[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/22506513/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/22541003/COAD-TP.mergedcluster.txt"

nPatients in clinical file=458, in cluster file=459, common to both=457
[1]  12 457
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4  5 
33 18 49 28 25 
 1  2  3  4  5 
33 18 49 28 25 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
44 70 39 
 1  2  3 
44 70 39 
[1] "CN_CNMF"
[1] 3
  1   2   3 
 53 219 177 
  1   2   3 
 53 219 177 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 84 103 106 
  1   2   3 
 84 103 106 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
 87 144 127 
  1   2   3 
 87 144 127 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
52 33 34 38 43 87 25 20 26 
 1  2  3  4  5  6  7  8  9 
52 33 34 38 43 87 25 20 26 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
127  95  98 135 
  1   2   3   4 
127  95  98 135 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 79 108  96 133  39 
  1   2   3   4   5 
 79 108  96 133  39 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
 61  88  72  78 107 
  1   2   3   4   5 
 61  88  72  78 107 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
79 55 47 17 56 21 27 43 61 
 1  2  3  4  5  6  7  8  9 
79 55 47 17 56 21 27 43 61 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
18 20 16 11 11  9 
 1  2  3  4  5  6 
18 20 16 11 11  9 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
12  9  8 12  9  7 13  9  6 
 1  2  3  4  5  6  7  8  9 
12  9  8 12  9  7 13  9  6 
[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 457 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=89,	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=252,	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=10,	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 457 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  56 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  78 311  56 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  78 311  56 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  78 311  56 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
269 105  83 
[1] "table(vv)"
vv
 N0  N1  N2 
269 105  83 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
269 105  83 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
269 105  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 25  7
  subtype2 14  2
  subtype3 36 10
  subtype4 22  6
  subtype5 19  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      32       16       46       28       24 
subtype1 subtype2 subtype3 subtype4 subtype5 
       7        2       10        6        5 
$subtype1
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3715 
       13.02         8.05         0.99        17.95         0.92        19.04 
TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3555 
       24.00        46.65        42.90        32.75         1.02        29.95 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3845 
       26.99        10.06        33.04         1.02        15.95         0.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       31.00         2.01        33.01        26.01         2.01        25.02 
TCGA-AA-3980 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R 
       27.02        38.04        19.00        30.02        18.05         0.99 
TCGA-AA-A01Q TCGA-AA-A02R 
        1.02        22.03 

$subtype2
TCGA-AA-3520 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 TCGA-A6-2674 TCGA-A6-3807 
       24.03        24.03        29.98         2.01        43.76        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3538 TCGA-AA-3812 TCGA-AA-3842 
       33.34        36.53         1.02        26.01        35.05        37.02 
TCGA-AA-3866 TCGA-AA-3973 TCGA-AA-A01D TCGA-AA-A01K 
       17.03        13.05        10.98        31.00 

$subtype3
TCGA-A6-2677 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 
       24.33        36.03        19.07        34.03        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L 
       14.93        31.07        50.99        26.01        24.00        38.04 
TCGA-AA-A00Z TCGA-A6-2683 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3534 TCGA-AA-3542 
       21.99        16.57        38.99         9.07        29.00        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       33.99        21.01        24.00         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3955 
       15.02        36.95        10.06        27.02        18.05        20.98 
TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A00Q 
       21.99        34.06         7.96        13.94        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A02E TCGA-AA-A02F 
       14.99        15.02        15.02        32.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 
        2.01         5.03        41.00        16.31 

$subtype4
TCGA-AA-3522 TCGA-AA-3556 TCGA-AA-A024 TCGA-A6-2678 TCGA-AA-3526 TCGA-AA-3544 
       37.05        23.01        39.06        42.28        19.07        14.01 
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-3696 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 
        5.03         0.99        38.99         0.00        36.03        30.05 
TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3994 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U 
       53.00        24.00        27.02        18.05         4.01        17.03 
TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 
       34.98        12.00        31.00        51.98 

$subtype5
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3986 
       13.02        19.99        36.00        30.05        12.99        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3831 
        0.00        29.00        50.04        37.05        25.02        17.98 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.00        33.07        32.05         0.99        31.07 
TCGA-AA-3956 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4071 
       34.03        36.03        16.08        27.02        34.03         0.95 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.00     1.02     2.01     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   46.65    43.76    50.99    54.02    50.04 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.020   27.995   21.500   23.505   26.020 
[1] "0.0 - 46.6 (19.0)" "1.0 - 43.8 (28.0)" "2.0 - 51.0 (21.5)"
[4] "0.0 - 54.0 (23.5)" "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        2        13         3         3          0          4
  subtype2       3        1         4         0         0          1          0
  subtype3       9        2        10         0         3          2          4
  subtype4       6        5         8         2         1          0          3
  subtype5       5        2        10         0         1          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          0        1         0
  subtype2          4        5         0
  subtype3          8       11         0
  subtype4          0        2         1
  subtype5          4        2         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6        3        9        6        5
  STAGE II          2        1        2        5        2
  STAGE IIA        13        4       10        8       10
  STAGE IIB         3        0        0        2        0
  STAGE III         3        0        3        1        1
  STAGE IIIA        0        1        2        0        0
  STAGE IIIB        4        0        4        3        1
  STAGE IIIC        0        4        8        0        4
  STAGE IV          1        5       11        2        2
  STAGE IVA         0        0        0        1        0
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  6 22  4
  subtype2  0  4 12  2
  subtype3  2 11 32  4
  subtype4  0  6 18  4
  subtype5  1  4 19  1
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        0        2        0        1
  T2        6        4       11        6        4
  T3       22       12       32       18       19
  T4        4        2        4        4        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 25  5  3
  subtype2  8  2  8
  subtype3 23 13 13
  subtype4 21  6  1
  subtype5 17  2  6
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       25        8       23       21       17
  N1        5        2       13        6        2
  N2        3        8       13        1        6
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 31  1
  subtype2 13  5
  subtype3 38 11
  subtype4 25  3
  subtype5 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    1
  subtype2   13    5
  subtype3   38   11
  subtype4   25    3
  subtype5   22    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       31       13       38       25       22
  1        1        5       11        3        2
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 24  9
  subtype2 10  8
  subtype3 25 24
  subtype4  9 19
  subtype5  7 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    9
  subtype2   10    8
  subtype3   25   24
  subtype4    9   19
  subtype5    7   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       10       25        9        7
  MALE          9        8       24       19       18
[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"
D1V8, binary
          cls
clus        0  1
  subtype1 26  0
  subtype2 14  0
  subtype3 40  2
  subtype4 24  0
  subtype5 20  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    0
  subtype2   14    0
  subtype3   40    2
  subtype4   24    0
  subtype5   20    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        26       14       40       24       20
  YES        0        0        2        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1 22 11
  subtype2 16  2
  subtype3 49  0
  subtype4 20  7
  subtype5 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   11
  subtype2   16    2
  subtype3   49    0
  subtype4   20    7
  subtype5   22    2
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                22       16       49       20       22
  COLON MUCINOUS ADENOCARCINOMA       11        2        0        7        2
[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
  subtype1 28  0  1
  subtype2 15  0  3
  subtype3 38  1 10
  subtype4 25  0  3
  subtype5 22  0  2
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       28       15       38       25       22
  R1        0        0        1        0        0
  R2        1        3       10        3        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"
D1V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     3
  subtype2                         0     4
  subtype3                         1     2
  subtype4                         0     1
  subtype5                         0     1
D1V12, multiclass
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        4        3        1        1 
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype3"
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                            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"
D1V13, binary
          cls
clus       0
  subtype1 3
  subtype2 4
  subtype3 3
  subtype4 1
  subtype5 1
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 33 10
  subtype2 51 17
  subtype3 32  3
subtype1 subtype2 subtype3 
      43       68       35 
subtype1 subtype2 subtype3 
      10       17        3 
$subtype1
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       13.02         8.05         0.99        17.95        23.01         0.92 
TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       19.04        29.98        24.00        46.65        43.76        42.90 
TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       33.34        32.75         1.02         1.02        19.07        29.95 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 
       26.99        10.06        33.04         1.02        15.95        37.02 
TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00         0.00        36.03        53.00        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       33.01        26.01         2.01        25.02        27.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01Q 
       30.02        18.05         4.01         0.99        10.98         1.02 
TCGA-AA-A02R 
       22.03 

