17.23        37.74        20.02        65.98        37.02 
TCGA-AG-4022 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       46.03         0.72        21.01        15.02        10.98         5.95 
TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6885 TCGA-EI-6917 
        5.29       129.27        24.13         2.40        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6864 
       32.19         0.66         0.69        12.46 

$subtype2
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3581 TCGA-AG-3732 TCGA-AG-3902 
       19.10        14.50        15.39         7.07        32.98        32.02 
TCGA-AH-6547 TCGA-CI-6622 TCGA-CI-6624 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6884 
        1.45         6.97         4.73        20.55        20.91        10.78 
TCGA-G5-6235 
       55.76 

$subtype3
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3599 TCGA-AG-3725 
       16.83        10.39        32.02        34.03        12.03        20.98 
TCGA-AG-3887 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A015 TCGA-AG-A02N 
       36.95         3.98        20.98        13.94        36.03        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6903 TCGA-BM-6198 
       41.00        38.56        17.49         0.69         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6682 
        6.05        33.17        15.02        13.97        19.99         4.01 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 
       19.96        17.00        18.28        17.69        16.41         8.61 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6641 
        0.53         1.12        18.28        26.43 

$subtype4
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3742 TCGA-AH-6897 
       86.63        11.84        34.03        19.99         0.99        26.43 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37        12.39        78.12         7.17        11.01         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        8.98        27.95         5.03       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       51.48        32.61         0.49        15.85        16.34        16.31 
TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6863 TCGA-G5-6572 
       11.51        11.97         0.76        47.08 

$subtype5
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        34.49        10.39        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02        36.03        20.05        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-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
       13.94        19.99         7.99         0.99        29.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        38.04       117.11 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     1.45     0.53     0.49     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    55.76    61.97   126.44   117.11 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.345   15.390   17.245   16.080   18.495 
[1] "0.4 - 129.3 (17.3)" "1.4 - 55.8 (15.4)"  "0.5 - 62.0 (17.2)" 
[4] "0.5 - 126.4 (16.1)" "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         7         0         0         0          2
  subtype2       4        0         2         1         0         1          1
  subtype3       8        1         7         0         1         1          4
  subtype4       5        0         7         1         1         0          2
  subtype5      12        5        17         0         0         4          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          7        2         4
  subtype2          3          0        0         1
  subtype3          3          2        3         2
  subtype4          6          2        1         2
  subtype5          9          3       11         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        4        8        5       12
  STAGE II          2        0        1        0        5
  STAGE IIA         7        2        7        7       17
  STAGE IIB         0        1        0        1        0
  STAGE IIC         0        0        1        1        0
  STAGE III         0        1        1        0        4
  STAGE IIIA        2        1        4        2        0
  STAGE IIIB        3        3        3        6        9
  STAGE IIIC        7        0        2        2        3
  STAGE IV          2        0        3        1       11
  STAGE IVA         4        1        2        2        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  2 23  4
  subtype2  0  4  8  2
  subtype3  3  9 21  1
  subtype4  2  4 18  3
  subtype5  4 10 43  4
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        3        2        4
  T2        2        4        9        4       10
  T3       23        8       21       18       43
  T4        4        2        1        3        4
[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 10  7 11
  subtype2  8  5  1
  subtype3 18  9  6
  subtype4 14  9  4
  subtype5 35 15 11
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10        8       18       14       35
  N1        7        5        9        9       15
  N2       11        1        6        4       11
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 22  5
  subtype2  8  0
  subtype3 25  4
  subtype4 22  3
  subtype5 50 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    5
  subtype2    8    0
  subtype3   25    4
  subtype4   22    3
  subtype5   50   11
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       22        8       25       22       50
  1        5        0        4        3       11
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 15 14
  subtype2  6  8
  subtype3 12 22
  subtype4 14 14
  subtype5 28 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   14
  subtype2    6    8
  subtype3   12   22
  subtype4   14   14
  subtype5   28   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       15        6       12       14       28
  MALE         14        8       22       14       33
[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"
D7V8, binary
          cls
clus        0  1
  subtype1 17  3
  subtype2  9  1
  subtype3 21  4
  subtype4 13  2
  subtype5 33 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    3
  subtype2    9    1
  subtype3   21    4
  subtype4   13    2
  subtype5   33   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        17        9       21       13       33
  YES        3        1        4        2       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 26  3
  subtype2 12  0
  subtype3 27  6
  subtype4 28  0
  subtype5 54  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    3
  subtype2   12    0
  subtype3   27    6
  subtype4   28    0
  subtype5   54    4
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                26       12       27       28       54
  RECTAL MUCINOUS ADENOCARCINOMA        3        0        6        0        4
[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 21  0  1  2
  subtype2  7  1  0  0
  subtype3 28  0  1  1
  subtype4 18  0  0  2
  subtype5 49  1 10  0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       21        7       28       18       49
  R1        0        1        0        0        1
  R2        1        0        1        0       10
  RX        2        0        1        2        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"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    24
  subtype2     0                         0    11
  subtype3     0                         0    23
  subtype4     0                         4    20
  subtype5     0                         1     3
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        1        0        0        4        1
  WHITE                           24       11       23       20        3
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 21  6
  subtype2 34  1
  subtype3 10  2
  subtype4 17  3
  subtype5 25  6
  subtype6 16  1
  subtype7 17  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      27       35       12       20       31       17       19 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        1        2        3        6        1        2 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-4021 TCGA-DC-6156 
       24.13        17.23        86.63        65.98         3.98        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       27.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 
      129.27        24.13         2.40        15.85        16.31        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       13.64        11.97        31.30         0.39         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.76        12.46        47.08 

