[1] "ofn"        "-oTCOAD-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/COAD-TP/19775087/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/20125559/COAD-TP.mergedcluster.txt"

nPatients in clinical file=457, in cluster file=459, common to both=456
[1]  12 456
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
38 61 30 24 
 1  2  3  4 
38 61 30 24 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
46 73 34 
 1  2  3 
46 73 34 
[1] "CN_CNMF"
[1] 3
  1   2   3 
202 168  77 
  1   2   3 
202 168  77 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
119  98  75 
  1   2   3 
119  98  75 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
 87 144 126 
  1   2   3 
 87 144 126 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
52 33 34 38 43 86 25 20 26 
 1  2  3  4  5  6  7  8  9 
52 33 34 38 43 86 25 20 26 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
120 108  91 135 
  1   2   3   4 
120 108  91 135 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 79 107  96 133  39 
  1   2   3   4   5 
 79 107  96 133  39 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
160  66 180 
  1   2   3 
160  66 180 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
136  50  79 141 
  1   2   3   4 
136  50  79 141 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
29 32 24 
 1  2  3 
29 32 24 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
12 22 17 24 10 
 1  2  3  4  5 
12 22 17 24 10 
[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 456 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=86,	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=288,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	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=16,	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=13,	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=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=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 456 columns, 1 survival variables, and 12 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"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  78 311  55 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  78 311  55 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  78 311  55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  78 311  55 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
268 105  83 
[1] "table(vv)"
vv
 N0  N1  N2 
268 105  83 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
268 105  83 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
268 105  83 
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=21, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 27  8
  subtype2 44 13
  subtype3 25  5
  subtype4 20  4
subtype1 subtype2 subtype3 subtype4 
      35       57       30       24 
subtype1 subtype2 subtype3 subtype4 
       8       13        5        4 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       46.65        43.76        42.90        33.34        32.75        36.53 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3672 
        1.02        13.02         0.99        17.95        29.95         0.92 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3842 
       26.99        19.04        10.06        33.04        15.95        37.02 
TCGA-AA-3845 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
        0.00        17.03        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00D 
       26.01        24.00         2.01        25.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A02R 
       30.02        18.05         0.99        10.98        22.03 

$subtype2
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3517 TCGA-AA-3519 
       24.33        42.28        16.57        34.65        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       36.03         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       12.99        33.99        21.01        24.00        19.99        19.99 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3812 
        2.01        14.01        15.02        19.00         5.03        35.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 
       38.99        36.95        10.06        31.07        31.07        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 
       27.02        18.05         2.01        20.98        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       13.05        34.06        26.01        24.00         7.96        34.03 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       38.04        27.02        42.02        14.99        21.99         1.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       15.02        32.02        31.00         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 
        5.03        41.00        16.31 

$subtype3
TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3556 
        1.02        37.05         8.05        19.07        14.01        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
       20.98        13.94        54.02        47.05        11.01         5.98 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 
        0.99         1.02         0.00        36.03        30.05        53.00 
TCGA-AA-3941 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U 
       24.00        27.02        13.94        18.05         4.01        17.03 
TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01Q TCGA-AA-A024 TCGA-AA-A029 
       34.98        12.00        31.00         1.02        39.06        51.98 

$subtype4
TCGA-AA-3520 TCGA-AA-3532 TCGA-AA-3552 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       24.03        29.00        13.02        50.04        47.01        37.05 
TCGA-AA-3692 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3850 
       36.00        25.02        17.98        14.93        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3956 
       33.07        32.05         0.99        30.05        12.99        34.03 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AY-4071 
       36.03        16.08        27.02        27.02        19.07         0.95 

subtype1 subtype2 subtype3 subtype4 
       0        0        0        0 
subtype1 subtype2 subtype3 subtype4 
   46.65    50.99    54.02    50.04 
subtype1 subtype2 subtype3 subtype4 
   24.00    24.00    18.56    26.02 
[1] "0.0 - 46.6 (24.0)" "0.0 - 51.0 (24.0)" "0.0 - 54.0 (18.6)"
[4] "0.0 - 50.0 (26.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       6        1        14         3         3          1          3
  subtype2      11        2        12         0         2          2          5
  subtype3       7        6         9         2         1          0          3
  subtype4       5        3        10         0         2          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        5         0
  subtype2         13       14         0
  subtype3          0        1         1
  subtype4          2        1         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           6       11        7        5
  STAGE II          1        2        6        3
  STAGE IIA        14       12        9       10
  STAGE IIB         3        0        2        0
  STAGE III         3        2        1        2
  STAGE IIIA        1        2        0        0
  STAGE IIIB        3        5        3        1
  STAGE IIIC        1       13        0        2
  STAGE IV          5       14        1        1
  STAGE IVA         0        0        1        0
[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  7 24  6
  subtype2  2 12 42  5
  subtype3  0  7 19  4
  subtype4  1  5 18  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        2        0        1
  T2        7       12        7        5
  T3       24       42       19       18
  T4        6        5        4        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 25  5  8
  subtype2 27 15 19
  subtype3 24  5  1
  subtype4 18  3  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       25       27       24       18
  N1        5       15        5        3
  N2        8       19        1        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 32  5
  subtype2 47 14
  subtype3 28  2
  subtype4 22  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32    5
  subtype2   47   14
  subtype3   28    2
  subtype4   22    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       32       47       28       22
  1        5       14        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"
D1V7, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 31 30
  subtype3 10 20
  subtype4  9 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   31   30
  subtype3   10   20
  subtype4    9   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       31       10        9
  MALE         13       30       20       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1 30  0
  subtype2 49  1
  subtype3 24  0
  subtype4 20  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2   49    1
  subtype3   24    0
  subtype4   20    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        30       49       24       20
  YES        0        1        0        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"
D1V9, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 60  1
  subtype3 22  7
  subtype4 22  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   60    1
  subtype3   22    7
  subtype4   22    1
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                25       60       22       22
  COLON MUCINOUS ADENOCARCINOMA       13        1        7        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"
          vv
clus       R0 R1 R2
  subtype1 32  0  3
  subtype2 47  1 13
  subtype3 28  0  2
  subtype4 21  0  1
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       32       47       28       21
  R1        0        1        0        0
  R2        3       13        2        1
[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"
D1V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     6
  subtype2                         1     4
  subtype3                         0     0
  subtype4                         0     1
D1V12, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype4 
       6        5        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            6        4
[1] 2 2
[1] FALSE
D1V13, binary
          cls
clus       0
  subtype1 6
  subtype2 5
  subtype3 0
  subtype4 1
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 34 10
  subtype2 55 17
  subtype3 27  3
subtype1 subtype2 subtype3 
      44       72       30 
subtype1 subtype2 subtype3 
      10       17        3 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3514 
       46.65        43.76        42.90        33.34        32.75         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3543 TCGA-AA-3554 
       13.02         1.02         8.05        19.07         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       29.95        23.01         0.92        26.99        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3852 
       33.04         1.02        15.95        37.02         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        53.00        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3994 
       26.01        24.00         2.01        25.02        27.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01D 
       38.04        30.02        18.05         4.01         0.99        10.98 
TCGA-AA-A01Q TCGA-AA-A02R 
        1.02        22.03 

$subtype2
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3519 
       24.33        42.28        16.57        34.65        36.53         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         0.00        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3560 
       29.00        14.01        33.99        21.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       13.94        54.02         2.01        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3818 TCGA-AA-3819 
       11.01         5.98        36.00         5.03         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       17.98        38.99        14.93        10.06         0.00        33.07 
TCGA-AA-3855 TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       32.05        30.05        27.02        18.05        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       50.99        13.05        26.01        24.00        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       13.94        19.00        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A024 TCGA-AA-A029 
       32.02        12.00        31.00        31.00        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 
        2.96        39.98         2.01         5.03        41.00        16.31 

$subtype3
TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 
       38.99        29.00        26.01        12.99        13.02        24.00 
TCGA-AA-3562 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3812 
       19.99        14.01        15.02        37.05        19.00        35.05 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 
       36.95        17.03         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       17.03        24.03         2.01        20.98        34.03        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4071 
       36.03        16.08        34.06        27.02        34.03         0.95 

subtype1 subtype2 subtype3 
    0.00     0.00     0.95 
subtype1 subtype2 subtype3 
   53.00    54.02    38.99 
subtype1 subtype2 subtype3 
  22.520   22.995   24.015 
[1] "0.0 - 53.0 (22.5)" "0.0 - 54.0 (23.0)" "0.9 - 39.0 (24.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        14         4         3          1          5
  subtype2      12        7        20         1         4          2          4
  subtype3       8        2        11         0         1          0          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        5         0
  subtype2         10       12         1
  subtype3          5        4         0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9       12        8
  STAGE II          3        7        2
  STAGE IIA        14       20       11
  STAGE IIB         4        1        0
  STAGE III         3        4        1
  STAGE IIIA        1        2        0
  STAGE IIIB        5        4        3
  STAGE IIIC        1       10        5
  STAGE IV          5       12        4
  STAGE IVA         0        1        0
[1] 10  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 10 28  7
  subtype2  2 13 51  7
  subtype3  1  8 24  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        2        1
  T2       10       13        8
  T3       28       51       24
  T4        7        7        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 31  7  8
  subtype2 42 16 15
  subtype3 21  5  8
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       31       42       21
  N1        7       16        5
  N2        8       15        8
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 40  5
  subtype2 60 13
  subtype3 29  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    5
  subtype2   60   13
  subtype3   29    4
   clus
vv  subtype1 subtype2 subtype3
  0       40       60       29
  1        5       13        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"
D2V7, binary
          cls
clus        0  1
  subtype1 28 18
  subtype2 35 38
  subtype3 12 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   18
  subtype2   35   38
  subtype3   12   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       35       12
  MALE         18       38       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1 35  0
  subtype2 60  3
  subtype3 28  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    0
  subtype2   60    3
  subtype3   28    0
     clus
vv    subtype1 subtype2 subtype3
  NO        35       60       28
  YES        0        3        0
[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"
D2V9, binary
          cls
clus        0  1
  subtype1 27 18
  subtype2 69  4
  subtype3 33  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   18
  subtype2   69    4
  subtype3   33    0
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                27       69       33
  COLON MUCINOUS ADENOCARCINOMA       18        4        0
[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 39  0  3
  subtype2 60  1 12
  subtype3 29  0  4
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       39       60       29
  R1        0        1        0
  R2        3       12        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"
D2V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     5
  subtype2                         1     5
  subtype3                         0     1
D2V12, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       5        6        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
                           clus
vv                          subtype1 subtype2
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            5        5
[1] 2 2
[1] FALSE
D2V13, binary
          cls
clus       0
  subtype1 5
  subtype2 6
  subtype3 1
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 147  47
  subtype2 126  36
  subtype3  61  16
subtype1 subtype2 subtype3 
     194      162       77 
subtype1 subtype2 subtype3 
      47       36       16 
$subtype1
TCGA-3L-AA1B TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       15.62         9.53        46.65        43.76        42.90        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 
       13.94        37.05        37.25        37.02        14.53        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       33.53        22.09        22.06         8.38        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 
        7.04         3.02        58.03        63.98        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 
       24.03        37.05         8.05        19.07        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 
       17.95        29.95        23.01        61.02         6.97         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       47.05        11.01        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       38.99         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       53.00        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 
       26.01        24.00         2.01         2.01        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       27.02        38.04        30.02        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        34.98        10.98        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02R 
        1.02        35.01        35.01        26.01        39.06        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6386 
        0.72        10.88         0.46         0.92        27.09        17.82 
TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33        75.95        58.39         1.41        32.94         5.13 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77        12.10       100.01         3.19         3.06         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       20.02        37.02        26.04        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        14.99        12.99        14.04        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       11.01        12.03        45.40        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 
       43.27        17.85        12.49        16.14         3.68        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        12.00        10.26 
TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 
       24.43        49.91        13.32       140.38       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
      139.17        81.37        60.79        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       35.74        35.74         6.18        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6302 
       16.24        47.41        35.31       133.18        23.51        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       53.62        85.48        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA 
       35.80        26.17        74.79        79.69        19.33         9.93 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       31.30        70.03 