$subtype2
TCGA-A6-2677 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 
       24.33        24.03        37.05        36.03        19.07        34.03 
TCGA-AA-3560 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       19.99        36.00        14.93        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-A6-2678 
       26.01        24.00        38.04        21.99        39.06        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3534 
       16.57        34.65        36.53         9.07         0.00        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 
       14.01        33.99        21.01        20.98        13.94        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
        2.01        50.04        47.05        11.01         5.98         5.03 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3861 TCGA-AA-3869 
        0.99        38.99        10.06        33.07        30.05        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3973 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-A004 
       18.05        24.00        13.05        27.02         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        18.05        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       31.00        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AY-4070 
       41.00        16.31 

$subtype3
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3867 
       13.02        19.99        19.00        31.07        30.05        24.03 
TCGA-AA-3986 TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 
       19.07        38.99        29.00        26.01        12.99        24.00 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3819 
       14.01        47.01        15.02        37.05        35.05        25.02 
TCGA-AA-3831 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 
       17.98        36.95        17.03         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
       31.07        17.03        20.98        34.03        21.99        36.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4071 
       16.08        34.06        27.02        34.03         0.95 

subtype1 subtype2 subtype3 
       0        0        0 
subtype1 subtype2 subtype3 
   53.00    54.02    47.01 
subtype1 subtype2 subtype3 
  22.030   22.995   24.030 
[1] "0.0 - 53.0 (22.0)" "0.0 - 54.0 (23.0)" "0.0 - 47.0 (24.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       8        3        14         4         3          1          5
  subtype2      10        7        18         1         3          2          4
  subtype3      11        2        13         0         2          0          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        4         0
  subtype2         11       13         1
  subtype3          4        4         0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8       10       11
  STAGE II          3        7        2
  STAGE IIA        14       18       13
  STAGE IIB         4        1        0
  STAGE III         3        3        2
  STAGE IIIA        1        2        0
  STAGE IIIB        5        4        3
  STAGE IIIC        1       11        4
  STAGE IV          4       13        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  9 28  6
  subtype2  2 10 50  8
  subtype3  1 12 25  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        2        1
  T2        9       10       12
  T3       28       50       25
  T4        6        8        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 30  7  7
  subtype2 38 15 17
  subtype3 26  6  7
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       30       38       26
  N1        7       15        6
  N2        7       17        7
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 39  4
  subtype2 56 14
  subtype3 34  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    4
  subtype2   56   14
  subtype3   34    4
   clus
vv  subtype1 subtype2 subtype3
  0       39       56       34
  1        4       14        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 27 17
  subtype2 34 36
  subtype3 14 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   17
  subtype2   34   36
  subtype3   14   25
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       34       14
  MALE         17       36       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"
D2V8, binary
          cls
clus        0  1
  subtype1 34  0
  subtype2 57  3
  subtype3 33  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    0
  subtype2   57    3
  subtype3   33    0
     clus
vv    subtype1 subtype2 subtype3
  NO        34       57       33
  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 25 18
  subtype2 66  4
  subtype3 38  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   18
  subtype2   66    4
  subtype3   38    0
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                25       66       38
  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  2
  subtype2 55  1 13
  subtype3 34  0  4
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       39       55       34
  R1        0        1        0
  R2        2       13        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] "subtype2" "subtype1" "subtype1" "subtype1" "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  38  13
  subtype2 163  51
  subtype3 134  37
subtype1 subtype2 subtype3 
      51      214      171 
subtype1 subtype2 subtype3 
      13       51       37 
$subtype1
TCGA-A6-2682 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3939 TCGA-AA-A00Z TCGA-3L-AA1B 
       13.94        13.02        23.01        12.99        21.99        15.62 
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-4107 TCGA-AA-3489 TCGA-AA-3558 TCGA-AA-3673 
       39.45        43.76        32.45         7.04        20.98        50.04 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3856 TCGA-AA-3968 TCGA-AA-A004 
        5.03        10.06         0.99         0.99        21.99        13.94 
TCGA-AA-A01I TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02O TCGA-AY-A54L TCGA-AY-A69D 
       31.00        26.01        51.98         0.92        17.26        17.85 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5254 
        5.13        65.00        49.41        12.10         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 
       12.46        12.59        12.20        20.02        25.02        29.06 
TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6165 TCGA-CM-6677 TCGA-D5-6539 
       22.98        15.02        15.02        16.04        11.08        12.49 
TCGA-DM-A0X9 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6626 
      119.70        12.59         7.50         1.55        47.41        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-QG-A5YW 
       74.79        18.18        29.46 

$subtype2
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3524 
       24.33        45.60        14.53         1.02        24.03        36.03 
TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       34.03        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3972 
       85.05        14.93        31.07        24.03        29.98        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 
       26.01        24.00        38.04        15.52       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6625 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 
       91.79        17.85         4.80         1.61        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       42.28        44.91        35.11        16.57        34.65        36.53 
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-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52        24.13        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        5.03         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       24.00        13.94        78.08         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 
       15.02         5.98        37.05        25.02        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07        32.05        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05         2.01        24.00        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       16.08        13.05        34.06        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       32.02        12.00        31.00         1.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
        2.96        39.98         2.01         5.03        41.00        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        5.79        22.42        27.42        26.47        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       16.31         0.95        33.01        18.84       109.28         5.65 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-6715 
       22.36        62.79        29.56         5.23        11.74        12.59 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
       14.30       148.01        21.99         2.01         8.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08        32.02         5.03        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       29.03        21.99        13.02        15.02        11.01        11.08 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        25.48        15.12        17.85        17.13 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      140.38        44.32       131.51        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.97         8.61        31.96        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        0.53         8.35        82.39        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V 
       39.42        61.91        36.00        26.43        10.98        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       21.90        38.70        60.13        11.90 