$subtype2
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3591 
       43.04        19.10        14.50        15.39        10.39        34.03 
TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3902 TCGA-AG-4022 TCGA-AH-6544 
       20.98        37.02        32.98        32.02        46.03        38.56 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.45         1.81         6.05        33.17         6.97         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6160 TCGA-DC-6681 TCGA-EI-6506 TCGA-EI-6508 
       12.39        21.01        19.99         5.95        20.55        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-7004 
       18.28        17.69        16.41         8.61        10.78         8.45 
TCGA-F5-6465 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       49.51         1.12        18.28        55.76        26.43 

$subtype3
TCGA-AF-3911 TCGA-AF-6655 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-6158 
       37.74        20.02         0.69         0.72        10.19        10.98 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6814 
        5.29        19.96        17.46         9.96        28.57         0.53 

$subtype4
TCGA-AF-5654 TCGA-AF-A56N TCGA-AG-3592 TCGA-AG-3742 TCGA-AH-6549 TCGA-AH-6897 
       16.83        11.84        34.03         0.99        17.49        26.43 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        9.37        78.12         7.17        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 
        8.98        13.97        51.48        32.61         0.49        17.00 
TCGA-EI-6513 TCGA-F5-6811 
       16.34        32.19 

$subtype5
TCGA-AF-2692 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       13.55        10.39        36.03         8.02        36.03        20.05 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       46.03        34.03        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3894 
       29.98        19.99         1.02        17.95        17.03        14.01 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A00Y 
       48.03        28.04        36.03         1.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       15.95         9.07        70.03        64.01         1.94        38.96 
TCGA-AG-A036 
      117.11 

$subtype6
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.49        12.00        32.02         2.01        50.04        12.03 
TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 
       13.94        19.04        36.95        13.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
        6.02        36.03        10.98        61.97        41.00 