$subtype2
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 
        4.80         1.61        39.45        43.76        43.43        24.33 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       44.91        35.11        45.60        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.45        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       29.16        22.52        24.13        25.08        20.61        24.69 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 
       20.28        61.84        56.25         5.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        9.07        34.03        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       21.01        13.02        19.99        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       14.01        50.04        15.02        37.05        19.00        85.05 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 
        0.99        31.07        17.03        27.02        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W 
       26.01         7.96        34.03        38.04        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01T 
       21.99         1.02        15.02        32.02        12.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
        2.96        39.98         2.01        41.00        40.96        15.52 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42         0.20        16.44        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
        0.95        33.01        17.26        17.85        18.84       109.28 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5256 
       22.36        65.00        29.56         5.23         1.61         2.14 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        0.07        14.30        49.08         9.99         1.91        25.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        8.02        13.02        29.06        22.03        32.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 
       15.02        17.03         2.96        29.03        16.04        15.02 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 
       11.08        10.06        19.59        56.09        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 
       15.12        17.13        11.38       130.65        92.75        12.59 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 
      131.51        14.04        26.47       119.93        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6297 
       31.96        33.67        13.25         0.53        28.21        82.39 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       65.85        55.04        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GC 
       36.00        91.79        46.75        18.18        19.33        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-T9-A92H 
       17.85        16.80        42.77        29.46        21.90        11.90 

$subtype3
TCGA-4T-AA8H TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 
       12.66        27.09        25.18         9.63         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        1.02        35.01         1.02        36.03        19.07         0.00 
TCGA-AA-3538 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       26.01        24.00        20.98        78.08         6.05        54.02 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3858 TCGA-AA-3867 
       47.01         5.98        36.00         5.03        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       29.98        24.00        27.02        13.94        19.00        18.05 
TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
       17.03         1.02        37.02        51.98         5.03         0.92 
TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
        5.79        21.44         5.65       106.75        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5797 TCGA-CK-4952 TCGA-CM-4751 
       49.41        11.74        12.69         3.29        15.62        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 
       22.98        30.08        21.99        13.02        11.01        11.08 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       12.26        55.92         4.80        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB 
       12.43         9.04       119.70        38.20         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A28H TCGA-F4-6805 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6306 
        6.12       117.07        34.42         8.35        74.56        44.68 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       10.98        15.65        32.98         8.42        30.28 

subtype1 subtype2 subtype3 
    0.00     0.07     0.00 
subtype1 subtype2 subtype3 
  148.01   131.51   119.70 
subtype1 subtype2 subtype3 
  21.565   22.195   19.070 
[1] "0.0 - 148.0 (21.6)" "0.1 - 131.5 (22.2)" "0.0 - 119.7 (19.1)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      39        1       13        75         6         0        11
  subtype2      21        0        5        42         2         1         7
  subtype3      14        0       10        16         0         0         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1         23         14       12         2         1
  subtype2          7         23         18       24        12         1
  subtype3          1         13          8        9         3         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          39       21       14
  STAGE IA          1        0        0
  STAGE II         13        5       10
  STAGE IIA        75       42       16
  STAGE IIB         6        2        0
  STAGE IIC         0        1        0
  STAGE III        11        7        3
  STAGE IIIA        1        7        1
  STAGE IIIB       23       23       13
  STAGE IIIC       14       18        8
  STAGE IV         12       24        9
  STAGE IVA         2       12        3
  STAGE IVB         1        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   5  38 131  27
  subtype2   5  24 120  19
  subtype3   1  15  54   7
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        5        1
  T2       38       24       15
  T3      131      120       54
  T4       27       19        7
[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 137  35  30
  subtype2  79  52  37
  subtype3  44  18  15
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      137       79       44
  N1       35       52       18
  N2       30       37       15
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 159  15
  subtype2 110  37
  subtype3  55  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  159   15
  subtype2  110   37
  subtype3   55   12
   clus
vv  subtype1 subtype2 subtype3
  0      159      110       55
  1       15       37       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"
D3V7, binary
          cls
clus         0   1
  subtype1 102 100
  subtype2  74  94
  subtype3  35  42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102  100
  subtype2   74   94
  subtype3   35   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      102       74       35
  MALE        100       94       42
[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"
D3V8, binary
          cls
clus         0   1
  subtype1 155   3
  subtype2 140   4
  subtype3  58   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  155    3
  subtype2  140    4
  subtype3   58    2
     clus
vv    subtype1 subtype2 subtype3
  NO       155      140       58
  YES        3        4        2
[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"
D3V9, binary
          cls
clus         0   1
  subtype1 151  48
  subtype2 161   6
  subtype3  70   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151   48
  subtype2  161    6
  subtype3   70    6
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               151      161       70
  COLON MUCINOUS ADENOCARCINOMA       48        6        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"
          vv
clus        R0  R1  R2  RX
  subtype1 146   2   5  16
  subtype2 121   1  13   6
  subtype3  52   0   7   3
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      146      121       52
  R1        2        1        0
  R2        5       13        7
  RX       16        6        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                        25
  subtype2                                0     3                        25
  subtype3                                0     2                         8
          vv
clus       WHITE
  subtype1    98
  subtype2    78
  subtype3    35
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   6        3        2
  BLACK OR AFRICAN AMERICAN              25       25        8
  WHITE                                  98       78       35
[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"
D3V13, binary
          cls
clus         0   1
  subtype1   1 125
  subtype2   3  96
  subtype3   0  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  125
  subtype2    3   96
  subtype3    0   44
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO      125       96       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 91 26
  subtype2 72 24
  subtype3 56 18
subtype1 subtype2 subtype3 
     117       96       74 
subtype1 subtype2 subtype3 
      26       24       18 
$subtype1
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 
       15.62         4.80        39.45        43.76        43.43        24.33 
TCGA-A6-2680 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       35.11        36.53        32.91        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        22.52        24.13        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       24.69        20.28        56.25         5.03         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
        1.02        62.96         6.97        61.02        78.08         6.05 
TCGA-AA-3697 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 
       85.05        15.52         0.79        22.42        16.44         0.46 
TCGA-AU-3779 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       14.50        33.01       109.28       106.75        22.36        65.00 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       29.56         1.61         2.14         0.07        12.20        14.30 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4750 TCGA-CM-5341 
       49.08         9.99         1.91        37.02         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       22.03         5.03        15.02        17.03        15.02         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       16.04        21.99        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       11.01        10.06        56.09        55.92        18.25         1.32 
TCGA-D5-6537 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        4.80         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       11.38        38.20       130.65        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       139.17        26.47        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 
      117.07         8.61        33.67         0.53        47.41        28.21 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       39.42        35.93        61.91        36.00        46.75        18.18 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-T9-A92H 
        8.42        30.28        11.90 

$subtype2
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-3809 
       12.66         1.61        44.91        45.60        37.02        32.75 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 
       14.53        32.45        30.44        33.53        22.06        24.39 
TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3663 
       20.12        24.92         3.02        35.01        58.03         6.97 
TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
       19.04         0.07        21.37        56.55         0.72         5.79 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.20         0.92        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       19.33         5.65        32.94        88.21        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       11.74        12.69         3.25        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 
       15.62        51.32        21.14        82.95       124.27        20.02 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6675 
       25.02        27.02        32.02        15.02        14.04        13.05 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6531 
       11.08        12.03        45.40        12.26        19.59        17.75 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       15.12        17.13        16.14        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       24.43        92.75        12.59         7.50       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
        6.12        14.04        60.79        98.24        95.18        11.11 
TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6320 TCGA-G4-6321 
        6.18        41.42       133.18        74.56        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U 
       26.04        13.78        35.80        26.17        79.69        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-QL-A97D 
       19.33        19.33         9.93        15.65        31.30        21.90 