$subtype3
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       24.16        58.03        13.02        37.05         8.05        19.07 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        0.99        17.95         0.92        19.04        19.04        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
        2.01        19.07        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       75.95       100.01        22.09        35.80        26.17        79.69 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       12.66         9.53        46.65        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       37.02        32.75        31.63        33.53        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         3.02        35.01        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 
       19.07         0.00        29.00        29.95        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3821 
       54.02        47.05        11.01        26.99        35.05         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        38.99         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       36.03        53.00        31.00        33.01        26.01         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       25.02        27.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01P 
        4.01        27.02         0.99        34.98        10.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        1.02        35.01         1.02        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        24.53         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        21.44        17.82        19.33        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       32.94        88.21         6.77        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.14        82.95       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       27.02        15.02        15.02        12.00        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 
       14.04        12.95        13.05        11.01        12.03        20.19 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       20.42        43.27         4.80        16.14        15.58        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD 
        9.44        11.64        13.35        12.00        10.26        24.43 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
      135.65         7.76       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       47.87        34.42        41.42        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV 
       67.30        53.62        85.48        26.04        13.78        19.33 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
        9.93        31.30        70.03 

subtype1 subtype2 subtype3 
    0.92     0.53     0.00 
subtype1 subtype2 subtype3 
  119.70   148.01   139.17 
subtype1 subtype2 subtype3 
   16.04    24.00    22.06 
[1] "0.9 - 119.7 (16.0)" "0.5 - 148.0 (24.0)" "0.0 - 139.2 (22.1)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        0        5        18         0         0         2
  subtype2      29        0       12        48         3         1        11
  subtype3      35        1       12        66         7         0         7
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1          2          4        7         2         0
  subtype2          7         34         22       33        13         1
  subtype3          0         23         15        5         2         1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          10       29       35
  STAGE IA          0        0        1
  STAGE II          5       12       12
  STAGE IIA        18       48       66
  STAGE IIB         0        3        7
  STAGE IIC         0        1        0
  STAGE III         2       11        7
  STAGE IIIA        1        7        0
  STAGE IIIB        2       34       23
  STAGE IIIC        4       22       15
  STAGE IV          7       33        5
  STAGE IVA         2       13        2
  STAGE IVB         0        1        1
[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  12  37   4
  subtype2   6  32 155  26
  subtype3   5  33 113  25
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        6        5
  T2       12       32       33
  T3       37      155      113
  T4        4       26       25
[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  34   9  10
  subtype2 104  68  47
  subtype3 124  28  25
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       34      104      124
  N1        9       68       28
  N2       10       47       25
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus         0   1
  subtype1  38   9
  subtype2 146  47
  subtype3 144   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    9
  subtype2  146   47
  subtype3  144    8
   clus
vv  subtype1 subtype2 subtype3
  0       38      146      144
  1        9       47        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  25  28
  subtype2  96 123
  subtype3  92  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   28
  subtype2   96  123
  subtype3   92   85
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       25       96       92
  MALE         28      123       85
[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  44   0
  subtype2 185   6
  subtype3 141   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    0
  subtype2  185    6
  subtype3  141    3
     clus
vv    subtype1 subtype2 subtype3
  NO        44      185      141
  YES        0        6        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus         0   1
  subtype1  49   3
  subtype2 206  10
  subtype3 127  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    3
  subtype2  206   10
  subtype3  127   49
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                49      206      127
  COLON MUCINOUS ADENOCARCINOMA        3       10       49
[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  38   0   3   4
  subtype2 152   2  18   8
  subtype3 133   2   4  13
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       38      152      133
  R1        0        2        2
  R2        3       18        4
  RX        4        8       13
[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     4                         7
  subtype2                                0     2                        29
  subtype3                                0     5                        23
          vv
clus       WHITE
  subtype1    23
  subtype2   105
  subtype3    84
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        2        5
  BLACK OR AFRICAN AMERICAN               7       29       23
  WHITE                                  23      105       84
[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  32
  subtype2   2 129
  subtype3   1 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    2  129
  subtype3    1  108
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        1
  NOT HISPANIC OR LATINO       32      129      108
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 63 21
  subtype2 77 24
  subtype3 79 25
subtype1 subtype2 subtype3 
      84      101      104 
subtype1 subtype2 subtype3 
      21       24       25 
$subtype1
TCGA-A6-2682 TCGA-A6-6649 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6314 
       13.94        24.16        10.88        75.95       100.01        35.93 
TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B TCGA-5M-AAT6 TCGA-A6-2675 TCGA-A6-2685 
       91.79        79.69        15.62         9.53        43.43        37.25 
TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 
       31.63        22.09         8.38        25.08        21.76        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 
       19.66        16.24        24.92        61.84         9.63         7.04 
TCGA-AA-3510 TCGA-AD-6963 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4315 
       63.98        27.42        27.09         0.20        18.84        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 
        1.41         5.13        62.79        12.10         5.23         3.19 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 
       12.36        12.59        12.76        10.06       148.01        23.05 
TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 
       26.04        13.02        22.03        22.98        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 
       12.00        14.04        29.03        14.99        12.99        12.95 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
       20.19        20.42        43.27        17.85        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0XF 
       12.39         9.44        11.64        13.41        13.35        38.20 
TCGA-DM-A280 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
        7.76        31.96        11.11        35.74        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 
        1.55        34.42        43.04        13.25        35.31         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6627 TCGA-WS-AB45 
       67.30        53.62        85.48        39.42        74.79        70.03 

$subtype2
TCGA-A6-2677 TCGA-AA-3496 TCGA-AA-3697 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 
       24.33         1.02        85.05        15.52       106.75         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-4N-A93T 
       49.08        28.21        23.51        63.62        17.85         4.80 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-3810 TCGA-A6-5656 
       39.45        43.76        35.11        37.05        36.53        32.91 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       29.19        23.61        32.71        29.16        27.09        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3488 
       25.18        20.61        24.69        20.28        56.25         5.03 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 
        1.02        37.05        62.96         6.97        61.02        78.08 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-5543 
       24.53        22.42        16.44         0.46        14.50        33.01 
TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-6715 
      109.28        22.36        65.00        29.56        12.46        12.59 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
       21.99         2.01         8.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6172 
       17.03        15.02        16.04        21.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       11.08        11.01        10.06        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       25.48         4.80         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB 
        9.04        11.38       130.65        49.91        13.32        44.32 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 
      139.17        26.47        81.37       119.93        35.97         8.61 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 
       33.67         0.53        47.41        82.39        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GC 
       55.04        61.91        36.00        46.75        18.18        12.79 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-T9-A92H 
       42.77        32.98         8.42        38.70        11.90 

$subtype3
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3662 TCGA-AA-3713 TCGA-AD-6548 
       45.60        14.53        58.03         6.05        19.04        21.37 
TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-4T-AA8H 
       25.08         5.88        22.09        35.80        26.17        12.66 
TCGA-5M-AAT4 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5659 
        1.61        44.91        37.02        32.75        32.45        30.44 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       33.53        22.06        22.52        24.39        20.12         3.02 
TCGA-AA-3502 TCGA-AA-3663 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 
       35.01         6.97        12.16        83.24         5.79        26.47 
TCGA-AM-5821 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.92        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
        5.65        32.94        88.21        49.41         6.77        11.74 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.69        12.39        12.20        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        25.02        27.02        32.02        15.02 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 
       13.02        14.04        13.05        11.08        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 
       54.61        19.59        17.75        15.12        17.13        16.14 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 
       12.00        10.26       119.70        24.43        92.75        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A288 TCGA-DM-A28G 
      140.38         7.50       131.51       135.65        14.04        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 
      117.07        98.24        95.18         6.18        41.42       133.18 
TCGA-G4-6299 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A50V 
       74.56        26.43        26.04        13.78        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z2 
       19.33         9.93        15.65        16.80        29.46        31.30 
TCGA-QL-A97D TCGA-SS-A7HO 
       21.90        60.13 