$subtype7
TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        7.07        24.00         1.02         6.05         0.99        15.95 
TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 
        0.99        35.01         1.02        19.99        14.04        17.03 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A025 
       37.02         1.02        12.00        31.00        51.98        49.97 
TCGA-AG-A032 
       38.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.39     1.12     0.53     0.49     0.99     2.01     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  129.27    55.76    37.74    78.12   117.11    61.97    51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  15.850   18.280   10.585   15.680   19.990   19.040   15.950 
[1] "0.4 - 129.3 (15.8)" "1.1 - 55.8 (18.3)"  "0.5 - 37.7 (10.6)" 
[4] "0.5 - 78.1 (15.7)"  "1.0 - 117.1 (20.0)" "2.0 - 62.0 (19.0)" 
[7] "1.0 - 52.0 (15.9)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0        10         0         1         0          0
  subtype2       5        1         5         1         1         2          5
  subtype3       1        1         2         0         0         0          2
  subtype4       6        0         4         1         0         0          2
  subtype5       7        4         8         0         0         2          0
  subtype6       6        2         7         0         0         1          0
  subtype7       4        0         4         0         0         1          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          5          5        3         1
  subtype2          6          0        3         5
  subtype3          1          3        0         1
  subtype4          2          2        0         2
  subtype5          4          2        6         0
  subtype6          2          0        0         0
  subtype7          4          2        5         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        5        1        6        7        6        4
  STAGE II          0        1        1        0        4        2        0
  STAGE IIA        10        5        2        4        8        7        4
  STAGE IIB         0        1        0        1        0        0        0
  STAGE IIC         1        1        0        0        0        0        0
  STAGE III         0        2        0        0        2        1        1
  STAGE IIIA        0        5        2        2        0        0        0
  STAGE IIIB        5        6        1        2        4        2        4
  STAGE IIIC        5        0        3        2        2        0        2
  STAGE IV          3        3        0        0        6        0        5
  STAGE IVA         1        5        1        2        0        0        0
[1] 11  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  1 22  3
  subtype2  2  5 25  4
  subtype3  0  3  8  1
  subtype4  3  5 10  2
  subtype5  1  7 22  3
  subtype6  2  4 12  0
  subtype7  1  4 14  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        0        2        0        3        1        2        1
  T2        1        5        3        5        7        4        4
  T3       22       25        8       10       22       12       14
  T4        3        4        1        2        3        0        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 12  5  9
  subtype2 15 15  6
  subtype3  4  4  3
  subtype4 11  5  3
  subtype5 19  8  6
  subtype6 15  3  0
  subtype7  9  5  6
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       12       15        4       11       19       15        9
  N1        5       15        4        5        8        3        5
  N2        9        6        3        3        6        0        6
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 22  4
  subtype2 22  5
  subtype3  8  1
  subtype4 15  2
  subtype5 27  6
  subtype6 18  0
  subtype7 15  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    4
  subtype2   22    5
  subtype3    8    1
  subtype4   15    2
  subtype5   27    6
  subtype6   18    0
  subtype7   15    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       22       22        8       15       27       18       15
  1        4        5        1        2        6        0        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 13 14
  subtype2 19 17
  subtype3  1 11
  subtype4 10 10
  subtype5 14 19
  subtype6  8 10
  subtype7 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   14
  subtype2   19   17
  subtype3    1   11
  subtype4   10   10
  subtype5   14   19
  subtype6    8   10
  subtype7   10   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       13       19        1       10       14        8       10
  MALE         14       17       11       10       19       10       10
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 12  2
  subtype2 23  4
  subtype3  7  2
  subtype4 12  1
  subtype5 18  6
  subtype6 11  3
  subtype7 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    2
  subtype2   23    4
  subtype3    7    2
  subtype4   12    1
  subtype5   18    6
  subtype6   11    3
  subtype7   10    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        12       23        7       12       18       11       10
  YES        2        4        2        1        6        3        2
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus        0  1
  subtype1 27  0
  subtype2 30  4
  subtype3 11  1
  subtype4 20  0
  subtype5 31  1
  subtype6  9  7
  subtype7 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    0
  subtype2   30    4
  subtype3   11    1
  subtype4   20    0
  subtype5   31    1
  subtype6    9    7
  subtype7   19    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                27       30       11       20       31
  RECTAL MUCINOUS ADENOCARCINOMA        0        4        1        0        1
                                clus
vv                               subtype6 subtype7
  RECTAL ADENOCARCINOMA                 9       19
  RECTAL MUCINOUS ADENOCARCINOMA        7        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 19  0  1  1
  subtype2 23  1  1  0
  subtype3  9  0  0  1
  subtype4 13  0  0  3
  subtype5 26  1  6  0
  subtype6 17  0  0  0
  subtype7 16  0  4  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       19       23        9       13       26       17       16
  R1        0        1        0        0        1        0        0
  R2        1        1        0        0        6        0        4
  RX        1        0        1        3        0        0        0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    23
  subtype2     0                         0    29
  subtype3     1                         0    11
  subtype4     0                         2    16
  subtype5     0                         1     1
  subtype6     0                         0     1
  subtype7     0                         0     0
D8V12, multiclass
[1] "Remove cluster labels:" "subtype5"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      26       29       12       18        2        1 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype4" "subtype2" "subtype2" "subtype4" "subtype3" "subtype3"
[19] "subtype4" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
[61] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[67] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[73] "subtype3" "subtype1" "subtype4" "subtype1" "subtype1" "subtype3"
[79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[85] "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        0
  BLACK OR AFRICAN AMERICAN        3        0        0        2
  WHITE                           23       29       11       16
[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(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 12  5
  subtype2 35  6
  subtype3 15  2
  subtype4  9  1
  subtype5 46  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       41       17       10       53 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        6        2        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 
        5.95         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        28.57         0.66         0.69        47.08 