$subtype3
TCGA-5M-AAT6 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5664 
        9.53        13.94        37.05        37.25        31.63        22.09 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 
        8.38        25.08        24.16        21.76        23.87        19.66 
TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3510 TCGA-AD-6963 
       16.24        61.84         9.63         7.04        63.98        27.42 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       10.88        27.09        18.84        75.95        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
        5.13        62.79        12.10       100.01         5.23         3.19 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 
        3.06         3.29        12.76        10.06       148.01        23.05 
TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-6162 
       26.04        13.02        22.98        30.08        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6530 
       29.03        14.99        12.99        12.95        20.19        20.42 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       43.27        17.85        12.49        15.58         3.68         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A280 TCGA-F4-6460 TCGA-F4-6463 
       11.64         4.80         1.51         7.76        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
       35.74        47.87         1.55        34.42        16.24        13.25 
TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6625 
       35.31         8.35        67.30        53.62        85.48        91.79 
TCGA-G4-6627 TCGA-WS-AB45 
       74.79        70.03 

subtype1 subtype2 subtype3 
    0.07     0.07     1.41 
subtype1 subtype2 subtype3 
  140.38   135.65   148.01 
subtype1 subtype2 subtype3 
  23.610   20.070   19.925 
[1] "0.1 - 140.4 (23.6)" "0.1 - 135.7 (20.1)" "1.4 - 148.0 (19.9)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      17        0        6        33         1         1         3
  subtype2      20        1        3        32         3         0         3
  subtype3       6        0        5        29         1         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         21          8       11        10         1
  subtype2          1         14         10        4         3         1
  subtype3          1         12          7        8         3         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          17       20        6
  STAGE IA          0        1        0
  STAGE II          6        3        5
  STAGE IIA        33       32       29
  STAGE IIB         1        3        1
  STAGE IIC         1        0        0
  STAGE III         3        3        1
  STAGE IIIA        4        1        1
  STAGE IIIB       21       14       12
  STAGE IIIC        8       10        7
  STAGE IV         11        4        8
  STAGE IVA        10        3        3
  STAGE IVB         1        1        0
[1] 13  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  4 19 82 14
  subtype2  2 19 62 14
  subtype3  1  5 58 11
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        2        1
  T2       19       19        5
  T3       82       62       58
  T4       14       14       11
[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 66 34 19
  subtype2 61 19 18
  subtype3 43 20 12
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       66       61       43
  N1       34       19       20
  N2       19       18       12
[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 76 22
  subtype2 64  8
  subtype3 54 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76   22
  subtype2   64    8
  subtype3   54   11
   clus
vv  subtype1 subtype2 subtype3
  0       76       64       54
  1       22        8       11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 49 70
  subtype2 53 45
  subtype3 32 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49   70
  subtype2   53   45
  subtype3   32   43
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       49       53       32
  MALE         70       45       43
[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 92  3
  subtype2 77  1
  subtype3 66  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    3
  subtype2   77    1
  subtype3   66    1
     clus
vv    subtype1 subtype2 subtype3
  NO        92       77       66
  YES        3        1        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"
D4V9, binary
          cls
clus         0   1
  subtype1 113   4
  subtype2  79  18
  subtype3  59  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    4
  subtype2   79   18
  subtype3   59   16
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               113       79       59
  COLON MUCINOUS ADENOCARCINOMA        4       18       16
[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 81  0  3  7
  subtype2 60  2  1 11
  subtype3 49  0  1  6
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       81       60       49
  R1        0        2        0
  R2        3        1        1
  RX        7       11        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        23
  subtype2                                0     3                        19
  subtype3                                1     4                        15
          vv
clus       WHITE
  subtype1    81
  subtype2    71
  subtype3    53
D4V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   4        3        4
  BLACK OR AFRICAN AMERICAN              23       19       15
  WHITE                                  81       71       53
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
          cls
clus         0   1
  subtype1   2 103
  subtype2   1  86
  subtype3   1  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  103
  subtype2    1   86
  subtype3    1   69
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        1
  NOT HISPANIC OR LATINO      103       86       69
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  64  19
  subtype2 107  33
  subtype3 101  24
subtype1 subtype2 subtype3 
      83      140      125 
subtype1 subtype2 subtype3 
      19       33       24 
$subtype1
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2683 
       15.62        43.76        24.33        42.28        45.60        16.57 
TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5667 
       37.25        33.34        36.53        32.91        30.44        29.16 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 
       24.13         8.38        24.16        20.28         3.02        35.01 
TCGA-AA-3506 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3529 TCGA-AA-3532 
       58.03         1.02        24.03        37.05         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       29.00        13.02        24.00        19.99        19.99        61.02 
TCGA-AA-3678 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3852 
       47.01        19.04        35.05         0.99        25.02         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-A004 TCGA-AA-A00F 
       36.03         0.99        20.98        21.99        13.94        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       18.05        18.05        38.04        21.99         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02K 
       10.98        38.07         1.02        33.04         2.96        14.01 
TCGA-AA-A02W TCGA-AD-5900 TCGA-AY-6386 TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4682 
       41.00         0.07        17.82        19.33        18.84        22.36 
TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5863 
        3.25         1.91        25.02        29.06        22.98        15.02 
TCGA-CM-6167 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-6531 TCGA-DM-A280 TCGA-F4-6459 
       14.99        10.06        12.26        17.75         7.76         8.61 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6310 TCGA-G4-6323 
       35.74         6.18        13.25        47.41        63.62        13.78 
TCGA-G4-6625 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z1 
       91.79        19.33         9.93        12.79         8.42 

$subtype2
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 
        4.80        12.66         9.53        46.65        42.90        35.11 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       37.02        32.75        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3496 
       27.09        22.52        20.61        24.69        23.87         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3525 TCGA-AA-3530 
       63.98         6.97        38.99         9.07         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 
       34.03        33.99        29.95        20.98        13.94        54.02 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3831 
       19.00         5.03        85.05        19.04        10.06        17.98 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3930 
       14.93        10.06        30.05        53.00        27.02         2.01 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00E 
       50.99        13.05        34.06        27.02         7.96        30.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01I 
       42.02        17.03        14.99        34.98        32.02        31.00 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 
        2.01         5.03         0.92        39.98        40.96        56.55 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A69D 
        5.79         0.20        33.01        21.44        17.26        17.85 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94        65.00        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6747 
        2.14         0.07        12.20        14.30         9.99        82.95 
TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 
       37.02        22.03        15.02        15.02        15.02        21.99 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       11.01        13.05        11.08        12.03        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 TCGA-D5-6923 
       18.25        15.12         4.80        17.13         3.68        12.43 
TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       12.00       119.70        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C 
      140.38         7.50        44.32       131.51       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6806 
      119.93        35.97        60.79        95.18        31.96        41.42 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 
      133.18        28.21         8.35        82.39        85.48        61.91 
TCGA-G4-6320 TCGA-G4-6322 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.43        26.04        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-T9-A92H 
       21.90        11.90 

$subtype3
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6142 
       37.05        34.65        31.63        29.19        33.53        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A566 
       25.18        21.76        24.39        20.12        19.66        24.92 
TCGA-AA-3489 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
        7.04        17.95         0.92         5.98        26.99        33.04 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3862 
       15.95        38.99        36.95         0.00         0.00        30.05 
TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3971 TCGA-AA-3986 TCGA-AA-A00A 
       17.03        33.01        24.00        16.08        19.07        38.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A02R TCGA-AA-A03F 
        4.01         0.99        31.00         1.02        22.03        18.05 
TCGA-AD-6548 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4308 TCGA-AZ-4315 
       21.37         0.46         0.92        27.09       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-5797 
        1.41         5.13        12.10       100.01         5.23         3.29 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       12.76        10.06        21.14       124.27        23.05        20.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       26.04         8.02        13.02        30.08        32.02         5.03 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 
       17.03        12.00         2.96        29.03        16.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        14.04        12.95        11.08        11.01 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       19.59        20.19        20.42         1.32        43.27        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6924 
       12.49        16.14        15.58         1.48         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF 
        9.04         9.44        11.64         1.51        11.38        38.20 
TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6461 TCGA-F4-6569 
      130.65       135.65        14.04        26.47        11.11        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
       47.87         1.55        34.42        16.24        33.67         0.53 
TCGA-F4-6856 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        39.42        35.93        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        74.79        79.69        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL 
       19.33        15.65        17.85        16.80        30.28 

subtype1 subtype2 subtype3 
    0.00     0.07     0.00 
subtype1 subtype2 subtype3 
   91.79   140.38   135.65 
subtype1 subtype2 subtype3 
   19.99    24.28    20.02 
[1] "0.0 - 91.8 (20.0)"  "0.1 - 140.4 (24.3)" "0.0 - 135.7 (20.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      12        1        4        28         1         0         4
  subtype2      21        0       13        38         4         1         8
  subtype3      21        0        3        50         3         0         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         12         10        8         4         1
  subtype2          1         23         10       16         5         1
  subtype3          4         14         13        6         6         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          12       21       21
  STAGE IA          1        0        0
  STAGE II          4       13        3
  STAGE IIA        28       38       50
  STAGE IIB         1        4        3
  STAGE IIC         0        1        0
  STAGE III         4        8        6
  STAGE IIIA        2        1        4
  STAGE IIIB       12       23       14
  STAGE IIIC       10       10       13
  STAGE IV          8       16        6
  STAGE IVA         4        5        6
  STAGE IVB         1        1        0
[1] 13  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   0  16  61   9
  subtype2   2  22 101  19
  subtype3   4  20  85  17
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        2        4
  T2       16       22       20
  T3       61      101       85
  T4        9       19       17
[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 49 21 17
  subtype2 80 38 26
  subtype3 80 26 20
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49       80       80
  N1       21       38       26
  N2       17       26       20
[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"
D5V6, binary
          cls
clus         0   1
  subtype1  66  13
  subtype2 102  22
  subtype3 100  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   13
  subtype2  102   22
  subtype3  100   12
   clus
vv  subtype1 subtype2 subtype3
  0       66      102      100
  1       13       22       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"
D5V7, binary
          cls
clus        0  1
  subtype1 45 42
  subtype2 64 80
  subtype3 63 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   42
  subtype2   64   80
  subtype3   63   63
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       64       63
  MALE         42       80       63
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1  71   2
  subtype2 112   3
  subtype3 102   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71    2
  subtype2  112    3
  subtype3  102    2
     clus
vv    subtype1 subtype2 subtype3
  NO        71      112      102
  YES        2        3        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1  75  12
  subtype2 134   9
  subtype3 103  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   12
  subtype2  134    9
  subtype3  103   21
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                75      134      103
  COLON MUCINOUS ADENOCARCINOMA       12        9       21
[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  R2  RX
  subtype1  75   5   1
  subtype2  84  12  11
  subtype3 106   0   4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       75       84      106
  R2        5       12        0
  RX        1       11        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"
D5V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        12
  subtype2                                0     7                        19
  subtype3                                1     3                        16
          vv
clus       WHITE
  subtype1    32
  subtype2    67
  subtype3    82
D5V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   1        7        3
  BLACK OR AFRICAN AMERICAN              12       19       16
  WHITE                                  32       67       82
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
          cls
clus         0   1
  subtype1   0  45
  subtype2   2  85
  subtype3   0 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   45
  subtype2    2   85
  subtype3    0  102
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        0
  NOT HISPANIC OR LATINO       45       85      102
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 38 13
  subtype2 25  7
  subtype3 27  5
  subtype4 25 12
  subtype5 32  9
  subtype6 68 16
  subtype7 17  8
  subtype8 18  2
  subtype9 22  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      51       32       32       37       41       84       25       20 
subtype9 
      26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      13        7        5       12        9       16        8        2 
subtype9 
       4 
$subtype1
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 
       15.62        43.76        24.33        37.05        37.25        33.34 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 TCGA-AA-3502 
       32.91        30.44        22.52        24.16        21.76        35.01 
TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3553 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3866 
        1.02         0.00        24.00        35.05         0.99        17.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AD-5900 TCGA-AM-5820 TCGA-AZ-4308 TCGA-AZ-6600 
       18.05        18.05         0.07         0.46       109.28        12.10 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-5860 
        3.19         3.29        12.76        14.30         1.91        32.02 
TCGA-CM-5868 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-6534 
       17.03        21.99        14.99        13.02        11.08        43.27 
TCGA-D5-6922 TCGA-D5-6926 TCGA-DM-A1D6 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6463 
        4.41         9.04        49.91        26.47         8.61        35.74 
TCGA-F4-6704 TCGA-F4-6854 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6314 
        1.55         0.53        23.51        65.85        63.62        35.93 
TCGA-G4-6625 TCGA-NH-A6GA TCGA-QG-A5Z1 
       91.79         9.93         8.42 