subtype1 subtype2 subtype3 
    0.20     0.46     0.92 
subtype1 subtype2 subtype3 
  148.01   139.17   140.38 
subtype1 subtype2 subtype3 
  21.090   24.530   21.405 
[1] "0.2 - 148.0 (21.1)" "0.5 - 139.2 (24.5)" "0.9 - 140.4 (21.4)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       8        0        5        30         1         0         2
  subtype2      14        0        7        27         1         1         1
  subtype3      21        1        3        36         4         0         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          0         14          9        9         3         0
  subtype2          4         19          5        8        10         1
  subtype3          1         14         12        6         3         1
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8       14       21
  STAGE IA          0        0        1
  STAGE II          5        7        3
  STAGE IIA        30       27       36
  STAGE IIB         1        1        4
  STAGE IIC         0        1        0
  STAGE III         2        1        3
  STAGE IIIA        0        4        1
  STAGE IIIB       14       19       14
  STAGE IIIC        9        5       12
  STAGE IV          9        8        6
  STAGE IVA         3       10        3
  STAGE IVB         0        1        1
[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  2  6 63 13
  subtype2  3 17 71 12
  subtype3  2 20 68 15
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        3        2
  T2        6       17       20
  T3       63       71       68
  T4       13       12       15
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 46 23 15
  subtype2 58 32 13
  subtype3 67 18 21
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       46       58       67
  N1       23       32       18
  N2       15       13       21
[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 60 12
  subtype2 66 19
  subtype3 71 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   12
  subtype2   66   19
  subtype3   71   10
   clus
vv  subtype1 subtype2 subtype3
  0       60       66       71
  1       12       19       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 37 47
  subtype2 43 60
  subtype3 55 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   47
  subtype2   43   60
  subtype3   55   51
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37       43       55
  MALE         47       60       51
[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 78  1
  subtype2 84  3
  subtype3 87  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78    1
  subtype2   84    3
  subtype3   87    1
     clus
vv    subtype1 subtype2 subtype3
  NO        78       84       87
  YES        1        3        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1 66 17
  subtype2 99  3
  subtype3 86 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   17
  subtype2   99    3
  subtype3   86   19
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                66       99       86
  COLON MUCINOUS ADENOCARCINOMA       17        3       19
[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 57  0  1  6
  subtype2 72  0  2  5
  subtype3 64  3  2 13
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       57       72       64
  R1        0        0        3
  R2        1        2        2
  RX        6        5       13
[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                                1     4                        17
  subtype2                                0     2                        18
  subtype3                                0     5                        23
          vv
clus       WHITE
  subtype1    60
  subtype2    73
  subtype3    72
D4V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        2        5
  BLACK OR AFRICAN AMERICAN              17       18       23
  WHITE                                  60       73       72
[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 77
  subtype2  1 89
  subtype3  1 95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   77
  subtype2    1   89
  subtype3    1   95
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        1
  NOT HISPANIC OR LATINO       77       89       95
[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  20
  subtype2 106  34
  subtype3 102  24
subtype1 subtype2 subtype3 
      84      140      126 
subtype1 subtype2 subtype3 
      20       34       24 
$subtype1
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3522 
       24.33        45.60        24.16        58.03        24.03        37.05 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3713 TCGA-AA-A00L TCGA-AA-A00Z 
       13.02        19.99        19.99        19.04        38.04        21.99 
TCGA-G4-6310 TCGA-G4-6625 TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2683 
       63.62        91.79        15.62        43.76        42.28        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-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3514 
       24.13         8.38        20.28         3.02        35.01         1.02 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3655 TCGA-AA-3678 
        0.00        29.00        29.00        24.00        61.02        47.01 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       35.05         0.99        25.02         0.00        36.03         0.99 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       20.98        21.99        13.94        34.03        18.05        18.05 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T 
       15.02        15.02        10.98        38.07         1.02        33.04 
TCGA-AA-A02E TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-5900 TCGA-AY-6196 TCGA-AY-6386 
        2.96        14.01        41.00        12.16         0.20        17.82 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4682 TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4747 
       19.33        18.84        22.36        12.39         2.01        25.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5863 TCGA-CM-6167 TCGA-CM-6679 TCGA-D5-5538 
       29.06        22.98        15.02        14.99        10.06        54.61 
TCGA-D5-6531 TCGA-DM-A280 TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6809 
       17.75         7.76         8.61        35.74         6.18        13.25 
TCGA-F4-6855 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z1 
       47.41        13.78        19.33         9.93        12.79         8.42 

$subtype2
TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3688 TCGA-AA-3697 
        1.02         8.05        19.07        34.03        19.00        85.05 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3972 TCGA-AA-A024 TCGA-AZ-6608 TCGA-G4-6294 
       19.04        14.93        50.99        39.06         1.94        28.21 
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-3510 
       27.09        22.52        20.61        24.69        23.87        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3558 
        6.97        38.99         9.07        33.99        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3848 
       13.94        54.02         5.03        10.06        17.98        10.06 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3973 TCGA-AA-3975 
       30.05        53.00        27.02         2.01        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00E TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02         7.96        30.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       34.98        32.02        31.00        35.01         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       51.98        39.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6197 
       40.96        83.24         5.79        26.47        33.01        21.44 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-5407 
       17.26        17.85         5.65        32.94        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77        29.56        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 
       12.36        12.46        12.59        12.20        14.30        21.99 
TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6161 
       82.95        37.02        22.03        15.02        15.02        15.02 
TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 
       21.99        11.01        13.05        11.08        12.03        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 
       55.92        18.25        15.12         4.80        17.13        12.39 
TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.43        12.00       119.70        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 
       81.37       119.93        35.97        60.79        95.18        31.96 
TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 
       41.42       133.18         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-AA-3554 TCGA-AA-3672 TCGA-AA-3862 TCGA-AA-3950 TCGA-AA-3986 TCGA-AD-6548 
       17.95         0.92        30.05        24.00        19.07        21.37 
TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
      100.01        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5660 
       79.69        17.85        37.05        34.65        31.63        29.19 
TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       33.53        25.08        25.18        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
       19.66        24.92         7.04         5.98        26.99        33.04 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3866 
       15.95        38.99        36.95         0.00         0.00        17.03 
TCGA-AA-3947 TCGA-AA-3971 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K 
       33.01        16.08        38.04         4.01         0.99        31.00 
TCGA-AA-A01Q TCGA-AA-A02R TCGA-AA-A03F TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        1.02        22.03        18.05         0.46         0.92        27.09 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6605 
      109.28        58.39         1.41         5.13        12.10         5.23 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
       12.59        12.76        10.06        21.14       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 
       20.02        26.04         8.02        13.02        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       12.99        13.02        15.02        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6534 
       11.01        19.59        20.19        20.42        25.48        43.27 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85        12.49        16.14        15.58         7.53        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04         9.44        11.64        13.35        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6461 
       38.20       130.65       135.65        14.04        26.47        11.11 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        34.42        43.04        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.31        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 
       44.68        55.04        39.42        36.00        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-SS-A7HO 
       18.18        19.33        15.65        16.80        38.70        60.13 