$subtype2
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 
       19.10        15.39        20.02        10.39        34.03        34.03 
TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       20.98        37.02        46.03        38.56         1.45         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12        21.01        11.01         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
       19.99         4.01         5.03        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       32.61        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       16.34        32.19        18.28        55.76        26.43 

$subtype3
TCGA-AF-5654 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-4021 TCGA-AG-A00C 
       16.83        32.98         0.99        35.01         3.98         6.02 
TCGA-AG-A025 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6156 TCGA-DC-6157 
       49.97        33.17         7.17        15.02        15.02        27.95 
TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-F5-6465 
      126.44         0.49         2.40        20.91        49.51 

$subtype4
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-4001 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       20.05        46.03        36.03        12.00        31.00        64.01 
TCGA-AG-A036 TCGA-AH-6549 TCGA-EI-6507 TCGA-F5-6810 
      117.11        17.49        19.96         0.39 

$subtype5
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 
       39.48        43.04        13.55        34.49        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        36.03        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-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       29.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W 
       20.98        13.94        37.02        36.03         9.07        70.03 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98         1.94        38.96        61.97        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     0.69     0.49     0.39     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    78.12   126.44   117.11    70.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.310   18.280   16.830   25.525   17.950 
[1] "0.7 - 129.3 (16.3)" "0.7 - 78.1 (18.3)"  "0.5 - 126.4 (16.8)"
[4] "0.4 - 117.1 (25.5)" "1.0 - 70.0 (17.9)" 
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"
D9V6, binary
          cls
clus        0  1
  subtype1 11  3
  subtype2 28  4
  subtype3 13  3
  subtype4  7  2
  subtype5 48  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    3
  subtype2   28    4
  subtype3   13    3
  subtype4    7    2
  subtype5   48    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       11       28       13        7       48
  1        3        4        3        2        8
[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"
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  9  2
  subtype2 21  6
  subtype3 10  1
  subtype4  5  2
  subtype5 35  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    2
  subtype2   21    6
  subtype3   10    1
  subtype4    5    2
  subtype5   35    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       21       10        5       35
  YES        2        6        1        2        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 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"
          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 19  3
  subtype2 51 10
  subtype3 47  8
subtype1 subtype2 subtype3 
      22       61       55 
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        20.05        46.03        37.02        35.01 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A01Y TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 
       36.03         3.98        64.01       117.11        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6508 
        6.05         4.73        57.24       129.27         0.49        20.91 
TCGA-EI-6513 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6641 
       16.34        28.57         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        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3732 
       20.02        10.39        34.03        34.03        20.98        32.98 
TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A025 TCGA-AH-6544 TCGA-AH-6547 
        0.99        46.03         6.02        49.97        38.56         1.45 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.72        10.19        33.17         6.97         9.37        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       51.48        32.61         2.40        20.55        19.96        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 
       18.28        15.85        17.69        16.31         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6235 
       31.30        32.19         0.66         0.69        18.28        55.76 
TCGA-G5-6572 
       47.08 

$subtype3
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       39.48        43.04        13.55        34.49        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        36.03        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-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       29.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       20.98        13.94        37.02        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        70.03        10.98         1.94        38.96        61.97 
TCGA-AG-A02X 
       41.00 

subtype1 subtype2 subtype3 
    0.39     0.66     0.99 
subtype1 subtype2 subtype3 
  129.27   126.44    70.03 
subtype1 subtype2 subtype3 
   25.28    17.23    17.03 
[1] "0.4 - 129.3 (25.3)" "0.7 - 126.4 (17.2)" "1.0 - 70.0 (17.0)" 
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"
D10V6, binary
          cls
clus        0  1
  subtype1 17  5
  subtype2 44  5
  subtype3 46 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    5
  subtype2   44    5
  subtype3   46   10
   clus
vv  subtype1 subtype2 subtype3
  0       17       44       46
  1        5        5       10
[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"
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 11  3
  subtype2 33  8
  subtype3 36  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    3
  subtype2   33    8
  subtype3   36    6
     clus
vv    subtype1 subtype2 subtype3
  NO        11       33       36
  YES        3        8        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"
D10V9, 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"
          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 11  3
  subtype3 11  3
  subtype4 11  2
subtype1 subtype2 subtype3 subtype4 
       9       14       14       13 
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        37.02        33.17        15.02         5.03        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-F5-6811 
       27.95        10.98        32.19 