$subtype2
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-5664 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3854 
        4.80        12.66        22.09        23.87        63.98        36.03 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01P 
       13.94        38.04        21.99         1.02        10.98        38.07 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02E TCGA-AD-6889 
        1.02        33.04        35.01        39.06         2.96        56.55 
TCGA-AD-6899 TCGA-AY-A71X TCGA-AZ-4682 TCGA-CA-5796 TCGA-CK-6747 TCGA-CM-4746 
        5.79        19.33        22.36         3.25        82.95        37.02 
TCGA-CM-6680 TCGA-D5-6920 TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6806 TCGA-QG-A5YV 
       12.03         3.68       139.17        60.79        41.42        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       32.98        31.30 

$subtype3
TCGA-A6-2678 TCGA-A6-6650 TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3561 TCGA-AA-3848 
       42.28        20.61         9.07        33.99        13.94        10.06 
TCGA-AA-3989 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
        7.96        30.02        34.03        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A029 
       34.98        15.02        32.02        31.00        35.01        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6965 
       39.98         5.03         0.92        39.98        40.96         0.20 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CM-6679 TCGA-D5-6535 
       33.01        17.26        29.56         1.61        10.06        15.12 
TCGA-DM-A1D9 TCGA-QG-A5YW 
      140.38        29.46 

$subtype4
TCGA-5M-AAT6 TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3558 TCGA-AA-3844 
        9.53        42.90        22.06        32.71        20.98        14.93 
TCGA-AA-3930 TCGA-AA-A01X TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-6598 
        2.01        26.01         5.65        32.94        65.00        49.41 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-5914 TCGA-CM-5861 TCGA-CM-5864 
       11.74        12.69         0.07         9.99        15.02        15.02 
TCGA-CM-6675 TCGA-D5-6532 TCGA-D5-6538 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       13.05        18.25        17.13        12.00        11.38       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28C 
       92.75        13.32         7.50       131.51        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 TCGA-G4-6299 TCGA-G4-6315 TCGA-QL-A97D 
      119.93        95.18        11.11        74.56        61.91        21.90 
TCGA-T9-A92H 
       11.90 

$subtype5
TCGA-A6-2672 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       46.65        35.11        16.57        37.02        32.75        36.53 
TCGA-A6-5667 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3530 
       29.16         7.04         3.02        58.03        38.99        19.07 
TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3688 
       34.03        19.99        61.02        54.02        47.01        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3864 
       17.98        38.99         0.00         0.00         0.99        53.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       33.01        20.98        21.99        16.08        50.99        34.06 
TCGA-AA-3982 TCGA-CA-5255 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       27.02         3.06        29.06        22.03        22.98 

$subtype6
TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 
       45.60        34.65        31.63        29.19        25.08        25.18 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3511 TCGA-AA-3532 TCGA-AA-3554 
       24.39        20.12        19.66         6.97        29.00        17.95 
TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3862 
        0.92         5.98        15.95        36.95         0.00        30.05 
TCGA-AA-3869 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R 
       27.02        24.00        19.07        38.04         4.01         0.99 
TCGA-AA-A01Q TCGA-AA-A03F TCGA-AD-6548 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-A69D 
        1.02        18.05        21.37         0.92        27.09        17.85 
TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-AZ-6605 
       18.84        58.39         1.41         5.13       100.01         5.23 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 
       10.06        21.14       124.27        23.05        20.02        13.02 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 
        5.03         2.96        12.99        14.04        12.95        11.01 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6539 
       19.59        20.19        20.42         1.32         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1HB 
       16.14        15.58         9.44        11.64         1.51       135.65 
TCGA-DM-A28F TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.97        35.74        47.87        34.42        16.24        33.67 
TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
       35.31        67.30        44.68        55.04        39.42        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       22.09        35.80        26.17        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL 
       18.18        19.33        15.65        17.85        16.80        30.28 

$subtype7
TCGA-A6-5661 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3552 
       33.53        24.03        37.05         8.05        29.00        13.02 
TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02R TCGA-AY-6197 
       33.04        30.05         2.01        14.01        22.03        21.44 
TCGA-AZ-6599 TCGA-CA-5256 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6170 
        6.77         2.14        26.04        30.08        12.00        15.02 
TCGA-D5-6531 TCGA-D5-6536 TCGA-DM-A1D8 TCGA-DM-A280 TCGA-F4-6570 TCGA-G4-6293 
       17.75        17.85        12.59         7.76         6.18       133.18 
TCGA-G4-6304 
       53.62 

$subtype8
TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-AA-3819 TCGA-AA-3973 
       23.61        27.09        24.13         8.38        25.02        13.05 
TCGA-AY-6386 TCGA-AZ-5407 TCGA-CA-6716 TCGA-CM-6161 TCGA-CM-6172 TCGA-CM-6676 
       17.82        88.21        12.20        15.02        11.01        11.08 
TCGA-F4-6460 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6320 
       31.96        28.21         8.35        82.39        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 
       26.04        13.78 