subtype1 subtype2 subtype3 
    0.00     0.92     0.00 
subtype1 subtype2 subtype3 
   91.79   140.38   135.65 
subtype1 subtype2 subtype3 
  20.135   24.280   20.305 
[1] "0.0 - 91.8 (20.1)"  "0.9 - 140.4 (24.3)" "0.0 - 135.7 (20.3)"
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       14        38         4         1         7
  subtype3      21        0        3        49         4         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         11       16         5         1
  subtype3          3         13         13        6         6         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          12       21       21
  STAGE IA          1        0        0
  STAGE II          4       14        3
  STAGE IIA        28       38       49
  STAGE IIB         1        4        4
  STAGE IIC         0        1        0
  STAGE III         4        7        6
  STAGE IIIA        2        1        3
  STAGE IIIB       12       23       13
  STAGE IIIC       10       11       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  18
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        2        4
  T2       16       22       20
  T3       61      101       85
  T4        9       19       18
[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 81 26 20
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49       80       81
  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 103  22
  subtype3 101  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   13
  subtype2  103   22
  subtype3  101   12
   clus
vv  subtype1 subtype2 subtype3
  0       66      103      101
  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 64 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   42
  subtype2   64   80
  subtype3   64   63
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       64       64
  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  73   2
  subtype2 116   3
  subtype3 109   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    2
  subtype2  116    3
  subtype3  109    2
     clus
vv    subtype1 subtype2 subtype3
  NO        73      116      109
  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 104  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   12
  subtype2  134    9
  subtype3  104   21
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                75      134      104
  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  R1  R2  RX
  subtype1  75   0   5   1
  subtype2  85   1  12  11
  subtype3 107   0   0   4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       75       85      107
  R1        0        1        0
  R2        5       12        0
  RX        1       11        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                        17
          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       17
  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  86
  subtype3   0 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   45
  subtype2    2   86
  subtype3    0  103
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        0
  NOT HISPANIC OR LATINO       45       86      103
[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 24  8
  subtype3 27  5
  subtype4 25 12
  subtype5 32  9
  subtype6 70 16
  subtype7 17  8
  subtype8 18  2
  subtype9 21  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      51       32       32       37       41       86       25       20 
subtype9 
      26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      13        8        5       12        9       16        8        2 
subtype9 
       5 
$subtype1
TCGA-A6-2677 TCGA-A6-6649 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
       24.33        24.16        23.51        63.62        35.93        91.79 
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5656 
       15.62        43.76        37.05        37.25        33.34        32.91 
TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3529 
       30.44        22.52        21.76        35.01         1.02         0.00 
TCGA-AA-3553 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3866 TCGA-AA-A00J TCGA-AA-A00K 
       24.00        35.05         0.99        17.03        18.05        18.05 
TCGA-AD-5900 TCGA-AM-5820 TCGA-AZ-4308 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 
       12.16         0.46       109.28        12.10         3.19        12.59 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6166 
       12.76        14.30         2.01        32.02        17.03        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-6534 TCGA-D5-6922 TCGA-D5-6926 
       14.99        13.02        11.08        43.27        10.13         9.04 
TCGA-DM-A1D6 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6854 
       49.91        26.47         8.61        35.74         1.55         0.53 
TCGA-G4-6303 TCGA-NH-A6GA TCGA-QG-A5Z1 
       65.85         9.93         8.42 

$subtype2
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-5664 
       38.04        21.99        39.06         4.80        12.66        22.09 
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3854 TCGA-AA-A004 TCGA-AA-A017 TCGA-AA-A01D 
       23.87        63.98        36.03        13.94        15.02        10.98 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A02E TCGA-AD-6889 
       38.07         1.02        33.04         1.02         2.96        83.24 
TCGA-AD-6899 TCGA-AY-A71X TCGA-AZ-4682 TCGA-CA-5796 TCGA-CK-6747 TCGA-CM-4746 
        5.79        19.33        22.36        12.39        82.95        37.02 
TCGA-CM-6680 TCGA-D5-6920 TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6806 TCGA-QG-A5YV 
       12.03        12.39       139.17        60.79        41.42        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       32.98        31.30 

$subtype3
TCGA-AZ-6608 TCGA-A6-2678 TCGA-A6-6650 TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3561 
        1.94        42.28        20.61         9.07        33.99        13.94 
TCGA-AA-3848 TCGA-AA-3989 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
       10.06         7.96        30.02        34.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01R 
       14.99        34.98        15.02        32.02        31.00        35.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J 
       51.98        39.98         5.03         0.92        39.98        40.96 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-A54L TCGA-AZ-6603 TCGA-CM-6679 TCGA-D5-6535 
       26.47        33.01        17.26        29.56        10.06        15.12 
TCGA-DM-A1D9 TCGA-QG-A5YW 
      140.38        29.46 

$subtype4
TCGA-AA-3844 TCGA-5M-AAT6 TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3558 
       14.93         9.53        42.90        22.06        32.71        20.98 
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        12.59        21.99        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-AA-3506 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3697 
       58.03        19.07        34.03        19.99        19.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3972 TCGA-A6-2672 TCGA-A6-2680 TCGA-A6-2683 
       19.04        19.04        50.99        46.65        35.11        16.57 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5667 TCGA-AA-3489 TCGA-AA-3492 
       37.02        32.75        36.53        29.16         7.04         3.02 
TCGA-AA-3517 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3710 
       38.99        61.02        54.02        47.01         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3856 
       10.06        17.98        38.99         0.00         0.00         0.99 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       53.00        33.01        20.98        21.99        16.08        34.06 
TCGA-AA-3982 TCGA-CA-5255 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       27.02        12.36        29.06        22.03        22.98 

$subtype6
TCGA-A6-2681 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3862 TCGA-AA-3950 TCGA-AA-3986 
       45.60        17.95         0.92        30.05        24.00        19.07 
TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       21.37       100.01        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 
       17.85        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-3681 
       24.39        20.12        19.66         6.97        29.00         5.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3869 TCGA-AA-A00A TCGA-AA-A00N 
       15.95        36.95         0.00        27.02        38.04         4.01 
TCGA-AA-A00R TCGA-AA-A01Q TCGA-AA-A03F TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
        0.99         1.02        18.05         0.92        27.09         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6605 
       17.85        18.84        58.39         1.41         5.13         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        14.04        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        25.48         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        13.35       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        43.04        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-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 
       46.75        74.79        18.18        19.33        15.65        16.80 
TCGA-RU-A8FL TCGA-SS-A7HO 
       38.70        60.13 

$subtype7
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3552 TCGA-A6-5661 TCGA-AA-3534 
       24.03        37.05         8.05        13.02        33.53        29.00 
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        12.46        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-G4-6294 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-AA-3819 
       28.21        23.61        27.09        24.13         8.38        25.02 
TCGA-AA-3973 TCGA-AY-6386 TCGA-AZ-5407 TCGA-CA-6716 TCGA-CM-6161 TCGA-CM-6172 
       13.05        17.82        88.21        12.20        15.02        11.01 
TCGA-CM-6676 TCGA-F4-6460 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6320 
       11.08        31.96         8.35        82.39        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 
       26.04        13.78 