$subtype2
TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4021 TCGA-AG-4022 TCGA-DC-6681 TCGA-DY-A1DE 
       37.74        14.50         3.98        46.03         5.95       129.27 
TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.31         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-G5-6572 
        0.66        47.08 

$subtype3
TCGA-AF-6655 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-BM-6198 TCGA-CI-6619 
       20.02        38.56         1.45        17.49        10.19         6.05 
TCGA-CI-6624 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-G5-6233 
        4.73         4.01         5.03        41.36        32.61        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype4
TCGA-AF-6672 TCGA-AG-3725 TCGA-AG-3732 TCGA-AH-6643 TCGA-CL-5918 TCGA-DC-4749 
       10.39        20.98        32.98         0.69         7.17        11.01 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6511 
       57.24        51.48        20.55        19.96        17.00        15.85 
TCGA-EI-6513 
       16.34 

subtype1 subtype2 subtype3 subtype4 
    5.03     0.39     1.45     0.69 
subtype1 subtype2 subtype3 subtype4 
   37.02   129.27    55.76    57.24 
subtype1 subtype2 subtype3 subtype4 
  24.130   22.440   17.885   17.000 
[1] "5.0 - 37.0 (24.1)"  "0.4 - 129.3 (22.4)" "1.4 - 55.8 (17.9)" 
[4] "0.7 - 57.2 (17.0)" 
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"
D11V6, binary
          cls
clus        0  1
  subtype1  6  3
  subtype2  8  3
  subtype3  7  2
  subtype4 10  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2    8    3
  subtype3    7    2
  subtype4   10    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        6        8        7       10
  1        3        3        2        1
[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"
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 6 1
  subtype2 8 2
  subtype3 6 1
  subtype4 8 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    8    2
  subtype3    6    1
  subtype4    8    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        8        6        8
  YES        1        2        1        2
[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  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"
          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  9  1
  subtype2 11  2
  subtype3 13  4
  subtype4  4  1
  subtype5  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       13       17        5        5 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        2        4        1        1 
$subtype1
TCGA-AF-2687 TCGA-AG-3731 TCGA-AG-4021 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       24.13        37.02         3.98        17.49         6.05        33.17 
TCGA-CI-6624 TCGA-DC-6682 TCGA-F5-6702 TCGA-F5-6810 
        4.73         4.01        28.57         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        46.03         1.45         5.95 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6571 
        5.03        57.24       129.27        16.31         9.96        31.30 
TCGA-F5-6812 
        0.66 

$subtype3
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3725 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       20.02        10.39        20.98        38.56         0.69        10.19 
TCGA-DC-4749 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       11.01        41.36        51.48        32.61        20.55        19.96 
TCGA-EI-6511 TCGA-EI-6513 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.85        16.34        18.28        55.76        26.43 

$subtype4
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        27.95        10.98 

$subtype5
TCGA-DC-6156 TCGA-EI-6509 TCGA-F5-6465 TCGA-F5-6811 TCGA-G5-6572 
       15.02        17.00        49.51        32.19        47.08 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     0.66     0.69     5.03    15.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   37.02   129.27    55.76    27.95    49.51 
subtype1 subtype2 subtype3 subtype4 subtype5 
   11.77    16.31    20.02    10.98    32.19 
[1] "0.4 - 37.0 (11.8)"  "0.7 - 129.3 (16.3)" "0.7 - 55.8 (20.0)" 
[4] "5.0 - 27.9 (11.0)"  "15.0 - 49.5 (32.2)"
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"
D12V6, binary
          cls
clus        0  1
  subtype1  4  5
  subtype2  9  1
  subtype3 11  2
  subtype4  4  0
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    9    1
  subtype3   11    2
  subtype4    4    0
  subtype5    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        4        9       11        4        3
  1        5        1        2        0        1
[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"
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  5  1
  subtype2  5  2
  subtype3 10  3
  subtype4  3  0
  subtype5  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    5    2
  subtype3   10    3
  subtype4    3    0
  subtype5    5    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         5        5       10        3        5
  YES        1        2        3        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 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"
          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"