$subtype9
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3555 TCGA-AA-3562 
       24.69        20.28        24.92         1.02        29.95        19.99 
TCGA-AA-A01K TCGA-AA-A02W TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5863 TCGA-CM-6164 
       31.00        41.00        25.02         8.02        15.02        29.03 
TCGA-CM-6165 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6898 TCGA-D5-6923 
       16.04        12.26        56.09        55.92         1.48        12.43 
TCGA-D5-6924 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DB TCGA-F4-6809 TCGA-F4-6855 
       14.30        38.20       130.65        44.32        13.25        47.41 
TCGA-NH-A5IV TCGA-NH-A6GC 
       19.33        12.79 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.00     1.02     0.20     0.07     0.00     0.00     2.01     8.35 
subtype9 
    1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  109.28   139.17   140.38   131.51    85.05   135.65   133.18    88.21 
subtype9 
  130.65 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  18.050   27.585   29.510   17.130   26.990   20.070   17.850   23.870 
subtype9 
  22.485 
[1] "0.0 - 109.3 (18.1)" "1.0 - 139.2 (27.6)" "0.2 - 140.4 (29.5)"
[4] "0.1 - 131.5 (17.1)" "0.0 - 85.0 (27.0)"  "0.0 - 135.7 (20.1)"
[7] "2.0 - 133.2 (17.9)" "8.3 - 88.2 (23.9)"  "1.0 - 130.7 (22.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      11        0        0        16         0         0         0
  subtype2       6        0        2        12         0         0         4
  subtype3       5        0        3         6         1         0         2
  subtype4       3        0        1        12         2         1         1
  subtype5       4        0        8        11         2         0         4
  subtype6      17        0        3        33         1         0         5
  subtype7       2        0        1        13         1         0         1
  subtype8       3        1        1         4         0         0         1
  subtype9       3        0        1         9         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1          9          6        7         2         0
  subtype2          0          3          4        1         1         0
  subtype3          2          5          4        3         1         0
  subtype4          0          4          7        4         2         1
  subtype5          1          6          1        6         0         0
  subtype6          2          9          7        4         5         0
  subtype7          0          3          1        2         0         0
  subtype8          0          6          0        3         1         0
  subtype9          1          4          3        0         3         1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          11        6        5        3        4       17        2
  STAGE IA          0        0        0        0        0        0        0
  STAGE II          0        2        3        1        8        3        1
  STAGE IIA        16       12        6       12       11       33       13
  STAGE IIB         0        0        1        2        2        1        1
  STAGE IIC         0        0        0        1        0        0        0
  STAGE III         0        4        2        1        4        5        1
  STAGE IIIA        1        0        2        0        1        2        0
  STAGE IIIB        9        3        5        4        6        9        3
  STAGE IIIC        6        4        4        7        1        7        1
  STAGE IV          7        1        3        4        6        4        2
  STAGE IVA         2        1        1        2        0        5        0
  STAGE IVB         0        0        0        1        0        0        0
            clus
vv           subtype8 subtype9
  STAGE I           3        3
  STAGE IA          1        0
  STAGE II          1        1
  STAGE IIA         4        9
  STAGE IIB         0        1
  STAGE IIC         0        0
  STAGE III         1        0
  STAGE IIIA        0        1
  STAGE IIIB        6        4
  STAGE IIIC        0        3
  STAGE IV          3        0
  STAGE IVA         1        3
  STAGE IVB         0        1
[1] 13  9
[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 11 32  9
  subtype2  0  6 23  4
  subtype3  1  7 22  4
  subtype4  0  4 26  8
  subtype5  0  7 33  3
  subtype6  3 16 58  9
  subtype7  0  2 20  3
  subtype8  1  2 15  1
  subtype9  1  3 18  4
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        0        0        1        0        0        3        0        1
  T2       11        6        7        4        7       16        2        2
  T3       32       23       22       26       33       58       20       15
  T4        9        4        4        8        3        9        3        1
    clus
vv   subtype9
  T1        1
  T2        3
  T3       18
  T4        4
[1] 4 9
[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 27 13 12
  subtype2 21  7  5
  subtype3 16 11  7
  subtype4 19  6 13
  subtype5 28 11  4
  subtype6 57 15 14
  subtype7 17  5  3
  subtype8  9  9  2
  subtype9 15  8  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       27       21       16       19       28       57       17        9
  N1       13        7       11        6       11       15        5        9
  N2       12        5        7       13        4       14        3        2
    clus
vv   subtype9
  N0       15
  N1        8
  N2        3
[1] 3 9
[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 37  9
  subtype2 25  2
  subtype3 26  4
  subtype4 27  7
  subtype5 36  6
  subtype6 64  9
  subtype7 20  2
  subtype8 13  4
  subtype9 20  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    9
  subtype2   25    2
  subtype3   26    4
  subtype4   27    7
  subtype5   36    6
  subtype6   64    9
  subtype7   20    2
  subtype8   13    4
  subtype9   20    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       37       25       26       27       36       64       20       13
  1        9        2        4        7        6        9        2        4
   clus
vv  subtype9
  0       20
  1        4
[1] 2 9
[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 24 28
  subtype2 18 15
  subtype3 18 16
  subtype4 16 22
  subtype5 20 23
  subtype6 36 50
  subtype7 15 10
  subtype8  9 11
  subtype9 16 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   28
  subtype2   18   15
  subtype3   18   16
  subtype4   16   22
  subtype5   20   23
  subtype6   36   50
  subtype7   15   10
  subtype8    9   11
  subtype9   16   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       24       18       18       16       20       36       15
  MALE         28       15       16       22       23       50       10
        clus
vv       subtype8 subtype9
  FEMALE        9       16
  MALE         11       10
[1] 2 9
[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 39  2
  subtype2 24  0
  subtype3 27  1
  subtype4 25  1
  subtype5 36  2
  subtype6 72  1
  subtype7 21  0
  subtype8 20  0
  subtype9 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    2
  subtype2   24    0
  subtype3   27    1
  subtype4   25    1
  subtype5   36    2
  subtype6   72    1
  subtype7   21    0
  subtype8   20    0
  subtype9   21    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        39       24       27       25       36       72       21       20
  YES        2        0        1        1        2        1        0        0
     clus
vv    subtype9
  NO        21
  YES        0
[1] 2 9
[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 44  8
  subtype2 27  6
  subtype3 32  2
  subtype4 36  1
  subtype5 39  4
  subtype6 72 13
  subtype7 22  3
  subtype8 19  1
  subtype9 21  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    8
  subtype2   27    6
  subtype3   32    2
  subtype4   36    1
  subtype5   39    4
  subtype6   72   13
  subtype7   22    3
  subtype8   19    1
  subtype9   21    4
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                44       27       32       36       39
  COLON MUCINOUS ADENOCARCINOMA        8        6        2        1        4
                               clus
vv                              subtype6 subtype7 subtype8 subtype9
  COLON ADENOCARCINOMA                72       22       19       21
  COLON MUCINOUS ADENOCARCINOMA       13        3        1        4
[1] 2 9
[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 R2 RX
  subtype1 40  1  3
  subtype2 25  1  1
  subtype3 25  3  1
  subtype4 15  3  6
  subtype5 36  5  1
  subtype6 71  1  3
  subtype7 20  2  0
  subtype8 12  1  1
  subtype9 21  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       40       25       25       15       36       71       20       12
  R2        1        1        3        3        5        1        2        1
  RX        3        1        1        6        1        3        0        1
    clus
vv   subtype9
  R0       21
  R2        0
  RX        0
[1] 3 9
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         8
  subtype2                                0     2                         8
  subtype3                                0     0                         4
  subtype4                                0     2                         4
  subtype5                                0     1                         1
  subtype6                                0     1                        13
  subtype7                                0     1                         1
  subtype8                                0     1                         4
  subtype9                                0     0                         4
          vv
clus       WHITE
  subtype1    30
  subtype2     9
  subtype3     7
  subtype4    28
  subtype5     9
  subtype6    55
  subtype7    13
  subtype8    13
  subtype9    17
D6V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        2        0        2        1
  BLACK OR AFRICAN AMERICAN               8        8        4        4        1
  WHITE                                  30        9        7       28        9
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0
  ASIAN                                   1        1        1        0
  BLACK OR AFRICAN AMERICAN              13        1        4        4
  WHITE                                  55       13       13       17
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
          cls
clus        0  1
  subtype1  0 42
  subtype2  0 17
  subtype3  0  9
  subtype4  1 32
  subtype5  1 10
  subtype6  0 69
  subtype7  0 14
  subtype8  0 18
  subtype9  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   42
  subtype2    0   17
  subtype3    0    9
  subtype4    1   32
  subtype5    1   10
  subtype6    0   69
  subtype7    0   14
  subtype8    0   18
  subtype9    0   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        0        1        1        0
  NOT HISPANIC OR LATINO       42       17        9       32       10       69
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            0        0        0
  NOT HISPANIC OR LATINO       14       18       21
[1] 2 9
[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  85  32
  subtype2  86  20
  subtype3  66  23
  subtype4 104  25
subtype1 subtype2 subtype3 subtype4 
     117      106       89      129 
subtype1 subtype2 subtype3 subtype4 
      32       20       23       25 
$subtype1
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2677 TCGA-A6-4105 
       15.62         4.80         1.61        39.45        24.33        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       32.91        30.44        29.19        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-A567 
       27.09        24.13        25.18        20.61        24.69        61.84 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3526 
        1.02        37.05        62.96         6.97        38.99        19.07 
TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3675 
       19.07        29.00        26.01        78.08         6.05        47.05 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3955 TCGA-AA-3976 
       37.05         5.03        85.05        24.03        20.98        26.01 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02F 
       38.04        27.02        31.00         1.02        26.01        39.98 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 
        5.03        14.01        41.00        15.52         0.79        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-4684 
        0.20        16.44        14.50        18.84        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
       62.79        29.56         1.61         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5344 
       12.20       148.01        49.08         9.99        25.02        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       21.99        15.02        11.08        11.01        45.40        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A0XF 
       18.25         1.32         4.80        17.13         4.80        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      131.51       139.17         6.12        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6854 
       35.97        60.79       117.07        31.96        33.67         0.53 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       28.21        23.51        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F7 TCGA-QG-A5YV 
       36.00        46.75        18.18        10.98        17.85        42.77 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-T9-A92H 
        8.42        30.28        11.90 

$subtype2
TCGA-4T-AA8H TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 
       12.66        33.53        22.06         8.38        24.16        24.39 
TCGA-A6-6780 TCGA-A6-A565 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3518 
       20.12        16.24         3.02        35.01        58.03         1.02 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       37.05         8.05        23.01        61.02         6.97        54.02 
TCGA-AA-3680 TCGA-AA-3713 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 
       11.01        19.04        33.07         0.00        36.03        30.05 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02Y 
       53.00         4.01        37.02        39.06        51.98        39.98 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       18.05        56.55        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.85        19.33        75.95        58.39         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
        5.13        88.21        49.41         6.77        12.10        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.69         3.06         3.25        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       15.62        51.32        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6171 TCGA-CM-6172 
       37.02        27.02        15.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 
       13.05        12.03        19.59        20.42        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.49        16.14         3.68         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
      119.70        24.43        49.91         7.50       135.65         7.76 
TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       14.04        98.24        95.18        41.42        35.31       133.18 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       53.62        85.48        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       35.80        26.17        19.33         9.93        15.65        12.79 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D 
       29.46        32.98        31.30        21.90 

$subtype3
TCGA-5M-AAT6 TCGA-A6-2675 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
        9.53        43.43        13.94        37.05        37.25        37.02 
TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       33.34        31.63        22.09        22.52        25.08        21.76 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       23.87        19.66        20.28        24.92        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3870 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6548 
        7.04         1.02        29.98        38.07         0.07        21.37 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         5.79        22.42        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AZ-4323 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 
       27.09         1.41       100.01         5.23         3.19        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-5349 
       10.06        14.30        21.14         1.91        22.98        30.08 
TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       32.02        12.00        16.04        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 
       12.95        11.08        10.06        12.26        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.75        43.27        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6932 TCGA-F4-6459 
       14.30         9.04         9.44        11.64        11.38         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       34.42        16.24        13.25        47.41         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6625 
       74.56        67.30        65.85        39.42        35.93        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A8F8 TCGA-WS-AB45 
       74.79        79.69        19.33        16.80        70.03 

$subtype4
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       43.76        46.65        43.76        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       35.11        45.60        16.57        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3519 
       32.45         5.03        63.98         1.02        13.02         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 
       24.03        36.03         0.00        34.03        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       17.95        29.95        19.99        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       10.06         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3862 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 
       34.03         2.01        21.99        36.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        18.05        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        12.00        31.00         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       33.04        35.01         2.96         2.01         0.92        22.03 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4748 
       40.96        16.31         0.95       109.28       106.75        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        8.02        13.02        29.06 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.00     0.07     0.00 
subtype1 subtype2 subtype3 subtype4 
  148.01   135.65   100.01   109.28 
subtype1 subtype2 subtype3 subtype4 
   25.02    21.67    17.75    22.03 
[1] "0.1 - 148.0 (25.0)" "0.0 - 135.7 (21.7)" "0.1 - 100.0 (17.8)"
[4] "0.0 - 109.3 (22.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      19        0        6        30         0         1         5
  subtype2      22        1        9        36         3         0         4
  subtype3      10        0        4        33         1         0         2
  subtype4      23        0       10        39         5         0        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         18          9       14        11         0
  subtype2          2         14          8        5         2         2
  subtype3          1         14          9       11         3         0
  subtype4          4         13         14       15         1         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          19       22       10       23
  STAGE IA          0        1        0        0
  STAGE II          6        9        4       10
  STAGE IIA        30       36       33       39
  STAGE IIB         0        3        1        5
  STAGE IIC         1        0        0        0
  STAGE III         5        4        2       10
  STAGE IIIA        2        2        1        4
  STAGE IIIB       18       14       14       13
  STAGE IIIC        9        8        9       14
  STAGE IV         14        5       11       15
  STAGE IVA        11        2        3        1
  STAGE IVB         0        2        0        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 23 80 14
  subtype2  2 21 72 12
  subtype3  1  9 65 16
  subtype4  5 24 93 13
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        2        1        5
  T2       23       21        9       24
  T3       80       72       65       93
  T4       14       12       16       13
[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 66 33 21
  subtype2 73 21 14
  subtype3 49 22 20
  subtype4 79 29 27
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       66       73       49       79
  N1       33       21       22       29
  N2       21       14       20       27
[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"
D7V6, binary
          cls
clus         0   1
  subtype1  75  25
  subtype2  77   9
  subtype3  63  14
  subtype4 116  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   25
  subtype2   77    9
  subtype3   63   14
  subtype4  116   16
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       75       77       63      116
  1       25        9       14       16
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 47 73
  subtype2 56 52
  subtype3 39 52
  subtype4 72 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   73
  subtype2   56   52
  subtype3   39   52
  subtype4   72   63
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       47       56       39       72
  MALE         73       52       52       63
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1  90   2
  subtype2  86   2
  subtype3  78   1
  subtype4 107   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90    2
  subtype2   86    2
  subtype3   78    1
  subtype4  107    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        90       86       78      107
  YES        2        2        1        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"
D7V9, binary
          cls
clus         0   1
  subtype1 116   2
  subtype2  81  25
  subtype3  77  14
  subtype4 114  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  116    2
  subtype2   81   25
  subtype3   77   14
  subtype4  114   20
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA               116       81       77      114
  COLON MUCINOUS ADENOCARCINOMA        2       25       14       20
[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  71   0   8   7
  subtype2  71   2   2  11
  subtype3  67   0   2   7
  subtype4 117   1  12   0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       71       71       67      117
  R1        0        2        0        1
  R2        8        2        2       12
  RX        7       11        7        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        18
  subtype2                                0     4                        24
  subtype3                                1     3                        13
  subtype4                                0     0                         3
          vv
clus       WHITE
  subtype1    69
  subtype2    57
  subtype3    69
  subtype4    18
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   4        4        3        0
  BLACK OR AFRICAN AMERICAN              18       24       13        3
  WHITE                                  69       57       69       18
[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"
D7V13, binary
          cls
clus        0  1
  subtype1  3 83
  subtype2  0 81
  subtype3  1 82
  subtype4  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   83
  subtype2    0   81
  subtype3    1   82
  subtype4    0   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        1        0
  NOT HISPANIC OR LATINO       83       81       82       21
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  60  19
  subtype2  81  24
  subtype3  69  24
  subtype4 101  25
  subtype5  30   8
subtype1 subtype2 subtype3 subtype4 subtype5 
      79      105       93      126       38 
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       24       24       25        8 
$subtype1
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 
       15.62        43.43        37.05        37.25        31.63        30.44 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       23.61        22.09        29.16        22.52        25.08        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       23.87        20.28        61.84        56.25         9.63         7.04 
TCGA-AA-3511 TCGA-AA-A01X TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-4323 
        6.97        26.01         5.79        22.42         0.46         1.41 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 
       62.79        29.56         5.23         3.29        12.76        14.30 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        1.91        25.02        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
        5.03        17.03         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       12.99        13.02        15.02        11.08        11.01        10.06 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       56.09        55.92        17.75        43.27        17.85         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A28A 
        4.41        12.43        14.30         9.04        11.38        26.47 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        8.61        31.96        35.74        34.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
        0.53        47.41        82.39        23.51        67.30        65.85 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6627 TCGA-NH-A8F8 
       63.62        39.42        35.93        91.79        74.79        16.80 
TCGA-QG-A5Z1 
        8.42 