$subtype9
TCGA-AA-3496 TCGA-AA-3562 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A566 TCGA-AA-3555 
        1.02        19.99        24.69        20.28        24.92        29.95 
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        54.61        56.09        55.92         7.53        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     0.92     2.01     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   23.115   29.510   18.250   26.990   20.305   17.850   23.870 
subtype9 
  24.805 
[1] "0.0 - 109.3 (18.1)" "1.0 - 139.2 (23.1)" "0.9 - 140.4 (29.5)"
[4] "2.0 - 131.5 (18.2)" "0.0 - 85.0 (27.0)"  "0.0 - 135.7 (20.3)"
[7] "2.0 - 133.2 (17.9)" "8.3 - 88.2 (23.9)"  "1.0 - 130.7 (24.8)"
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        9        11         2         0         3
  subtype6      17        0        3        32         2         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          5        3         1         0
  subtype4          0          4          7        4         2         1
  subtype5          1          6          1        6         0         0
  subtype6          1          8          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        9        3        1
  STAGE IIA        16       12        6       12       11       32       13
  STAGE IIB         0        0        1        2        2        2        1
  STAGE IIC         0        0        0        1        0        0        0
  STAGE III         0        4        2        1        3        5        1
  STAGE IIIA        1        0        2        0        1        1        0
  STAGE IIIB        9        3        5        4        6        8        3
  STAGE IIIC        6        4        5        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 10
  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       10        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 58 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       58       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 27  4
  subtype4 27  7
  subtype5 36  6
  subtype6 65  9
  subtype7 20  2
  subtype8 13  4
  subtype9 20  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    9
  subtype2   25    2
  subtype3   27    4
  subtype4   27    7
  subtype5   36    6
  subtype6   65    9
  subtype7   20    2
  subtype8   13    4
  subtype9   20    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       37       25       27       27       36       65       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 37 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   37   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       37       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 42  2
  subtype2 27  0
  subtype3 28  1
  subtype4 26  1
  subtype5 36  2
  subtype6 76  1
  subtype7 21  0
  subtype8 20  0
  subtype9 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    2
  subtype2   27    0
  subtype3   28    1
  subtype4   26    1
  subtype5   36    2
  subtype6   76    1
  subtype7   21    0
  subtype8   20    0
  subtype9   22    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        42       27       28       26       36       76       21       20
  YES        2        0        1        1        2        1        0        0
     clus
vv    subtype9
  NO        22
  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 73 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   73   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                73       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 R1 R2 RX
  subtype1 40  0  1  3
  subtype2 26  0  1  1
  subtype3 25  1  3  1
  subtype4 15  0  3  6
  subtype5 36  0  5  1
  subtype6 72  0  1  3
  subtype7 20  0  2  0
  subtype8 12  0  1  1
  subtype9 21  0  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       40       26       25       15       36       72       20       12
  R1        0        0        1        0        0        0        0        0
  R2        1        1        3        3        5        1        2        1
  RX        3        1        1        6        1        3        0        1
    clus
vv   subtype9
  R0       21
  R1        0
  R2        0
  RX        0
[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"
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                        14
  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              14        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 10
  subtype4  1 32
  subtype5  1 10
  subtype6  0 70
  subtype7  0 14
  subtype8  0 18
  subtype9  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   42
  subtype2    0   17
  subtype3    0   10
  subtype4    1   32
  subtype5    1   10
  subtype6    0   70
  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       10       32       10       70
                        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  90  34
  subtype2  77  16
  subtype3  71  26
  subtype4 103  26
subtype1 subtype2 subtype3 subtype4 
     124       93       97      129 
subtype1 subtype2 subtype3 subtype4 
      34       16       26       26 
$subtype1
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3662 TCGA-AA-3688 
       24.33        14.53        19.07        34.03         6.05        19.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3976 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 
       85.05        24.03        26.01        38.04        21.99        15.52 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-5656 
       17.85        15.62         4.80         1.61        39.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-A567 TCGA-AA-3494 
       24.13        25.18        20.61        24.69        61.84         1.02 
TCGA-AA-3495 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3526 TCGA-AA-3534 
       37.05        62.96         6.97        38.99        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3675 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3955 
       26.01        78.08        47.05        37.05         5.03        20.98 
TCGA-AA-3973 TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02F 
       13.05        27.02        31.00         1.02        26.01        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6963 
        2.01         5.03        14.01        41.00        24.53        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-4684 
       26.47        16.44        14.50        18.84        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       62.79        29.56        12.46        12.59        12.59        12.20 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
      148.01        21.99        25.02        22.03         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6170 
       17.03        15.02        14.04        29.03        21.99        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 
       11.08        11.01        45.40        56.09        18.25        25.48 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        4.80        17.13        13.41        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6854 TCGA-G4-6306 TCGA-G4-6307 
        8.61        31.96        33.67         0.53        44.68        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV 
       61.91        36.00        46.75        18.18        10.98        42.77 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        38.70        60.13        11.90 

$subtype2
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3713 
       24.16        58.03        37.05         8.05        23.01        19.04 
TCGA-AA-A024 TCGA-AZ-4313 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-4T-AA8H 
       39.06        75.95        22.09        35.80        26.17        12.66 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-A565 
       33.53        22.06         8.38        24.39        20.12        16.24 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3851 
        3.02        35.01        61.02         6.97        11.01        33.07 
TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-A01Z TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 
       36.03        30.05        37.02        39.98        18.05        83.24 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       58.39         5.65        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 
       11.74        12.69        12.36        12.39        17.56        85.45 
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-D5-6539 
       13.05        12.03        19.59        20.42        15.12        12.49 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D6 
       16.14        12.39        12.00       119.70        24.43        49.91 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M 
        7.50       135.65         7.76        14.04        98.24        95.18 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       41.42        35.31       133.18        53.62        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW 
       26.04        13.78        19.33        15.65        12.79        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D 
       32.98        31.30        21.90 

$subtype3
TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3870 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       13.94         1.02        29.98        21.37        25.08        10.88 
TCGA-AZ-6601 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2675 
      100.01        35.93        91.79        79.69         9.53        43.43 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5657 
       37.05        37.25        37.02        33.34        36.53        31.63 
TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 
       22.09        22.52        25.08        21.76        23.87        19.66 
TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-A01P 
       20.28        24.92        56.25         9.63         7.04        38.07 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       12.16         5.79        22.42         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6605 TCGA-AZ-6607 
        0.20         1.41        32.94         5.13         5.23         3.19 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6748 
       12.76        10.06        14.30        70.16        21.14         2.01 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 
       22.98        30.08        32.02        12.00        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 
       12.99        13.02        12.95        11.08        10.06        54.61 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 
       55.92        20.19        17.75        43.27        17.85        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-F4-6461 TCGA-F4-6463 
       11.64        13.35        11.38        10.26        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        34.42        43.04 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       13.25        47.41         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A8F8 
       65.85        39.42        74.79        19.33         9.93        16.80 
TCGA-WS-AB45 
       70.03 

$subtype4
TCGA-A6-2681 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3552 
       45.60        13.02        24.03        36.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3715 
       17.95        19.99        19.99         0.92        36.00        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        30.05        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AZ-4681 TCGA-A6-2671 TCGA-A6-2672 
       50.99        24.00        19.07       106.75        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3510 TCGA-AA-3514 
       34.65        32.75        32.45         5.03        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
        1.02         9.07         0.00        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3664 
       33.99        21.01        24.00        29.95        13.94        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
        0.00        17.03        10.06         0.00         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        36.03        16.08        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q 
       15.02        10.98        32.02        12.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02O 
       35.01        33.04         1.02        51.98         2.96         0.92 
TCGA-AA-A02R TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-CM-4748 
       22.03        40.96        16.31         0.95       109.28        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        8.02        13.02        29.06 

subtype1 subtype2 subtype3 subtype4 
    0.53     3.02     0.20     0.00 
subtype1 subtype2 subtype3 subtype4 
  148.01   135.65   100.01   109.28 
subtype1 subtype2 subtype3 subtype4 
   25.10    22.06    19.66    22.03 
[1] "0.5 - 148.0 (25.1)" "3.0 - 135.7 (22.1)" "0.2 - 100.0 (19.7)"
[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        7        31         1         1         4
  subtype2      21        1        6        31         2         0         4
  subtype3      11        0        4        37         1         0         2
  subtype4      23        0       13        38         6         0        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         18         10       17        11         0
  subtype2          1         13          7        4         2         2
  subtype3          1         15         10       12         3         0
  subtype4          4         13         14       12         1         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          19       21       11       23
  STAGE IA          0        1        0        0
  STAGE II          7        6        4       13
  STAGE IIA        31       31       37       38
  STAGE IIB         1        2        1        6
  STAGE IIC         1        0        0        0
  STAGE III         4        4        2       10
  STAGE IIIA        2        1        1        4
  STAGE IIIB       18       13       15       13
  STAGE IIIC       10        7       10       14
  STAGE IV         17        4       12       12
  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 85 16
  subtype2  2 20 62 10
  subtype3  1 10 70 17
  subtype4  5 24 93 13
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        2        1        5
  T2       23       20       10       24
  T3       85       62       70       93
  T4       16       10       17       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 69 35 23
  subtype2 63 20 12
  subtype3 54 23 21
  subtype4 82 27 26
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       69       63       54       82
  N1       35       20       23       27
  N2       23       12       21       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"
D7V6, binary
          cls
clus         0   1
  subtype1  80  28
  subtype2  66   8
  subtype3  69  15
  subtype4 119  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80   28
  subtype2   66    8
  subtype3   69   15
  subtype4  119   13
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       80       66       69      119
  1       28        8       15       13
[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 51 76
  subtype2 51 44
  subtype3 41 57
  subtype4 72 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   76
  subtype2   51   44
  subtype3   41   57
  subtype4   72   63
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       51       51       41       72
  MALE         76       44       57       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 101   2
  subtype2  81   2
  subtype3  89   1
  subtype4 106   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101    2
  subtype2   81    2
  subtype3   89    1
  subtype4  106    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       101       81       89      106
  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 123   2
  subtype2  72  21
  subtype3  81  17
  subtype4 112  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  123    2
  subtype2   72   21
  subtype3   81   17
  subtype4  112   22
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA               123       72       81      112
  COLON MUCINOUS ADENOCARCINOMA        2       21       17       22
[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  75   1  11   7
  subtype2  62   1   2  10
  subtype3  72   1   2   8
  subtype4 120   1   9   0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       75       62       72      120
  R1        1        1        1        1
  R2       11        2        2        9
  RX        7       10        8        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                        19
  subtype2                                0     4                        23
  subtype3                                1     3                        14
  subtype4                                0     0                         3
          vv
clus       WHITE
  subtype1    70
  subtype2    51
  subtype3    75
  subtype4    17
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              19       23       14        3
  WHITE                                  70       51       75       17
[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 86
  subtype2  0 74
  subtype3  1 90
  subtype4  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   86
  subtype2    0   74
  subtype3    1   90
  subtype4    0   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        1        0
  NOT HISPANIC OR LATINO       86       74       90       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"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  60  19
  subtype2  81  25
  subtype3  69  25
  subtype4 101  25
  subtype5  30   8
subtype1 subtype2 subtype3 subtype4 subtype5 
      79      106       94      126       38 
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       25       25       25        8 
$subtype1
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-3L-AA1B TCGA-A6-2675 
       23.51        63.62        35.93        91.79        15.62        43.43 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 
       37.05        37.25        31.63        30.44        23.61        22.09 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 
       29.16        22.52        25.08        21.76        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-A01X 
       61.84        56.25         9.63         7.04         6.97        26.01 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6603 
        5.79        22.42         0.46         1.41        62.79        29.56 
TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
        5.23        12.59        12.76        14.30         2.01        25.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
       22.03        22.98        30.08        32.02         5.03        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-5541 
       15.02        11.08        11.01        10.06        56.09        55.92 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.75        43.27        17.85         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 
       14.30         9.04        11.38        26.47         8.61        31.96 
TCGA-F4-6463 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       35.74        34.42        43.04        13.25         0.53        47.41 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6627 TCGA-NH-A8F8 
       82.39        67.30        65.85        39.42        74.79        16.80 
TCGA-QG-A5Z1 
        8.42 

$subtype2
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3662 TCGA-AA-3697 
       13.94        14.53         1.02        58.03         6.05        85.05 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       21.37        15.52         1.94        49.08         5.88        28.21 
TCGA-NH-A8F7 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-5656 
       17.85         4.80        12.66         1.61        39.45        32.91 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       29.19        32.71        27.09        24.13        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3495 TCGA-AA-3509 TCGA-AA-3526 
       24.69        20.12        24.92        37.05        62.96        19.07 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3675 TCGA-AA-3685 TCGA-AA-A01Z TCGA-AA-A02K 
       61.02        78.08        47.05        37.05        37.02        14.01 
TCGA-AA-A02Y TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       39.98        24.53        27.42        26.47        16.44        14.50 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4315 
       33.01        17.82        17.26        17.85        18.84        58.39 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
       22.36        65.00        12.46        12.59        12.20        17.56 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 
      148.01        21.99        82.95        15.02        15.02        21.99 
TCGA-CM-6172 TCGA-CM-6677 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6532 
       11.01        11.08        45.40        54.61        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6929 
       25.48        15.12         4.80        17.13        15.58        13.41 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      140.38        44.32       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6808 TCGA-G4-6293 
       35.97        60.79       117.07        95.18        33.67       133.18 
TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
        8.35        44.68        55.04        61.91        36.00        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       18.18        10.98        19.33        42.77        29.46        32.98 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       21.90        38.70        60.13        11.90 

$subtype3
TCGA-A6-6649 TCGA-AA-3713 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       24.16        19.04        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2686 
       22.09        35.80        26.17        79.69         9.53        37.02 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-A565 
       33.53        22.06         8.38        24.39        19.66        16.24 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3663 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 
        3.02        35.01         6.97        38.07        12.16        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 
        0.92        27.09         0.20        21.44        19.33         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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6718 
       11.74         3.19        12.69        12.36        12.39        10.06 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6751 
       85.45        70.16        15.62        51.32        21.14       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       23.05        20.02        27.02        15.02        15.02        12.00 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 
       14.04        12.95        13.05        12.03        19.59        20.42 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.49        16.14        12.39         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA 
       12.00        10.26        24.43        49.91         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
      135.65         7.76        98.24        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       47.87         1.55        41.42        35.31        74.56        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA 
       85.48        26.43        26.04        13.78        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 
       15.65        12.79        31.30        70.03 