$subtype2
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2682 TCGA-A6-4105 
        4.80        12.66         1.61        39.45        13.94        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 
       32.91        29.19        32.71        27.09        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3495 TCGA-AA-3496 
       20.61        24.69        20.12        24.92        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3526 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       58.03        62.96        19.07        61.02        78.08         6.05 
TCGA-AA-3675 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-A01Z TCGA-AA-A02K TCGA-AA-A02Y 
       47.05        37.05        85.05        37.02        14.01        39.98 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       21.37        15.52         0.79        27.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        33.01        17.82        17.26        17.85        18.84 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 
       58.39        22.36        65.00         1.61         2.14         0.07 
TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
       12.20        17.56       148.01        49.08         9.99        82.95 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6677 TCGA-D5-5537 
       15.02        15.02        21.99        11.01        11.08        45.40 
TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       12.26        20.19        18.25         1.32        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       17.13        15.58         4.80       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 
       92.75        13.32        12.59       140.38        44.32       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        6.12        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
      117.07        95.18        33.67       133.18        28.21         8.35 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       44.68        55.04        61.91        36.00        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       10.98        19.33        17.85        42.77        29.46        32.98 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       21.90        30.28        11.90 

$subtype3
TCGA-5M-AAT6 TCGA-A6-2686 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 
        9.53        37.02        33.53        22.06         8.38        24.16 
TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-A565 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3663 
       24.39        19.66        16.24         3.02        35.01         6.97 
TCGA-AA-3713 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       19.04        38.07         0.07        56.55         0.72        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4614 
        0.92        27.09        21.44        19.33        75.95         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       32.94         5.13        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       10.06        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 
      124.27        23.05        20.02        27.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 
       12.00        14.04        12.95        13.05        12.03        19.59 
TCGA-D5-6530 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       20.42        12.49        16.14         3.68         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA 
        1.51        12.00        10.26        24.43        49.91         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6569 
      131.51       135.65         7.76        98.24        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6299 
        6.18        47.87         1.55        41.42        35.31        74.56 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       53.62        85.48        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       35.80        26.17        79.69        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 
       12.79        31.30        70.03 

$subtype4
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3494 
       16.57        34.65        36.53        32.45         5.03         1.02 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       36.03         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       24.00        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 
        0.92        50.04        47.01        15.02        11.01        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       36.00         5.03        35.05         0.99        25.02        17.98 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        33.07        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       18.05         2.01        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03        21.99        36.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
        7.96        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 
       31.00        31.00         1.02        33.04        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 
       41.00        18.05        40.96        16.31         0.95       109.28 
TCGA-AZ-4681 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
      106.75        37.02        26.04         8.02        13.02        29.06 

$subtype5
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3516 
       46.65        43.76        42.90        33.34        32.75        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        1.02         8.05         0.99        17.95        29.95        23.01 
TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       54.02         5.98        26.99        19.04        10.06        33.04 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
        1.02        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
       31.00        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q 
       27.02        30.02        18.05         4.01         0.99         1.02 
TCGA-AA-A01R TCGA-AA-A02R 
       35.01        22.03 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.07     0.07     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.79   148.01   135.65   109.28    54.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.030   22.360   19.330   24.030   23.505 
[1] "0.5 - 91.8 (22.0)"  "0.1 - 148.0 (22.4)" "0.1 - 135.7 (19.3)"
[4] "0.0 - 109.3 (24.0)" "0.0 - 54.0 (23.5)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       9        0        3        25         1         0         2
  subtype2      15        0        8        34         0         1         4
  subtype3      20        1        4        31         2         0         3
  subtype4      24        0        9        35         2         0         8
  subtype5       6        0        5        13         4         0         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1         16          5        7         8         0
  subtype2          1         18          7        8         7         0
  subtype3          2         10         12        6         1         2
  subtype4          5         10         16       23         1         0
  subtype5          0          5          0        1         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           9       15       20       24        6
  STAGE IA          0        0        1        0        0
  STAGE II          3        8        4        9        5
  STAGE IIA        25       34       31       35       13
  STAGE IIB         1        0        2        2        4
  STAGE IIC         0        1        0        0        0
  STAGE III         2        4        3        8        4
  STAGE IIIA        1        1        2        5        0
  STAGE IIIB       16       18       10       10        5
  STAGE IIIC        5        7       12       16        0
  STAGE IV          7        8        6       23        1
  STAGE IVA         8        7        1        1        0
  STAGE IVB         0        0        2        0        0
[1] 13  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  1 10 55 13
  subtype2  2 16 78 11
  subtype3  3 18 60 14
  subtype4  4 27 91 11
  subtype5  1  6 26  6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        2        3        4        1
  T2       10       16       18       27        6
  T3       55       78       60       91       26
  T4       13       11       14       11        6
[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 39 28 12
  subtype2 66 24 17
  subtype3 60 18 18
  subtype4 73 29 31
  subtype5 29  6  4
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       39       66       60       73       29
  N1       28       24       18       29        6
  N2       12       17       18       31        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"
D8V6, binary
          cls
clus         0   1
  subtype1  52  15
  subtype2  70  15
  subtype3  65   9
  subtype4 107  24
  subtype5  37   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   15
  subtype2   70   15
  subtype3   65    9
  subtype4  107   24
  subtype5   37    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       52       70       65      107       37
  1       15       15        9       24        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"
D8V7, binary
          cls
clus        0  1
  subtype1 33 46
  subtype2 46 61
  subtype3 47 49
  subtype4 63 70
  subtype5 25 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   46
  subtype2   46   61
  subtype3   47   49
  subtype4   63   70
  subtype5   25   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       33       46       47       63       25
  MALE         46       61       49       70       14
[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"
D8V8, binary
          cls
clus         0   1
  subtype1  73   2
  subtype2  80   1
  subtype3  74   2
  subtype4 105   3
  subtype5  29   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    2
  subtype2   80    1
  subtype3   74    2
  subtype4  105    3
  subtype5   29    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        73       80       74      105       29
  YES        2        1        2        3        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"
D8V9, binary
          cls
clus         0   1
  subtype1  73   6
  subtype2  98   7
  subtype3  72  23
  subtype4 124   8
  subtype5  21  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    6
  subtype2   98    7
  subtype3   72   23
  subtype4  124    8
  subtype5   21   17
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                73       98       72      124       21
  COLON MUCINOUS ADENOCARCINOMA        6        7       23        8       17
[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  59   0   0   5
  subtype2  62   0   2   9
  subtype3  59   2   2  11
  subtype4 110   1  20   0
  subtype5  36   0   0   0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       59       62       59      110       36
  R1        0        0        2        1        0
  R2        0        2        2       20        0
  RX        5        9       11        0        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"
D8V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        13
  subtype2                                0     3                        24
  subtype3                                1     5                        17
  subtype4                                0     0                         4
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    60
  subtype2    65
  subtype3    68
  subtype4    15
  subtype5     5
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   3        3        5        0        0
  BLACK OR AFRICAN AMERICAN              13       24       17        4        0
  WHITE                                  60       65       68       15        5
[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"
D8V13, binary
          cls
clus        0  1
  subtype1  1 72
  subtype2  2 84
  subtype3  1 87
  subtype4  0 19
  subtype5  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   72
  subtype2    2   84
  subtype3    1   87
  subtype4    0   19
  subtype5    0    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        2        1        0        0
  NOT HISPANIC OR LATINO       72       84       87       19        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"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 125  32
  subtype2  49  17
  subtype3 130  40
subtype1 subtype2 subtype3 
     157       66      170 
subtype1 subtype2 subtype3 
      32       17       40 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       43.43        14.53        32.91        30.44        29.19        33.53 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       22.06        32.71        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3496 
       25.18        20.61        24.39        20.12        20.28         1.02 
TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 
        6.97        61.02        78.08         6.05         6.97        85.05 
TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       19.04         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       27.42         0.20         0.92        14.50        27.09        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       21.44        17.82         5.13        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       12.10        11.74         1.61        12.69         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
      124.27        23.05        27.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       15.02         2.96        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       20.19        20.42        17.75        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XD 
        3.68        12.43         4.80        12.00       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6570 
       60.79       117.07        98.24        95.18        35.74         6.18 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       33.67        47.41       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        39.42        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       79.69 

$subtype2
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5662 
       45.60        37.05        37.25        33.34        31.63        23.61 
TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.09        22.52         8.38        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X 
       23.87        19.66         7.04        27.02        38.07        26.01 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AZ-4323 
        0.72         5.79        22.42        10.88         0.46         1.41 
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 
       62.79       100.01        29.56         5.23         3.19         3.06 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-4748 TCGA-CM-6162 TCGA-CM-6167 
       12.76        10.06         1.91        26.04        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6898 
       12.99        12.95        10.06        19.59        43.27         1.48 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.41        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
       11.38        10.26         8.61        31.96        11.11        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6627 
        0.53        35.31        67.30        63.62        35.93        74.79 

$subtype3
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        13.94        16.57        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3494 
       32.75        36.53        32.45         5.03         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3514 
       37.05        35.01        58.03        62.96        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        30.05        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 
       34.03         2.01        21.99        36.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00J 
       27.02        19.07         7.96        27.02        19.00        18.05 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D 
       38.04        42.02        17.03        14.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       32.02        12.00        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       40.96        16.31         0.95       109.28        75.95        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-5256 
        5.65        32.94       106.75        22.36        65.00         2.14 
TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       70.16        20.02        37.02        25.02         8.02        13.02 
TCGA-CM-5341 TCGA-DM-A1D6 
       29.06        49.91 

subtype1 subtype2 subtype3 
    0.07     0.46     0.00 
subtype1 subtype2 subtype3 
  148.01   100.01   109.28 
subtype1 subtype2 subtype3 
  22.060   17.915   24.180 
[1] "0.1 - 148.0 (22.1)" "0.5 - 100.0 (17.9)" "0.0 - 109.3 (24.2)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      24        1        7        56         2         1         7
  subtype2       7        0        3        21         0         0         2
  subtype3      35        0       18        44         6         0        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         26         12       11         6         1
  subtype2          2         11          8        4         4         0
  subtype3          4         15         13       27         5         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          24        7       35
  STAGE IA          1        0        0
  STAGE II          7        3       18
  STAGE IIA        56       21       44
  STAGE IIB         2        0        6
  STAGE IIC         1        0        0
  STAGE III         7        2       12
  STAGE IIIA        2        2        4
  STAGE IIIB       26       11       15
  STAGE IIIC       12        8       13
  STAGE IV         11        4       27
  STAGE IVA         6        4        5
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   5  23 116  15
  subtype2   0   9  46  11
  subtype3   6  36 118  20
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        0        6
  T2       23        9       36
  T3      116       46      118
  T4       15       11       20
[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  97  40  23
  subtype2  33  19  14
  subtype3 108  37  35
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       97       33      108
  N1       40       19       37
  N2       23       14       35
[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"
D9V6, binary
          cls
clus         0   1
  subtype1 113  18
  subtype2  48   8
  subtype3 144  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113   18
  subtype2   48    8
  subtype3  144   32
   clus
vv  subtype1 subtype2 subtype3
  0      113       48      144
  1       18        8       32
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 74 86
  subtype2 27 39
  subtype3 90 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74   86
  subtype2   27   39
  subtype3   90   90
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       74       27       90
  MALE         86       39       90
[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"
D9V8, binary
          cls
clus         0   1
  subtype1 118   1
  subtype2  57   3
  subtype3 144   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118    1
  subtype2   57    3
  subtype3  144    4
     clus
vv    subtype1 subtype2 subtype3
  NO       118       57      144
  YES        1        3        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"
D9V9, binary
          cls
clus         0   1
  subtype1 143  14
  subtype2  52  14
  subtype3 153  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  143   14
  subtype2   52   14
  subtype3  153   25
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               143       52      153
  COLON MUCINOUS ADENOCARCINOMA       14       14       25
[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  94   1   2  15
  subtype2  43   0   0   5
  subtype3 145   2  23   2
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       94       43      145
  R1        1        0        2
  R2        2        0       23
  RX       15        5        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"
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        12
  subtype2                                1     3                         7
  subtype3                                0     1                         4
          vv
clus       WHITE
  subtype1   132
  subtype2    51
  subtype3    30
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   7        3        1
  BLACK OR AFRICAN AMERICAN              12        7        4
  WHITE                                 132       51       30
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
          cls
clus         0   1
  subtype1   1 146
  subtype2   0  59
  subtype3   0  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  146
  subtype2    0   59
  subtype3    0   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO      146       59       34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 101  32
  subtype2  40  10
  subtype3  58  18
  subtype4 105  29
subtype1 subtype2 subtype3 subtype4 
     133       50       76      134 
subtype1 subtype2 subtype3 subtype4 
      32       10       18       29 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5665 
       43.43        14.53        32.91        30.44        33.53        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       32.71        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3660 
        7.04        35.01         6.97         1.02        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3861 TCGA-AA-A010 
        6.05         6.97        85.05        19.04        30.05        34.98 
TCGA-AA-A01Z TCGA-AA-A02H TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       37.02         2.01        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       22.42        27.42        14.50        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 
        1.41         5.13        88.21        49.41        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 
       11.74         1.61        12.69         3.06         3.25        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 
       85.45        15.62        49.08        51.32        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       23.05        27.02        22.98        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       15.02         2.96        29.03        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.03        45.40        55.92        20.19        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       15.12         4.80        12.49        16.14        15.58         3.68 
TCGA-D5-6923 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.43        11.64       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76        14.04        26.47        81.37       119.93 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6806 
      117.07        98.24        95.18        11.11         6.18        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.24        33.67        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       82.39        53.62        44.68        85.48        39.42        36.00 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        26.04        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       79.69 

$subtype2
TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6654 TCGA-AD-5900 
       31.63        23.61        29.16        24.16        23.87         0.07 
TCGA-AD-6895 TCGA-AM-5820 TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 
        0.72         0.46        27.09        62.79       100.01        29.56 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 
        3.19        12.76        10.06        14.30        21.14         1.91 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       22.03        30.08        15.02        17.03        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6534 
       14.99        12.99        12.95        19.59        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       17.85         1.48         4.41         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       11.38        10.26         8.61        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 
       34.42        13.25         0.53        67.30        65.85        63.62 
TCGA-G4-6320 TCGA-G4-6627 
       26.43        74.79 

$subtype3
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6142 
       43.76        24.33        42.28        29.19        22.09        25.08 
TCGA-A6-6651 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3517 
       21.76         1.02         1.02        58.03        62.96        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        9.07        24.03         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3678 
       26.01        12.99        23.01        13.94        19.99        47.01 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
       11.01        36.00         5.03        25.02        17.98        38.99 
TCGA-AA-3852 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-3989 
        0.00        24.03        18.05        26.01        19.07         7.96 
TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02J TCGA-AA-A02K 
       38.04        17.03         1.02        26.01         5.03        14.01 
TCGA-AD-6548 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-6599 TCGA-CA-5256 
       21.37        10.88         0.20        16.31         6.77         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4750 
        3.29         0.07        12.20       148.01         9.99         8.02 
TCGA-CM-4752 TCGA-CM-6161 TCGA-CM-6166 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 
       13.02        15.02        21.99        12.26        56.09         1.32 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A282 TCGA-DM-A285 
       17.13        14.30         4.80        38.20       139.17         6.12 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6298 
       35.97        60.79        31.96        35.74         8.35        23.51 
TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6323 
       55.04        35.93        61.91        13.78 

$subtype4
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        46.65        42.90        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 
       33.34        32.75        36.53        32.45         5.03         3.02 
TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 
       37.05        63.98         1.02        13.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
        8.05        19.07        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3710 
       47.05        15.02         5.98        37.05        19.00        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        53.00        17.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       36.03        16.08        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00J 
       24.00        27.02        27.02        27.02        19.00        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       27.02        42.02        14.99        10.98        32.02        12.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       38.07        35.01        33.04        35.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.96        39.98         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AM-5821 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       40.96         0.92         0.95       109.28        75.95        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CK-4951 
        5.65        32.94       106.75        22.36        65.00        70.16 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-D5-6931 
       20.02        37.02        25.02        26.04        29.06        12.00 
TCGA-DM-A1HA TCGA-G4-6299 
      131.51        74.56 

subtype1 subtype2 subtype3 subtype4 
    0.79     0.07     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 
  140.38   100.01   148.01   131.51 
subtype1 subtype2 subtype3 subtype4 
  22.520   16.535   19.530   27.020 
[1] "0.8 - 140.4 (22.5)" "0.1 - 100.0 (16.5)" "0.0 - 148.0 (19.5)"
[4] "0.0 - 131.5 (27.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      20        0        7        50         4         1         5
  subtype2       6        0        2        19         0         0         1
  subtype3      11        1        4        19         0         0         5
  subtype4      29        0       15        33         4         0        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         17         11        9         5         1
  subtype2          2          9          2        3         4         0
  subtype3          2         12          8       14         1         0
  subtype4          2         14         12       16         5         0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          20        6       11       29
  STAGE IA          0        0        1        0
  STAGE II          7        2        4       15
  STAGE IIA        50       19       19       33
  STAGE IIB         4        0        0        4
  STAGE IIC         1        0        0        0
  STAGE III         5        1        5       10
  STAGE IIIA        2        2        2        2
  STAGE IIIB       17        9       12       14
  STAGE IIIC       11        2        8       12
  STAGE IV          9        3       14       16
  STAGE IVA         5        4        1        5
  STAGE IVB         1        0        0        0
[1] 13  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  4 20 95 17
  subtype2  1  6 39  4
  subtype3  2 13 56  7
  subtype4  4 29 90 18
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        1        2        4
  T2       20        6       13       29
  T3       95       39       56       90
  T4       17        4        7       18
[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 89 27 20
  subtype2 27 17  6
  subtype3 38 21 20
  subtype4 84 31 26
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       89       27       38       84
  N1       27       17       21       31
  N2       20        6       20       26
[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"
D10V6, binary
          cls
clus         0   1
  subtype1  97  15
  subtype2  36   7
  subtype3  55  15
  subtype4 117  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97   15
  subtype2   36    7
  subtype3   55   15
  subtype4  117   21
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       97       36       55      117
  1       15        7       15       21
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 57 79
  subtype2 23 27
  subtype3 40 39
  subtype4 71 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   79
  subtype2   23   27
  subtype3   40   39
  subtype4   71   70
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       57       23       40       71
  MALE         79       27       39       70
[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"
D10V8, binary
          cls
clus         0   1
  subtype1 105   2
  subtype2  40   2
  subtype3  59   1
  subtype4 115   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105    2
  subtype2   40    2
  subtype3   59    1
  subtype4  115    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       105       40       59      115
  YES        2        2        1        3
[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"
D10V9, binary
          cls
clus         0   1
  subtype1 118  16
  subtype2  40  10
  subtype3  71   6
  subtype4 119  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   16
  subtype2   40   10
  subtype3   71    6
  subtype4  119   21
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA               118       40       71      119
  COLON MUCINOUS ADENOCARCINOMA       16       10        6       21
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  76   1   3  11
  subtype2  37   0   0   5
  subtype3  51   1   9   5
  subtype4 118   1  13   1
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       76       37       51      118
  R1        1        0        1        1
  R2        3        0        9       13
  RX       11        5        5        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"
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        11
  subtype2                                1     3                         3
  subtype3                                0     4                         6
  subtype4                                0     0                         3
          vv
clus       WHITE
  subtype1   106
  subtype2    43
  subtype3    32
  subtype4    32
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   4        3        4        0
  BLACK OR AFRICAN AMERICAN              11        3        6        3
  WHITE                                 106       43       32       32
[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"
D10V13, binary
          cls
clus         0   1
  subtype1   0 116
  subtype2   1  48
  subtype3   0  40
  subtype4   0  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  116
  subtype2    1   48
  subtype3    0   40
  subtype4    0   35
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        0        0
  NOT HISPANIC OR LATINO      116       48       40       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 16 13
  subtype2 19 12
  subtype3 19  5
subtype1 subtype2 subtype3 
      29       31       24 
subtype1 subtype2 subtype3 
      13       12        5 
$subtype1
TCGA-A6-2675 TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-AD-6963 
       43.43         8.38        20.28         6.97        22.42        27.42 
TCGA-AD-6964 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CM-6674 TCGA-CM-6676 
       10.88         5.13        29.56         5.23        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-DM-A0XD 
       11.08        11.01        10.06        12.03        45.40        24.43 
TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A280 TCGA-DM-A282 
       38.20        13.32        12.59       140.38         7.76       139.17 
TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6625 
        6.12         6.18        33.67        74.56        91.79 

$subtype2
TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 
       31.63        29.16        25.08        24.16        21.76        23.87 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AD-5900 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6600 
       19.66         7.04         0.07         1.41        62.79        12.10 
TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 
      100.01         3.19        10.06        14.30        21.14         1.91 
TCGA-CM-5860 TCGA-CM-6167 TCGA-D5-6534 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       32.02        14.99        43.27         8.61        31.96        35.74 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 TCGA-G4-6314 
        1.55        34.42        16.24        13.25        67.30        35.93 
TCGA-G4-6627 
       74.79 

$subtype3
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6548 
       27.09        22.52        24.13        20.61        24.39        21.37 
TCGA-AD-6889 TCGA-AD-6965 TCGA-AZ-6598 TCGA-CM-4751 TCGA-D5-6533 TCGA-D5-6536 
       56.55         0.20        49.41        27.02         1.32        17.85 
TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F 
        4.41        14.30       130.65         7.50       131.51        35.97 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6628 
       28.21         8.35        65.85        44.68        85.48        79.69 

subtype1 subtype2 subtype3 
    5.13     0.07     0.20 
subtype1 subtype2 subtype3 
  140.38   100.01   131.51 
subtype1 subtype2 subtype3 
  12.950   21.760   25.705 
[1] "5.1 - 140.4 (12.9)" "0.1 - 100.0 (21.8)" "0.2 - 131.5 (25.7)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2        1        13         1          0          2
  subtype2       3        3         7         0          0          7
  subtype3       4        2         7         0          1          5
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        2         1
  subtype2          5        5         2
  subtype3          2        2         0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        3        4
  STAGE II          1        3        2
  STAGE IIA        13        7        7
  STAGE IIB         1        0        0
  STAGE IIIA        0        0        1
  STAGE IIIB        2        7        5
  STAGE IIIC        2        5        2
  STAGE IV          2        5        2
  STAGE IVA         1        2        0
[1] 9 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 21  5
  subtype2  1  2 25  4
  subtype3  0  5 17  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        1        0
  T2        2        2        5
  T3       21       25       17
  T4        5        4        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 18  4  7
  subtype2 13 11  8
  subtype3 14  7  3
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18       13       14
  N1        4       11        7
  N2        7        8        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 18  3
  subtype2 18  7
  subtype3 20  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    3
  subtype2   18    7
  subtype3   20    2
   clus
vv  subtype1 subtype2 subtype3
  0       18       18       20
  1        3        7        2
[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"
D11V7, binary
          cls
clus        0  1
  subtype1 14 15
  subtype2 15 17
  subtype3  9 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   15
  subtype2   15   17
  subtype3    9   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       15        9
  MALE         15       17       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0
  subtype1 21
  subtype2 28
  subtype3 16
[1] "NOT AVAILABLE: table only has an event [0]"
D11V9, binary
          cls
clus        0  1
  subtype1 25  2
  subtype2 25  7
  subtype3 24  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    2
  subtype2   25    7
  subtype3   24    0
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                25       25       24
  COLON MUCINOUS ADENOCARCINOMA        2        7        0
[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 RX
  subtype1 12  1
  subtype2 19  4
  subtype3 11  0
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       12       19       11
  RX        1        4        0
[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"
D11V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                1     2                         3
  subtype3                                0     1                         2
          vv
clus       WHITE
  subtype1    27
  subtype2    25
  subtype3    21
D11V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        2        1
  BLACK OR AFRICAN AMERICAN               1        3        2
  WHITE                                  27       25       21
[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"
D11V13, binary
          cls
clus        0
  subtype1 26
  subtype2 31
  subtype3 22
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1  6  5
  subtype2 14  8
  subtype3 12  5
  subtype4 16  8
  subtype5  6  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       22       17       24       10 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        8        5        8        4 
$subtype1
TCGA-A6-2675 TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-6901 TCGA-AZ-5403 TCGA-AZ-6600 
       43.43        20.28         7.04        22.42        62.79        12.10 
TCGA-AZ-6605 TCGA-CM-5860 TCGA-CM-6677 TCGA-CM-6679 TCGA-F4-6569 
        5.23        32.02        11.08        10.06        35.74 

$subtype2
TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-AD-6548 
       31.63        29.16        25.08        21.76        23.87        21.37 
TCGA-AZ-4323 TCGA-AZ-6603 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-6167 TCGA-D5-6922 
        1.41        29.56        14.30         1.91        14.99         4.41 
TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        6.12         8.61        31.96        34.42        16.24        13.25 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6627 
       67.30        65.85        35.93        74.79 

$subtype3
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6965 
       27.09        24.13        20.61        24.39        56.55         0.20 
TCGA-AZ-6598 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F 
       49.41        24.43       130.65         7.50       131.51        35.97 
TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 
       33.67        28.21         8.35        44.68        85.48 

$subtype4
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6781 TCGA-AD-5900 TCGA-AD-6963 
       22.52         8.38        24.16        19.66         0.07        27.42 
TCGA-AD-6964 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-6718 TCGA-CK-5916 
       10.88         5.13       100.01         3.19        10.06        21.14 
TCGA-CM-4751 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6534 TCGA-D5-6536 
       27.02        12.95        11.01        12.03        43.27        17.85 
TCGA-DM-A280 TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6625 TCGA-G4-6628 
        7.76         6.18         1.55        74.56        91.79        79.69 

$subtype5
TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF 
        6.97        11.08        45.40         1.32        14.30        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 
       13.32        12.59       140.38       139.17 

subtype1 subtype2 subtype3 subtype4 subtype5 
    5.23     1.41     0.20     0.07     1.32 
subtype1 subtype2 subtype3 subtype4 subtype5 
   62.79    74.79   131.51   100.01   140.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  20.280   22.815   28.210   15.400   13.810 
[1] "5.2 - 62.8 (20.3)"  "1.4 - 74.8 (22.8)"  "0.2 - 131.5 (28.2)"
[4] "0.1 - 100.0 (15.4)" "1.3 - 140.4 (13.8)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        2         4         1          0          1
  subtype2       1        0         4         0          1          6
  subtype3       2        2         6         0          0          3
  subtype4       4        1         8         0          0          3
  subtype5       1        1         5         0          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        1         0
  subtype2          2        5         2
  subtype3          2        1         0
  subtype4          3        2         1
  subtype5          1        0         0
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        2        4        1
  STAGE II          2        0        2        1        1
  STAGE IIA         4        4        6        8        5
  STAGE IIB         1        0        0        0        0
  STAGE IIIA        0        1        0        0        0
  STAGE IIIB        1        6        3        3        1
  STAGE IIIC        1        2        2        3        1
  STAGE IV          1        5        1        2        0
  STAGE IVA         0        2        0        1        0
[1] 9 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  8  3
  subtype2  0  2 19  1
  subtype3  1  2 13  1
  subtype4  1  3 16  4
  subtype5  0  1  7  2
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        1        1        0
  T2        1        2        2        3        1
  T3        8       19       13       16        7
  T4        3        1        1        4        2
[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  9  2  1
  subtype2  5 11  6
  subtype3 10  4  3
  subtype4 14  4  6
  subtype5  7  1  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        9        5       10       14        7
  N1        2       11        4        4        1
  N2        1        6        3        6        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  6  1
  subtype2 12  7
  subtype3 14  1
  subtype4 16  3
  subtype5  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2   12    7
  subtype3   14    1
  subtype4   16    3
  subtype5    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        6       12       14       16        8
  1        1        7        1        3        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"
D12V7, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2 17  5
  subtype3  7 10
  subtype4  8 16
  subtype5  5  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2   17    5
  subtype3    7   10
  subtype4    8   16
  subtype5    5    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1       17        7        8        5
  MALE         11        5       10       16        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"
D12V8, binary
          cls
clus        0
  subtype1 10
  subtype2 20
  subtype3 10
  subtype4 21
  subtype5  4
[1] "NOT AVAILABLE: table only has an event [0]"
D12V9, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2 19  3
  subtype3 17  0
  subtype4 19  5
  subtype5  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   19    3
  subtype3   17    0
  subtype4   19    5
  subtype5    8    0
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                11       19       17       19        8
  COLON MUCINOUS ADENOCARCINOMA        1        3        0        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"
          vv
clus       R0 RX
  subtype1  7  0
  subtype2 14  2
  subtype3  4  0
  subtype4 13  2
  subtype5  4  1
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7       14        4       13        4
  RX        0        2        0        2        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"
D12V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                0     1                         2
  subtype3                                0     1                         2
  subtype4                                1     1                         1
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    10
  subtype2    19
  subtype3    14
  subtype4    21
  subtype5     9
D12V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   0        1        1        1        0
  BLACK OR AFRICAN AMERICAN               1        2        2        1        0
  WHITE                                  10       19       14       21        9
[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"
D12V13, binary
          cls
clus        0
  subtype1 10
  subtype2 22
  subtype3 15
  subtype4 23
  subtype5  9
[1] "NOT AVAILABLE: table only has an event [0]"