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

$subtype5
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3715 
       13.02         8.05         0.99        17.95        23.01        19.04 
TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 
       24.00        46.65        43.76        42.90        33.34        32.75 
TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3811 
        1.02        29.95        54.02         5.98        26.99        10.06 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3854 
       33.04         1.02        15.95         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       53.00        31.00        33.01        26.01         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     1.02     0.20     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.79   148.01   135.65   109.28    54.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.090   25.050   19.460   24.015   23.505 
[1] "0.5 - 91.8 (22.1)"  "1.0 - 148.0 (25.1)" "0.2 - 135.7 (19.5)"
[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        9        33         1         1         3
  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         17          8        8         7         0
  subtype3          1         11         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        9        4        9        5
  STAGE IIA        25       33       31       35       13
  STAGE IIB         1        1        2        2        4
  STAGE IIC         0        1        0        0        0
  STAGE III         2        3        3        8        4
  STAGE IIIA        1        1        1        5        0
  STAGE IIIB       16       17       11       10        5
  STAGE IIIC        5        8       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 12
  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       12       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 67 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       67       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  72  15
  subtype3  66   9
  subtype4 107  24
  subtype5  37   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   15
  subtype2   72   15
  subtype3   66    9
  subtype4  107   24
  subtype5   37    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       52       72       66      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 47 61
  subtype3 47 49
  subtype4 63 70
  subtype5 25 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   46
  subtype2   47   61
  subtype3   47   49
  subtype4   63   70
  subtype5   25   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       33       47       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  75   2
  subtype2  86   1
  subtype3  80   2
  subtype4 107   3
  subtype5  29   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75    2
  subtype2   86    1
  subtype3   80    2
  subtype4  107    3
  subtype5   29    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        75       86       80      107       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  99   7
  subtype3  71  24
  subtype4 124   8
  subtype5  21  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    6
  subtype2   99    7
  subtype3   71   24
  subtype4  124    8
  subtype5   21   17
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                73       99       71      124       21
  COLON MUCINOUS ADENOCARCINOMA        6        7       24        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  63   1   2   9
  subtype3  61   2   2  11
  subtype4 110   1  20   0
  subtype5  36   0   0   0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       59       63       61      110       36
  R1        0        1        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                        25
  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       25       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 86
  subtype3  1 88
  subtype4  0 19
  subtype5  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   72
  subtype2    2   86
  subtype3    1   88
  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       86       88       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 46 13
  subtype2 72 14
  subtype3 55 16
  subtype4 56 19
  subtype5 74 29
subtype1 subtype2 subtype3 subtype4 subtype5 
      59       86       71       75      103 
subtype1 subtype2 subtype3 subtype4 subtype5 
      13       14       16       19       29 
$subtype1
TCGA-AA-3496 TCGA-AA-3662 TCGA-CK-5912 TCGA-G4-6294 TCGA-A6-2671 TCGA-A6-2675 
        1.02         6.05        49.08        28.21        43.76        43.43 
TCGA-A6-2679 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 
       44.91        32.45        32.91        30.44        29.19        32.71 
TCGA-A6-6137 TCGA-AA-3488 TCGA-AA-3509 TCGA-AA-3660 TCGA-AA-A00Q TCGA-AD-6890 
       27.09         5.03        62.96        78.08        42.02        24.53 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5407 
        5.79        26.47        14.50        33.01       109.28        88.21 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-6747 
        6.77        11.74        12.46        12.59        14.30        82.95 
TCGA-CK-6748 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 
        2.01        13.02        32.02         5.03        15.02        15.02 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5537 TCGA-D5-5538 
       21.99        13.02        15.02        11.01        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6538 TCGA-D5-6923 TCGA-D5-6924 
       56.09        55.92        18.25        17.13        12.43        14.30 
TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A 
       13.41       119.70       130.65        44.32       131.51        26.47 
TCGA-DM-A28G TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6317 
       60.79        33.67       133.18        82.39        36.00 

$subtype2
TCGA-A6-4105 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6298 
       14.53        85.05        19.04        21.37       100.01        23.51 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 
       22.09        35.80        26.17        79.69        33.53        22.06 
TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3663 
       25.18        24.39        20.12        19.66        61.02         6.97 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
       12.16        83.24        27.42         0.92        27.09         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5254 
       21.44        17.82         5.13        49.41        12.10        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.36        12.39        12.59        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 
       85.45        15.62        51.32        21.99        21.14       124.27 
TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       23.05        27.02        22.03        30.08        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       12.00        29.03        14.04        12.95        13.05        12.03 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        17.75        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
        4.80        12.49        16.14        15.58        12.39         9.44 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 
       12.00        10.26         7.50       135.65         7.76        14.04 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6295 
      117.07        98.24        95.18         6.18        35.31         8.35 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       53.62        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 
       26.04        13.78 

$subtype3
TCGA-A6-2681 TCGA-A6-6649 TCGA-AD-6895 TCGA-AD-6964 TCGA-DM-A285 TCGA-G4-6310 
       45.60        24.16        25.08        10.88         5.88        63.62 
TCGA-G4-6314 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5662 
       35.93        37.05        37.25        33.34        31.63        23.61 
TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 
       22.09        29.16        22.52         8.38        25.08        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3514 TCGA-AA-3818 
       24.69        23.87        20.28         7.04         1.02         0.99 
TCGA-AA-3833 TCGA-AA-3866 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A00O TCGA-AA-A01X 
       15.95        17.03        13.05        27.02        27.02        26.01 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
       22.42         0.46         1.41        62.79        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5348 
        3.19        12.20        12.76        25.02        26.04        22.98 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6679 
       17.03        14.04        16.04        14.99        12.99        10.06 
TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 
       19.59        43.27         7.53        10.13         9.04        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       13.35        11.38         8.61        31.96        11.11        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        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6627 
        0.53        47.41        67.30        65.85        74.79 

$subtype4
TCGA-AA-3688 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3952 
       19.00        31.07        30.05        24.03        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AD-6888 TCGA-AZ-6608 
       50.99        26.01        24.00        38.04        15.52         1.94 
TCGA-G4-6625 TCGA-A6-3810 TCGA-A6-6140 TCGA-A6-6650 TCGA-AA-3511 TCGA-AA-3673 
       91.79        36.53        24.13        20.61         6.97        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 
       47.01        15.02        37.05        10.06        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3855 
        1.02        17.98        37.02        17.03        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
        0.99        31.07         2.01        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-A00U 
       21.99        36.03        16.08        34.06        27.02        17.03 
TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       14.99        32.02         1.02        33.04        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A03J TCGA-AY-4071 TCGA-AZ-4682 
       39.98         2.01         5.03        40.96         0.95        22.36 
TCGA-AZ-4684 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       65.00         8.02        29.06        11.08        11.08        11.01 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6806 
      140.38       139.17        81.37       119.93        35.97        41.42 
TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6626 
       74.56        44.68        46.75 

$subtype5
TCGA-A6-2677 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        13.94        58.03        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3692 
       17.95        23.01        19.99        19.99         0.92        36.00 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 
       19.04        14.93        29.98        24.00        19.07        39.06 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       75.95       106.75        46.65        43.76        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-AA-3492 
       35.11        16.57        37.02        34.65        32.75         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 
        1.02        37.05        35.01        63.98        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       20.98        13.94        54.02         2.01        14.01        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3837 
       11.01         5.98         5.03        26.99        33.04        38.99 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 
        0.00        10.06         0.00         0.00        36.03        30.05 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       53.00        27.02        18.05        31.00        33.01        26.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00J 
        2.01        25.02        27.02         7.96        19.00        18.05 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01V 
       34.98        10.98        12.00        38.07        35.01         1.02 
TCGA-AA-A029 TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        14.01         0.92        22.03        39.98        18.05 
TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-CK-4951 TCGA-CM-4744 
       16.31        58.39         5.65        32.94        70.16        20.02 
TCGA-CM-4746 
       37.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.02     0.20     0.46     0.95     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
  133.18   148.01    74.79   140.38   106.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
  29.190   20.305   22.090   26.010   24.000 
[1] "1.0 - 133.2 (29.2)" "0.2 - 148.0 (20.3)" "0.5 - 74.8 (22.1)" 
[4] "0.9 - 140.4 (26.0)" "0.0 - 106.8 (24.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      12        0        3        17         1         1         1
  subtype2      12        1        6        29         2         0         5
  subtype3       7        0        2        22         1         0         1
  subtype4      11        0        4        28         0         0         5
  subtype5      24        0       14        24         4         0         8
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          0          8          6        9         2         0
  subtype2          0         17          7        4         1         1
  subtype3          2         14          6        7         7         0
  subtype4          5          6          3       10         4         0
  subtype5          0          7         12       12         1         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          12       12        7       11       24
  STAGE IA          0        1        0        0        0
  STAGE II          3        6        2        4       14
  STAGE IIA        17       29       22       28       24
  STAGE IIB         1        2        1        0        4
  STAGE IIC         1        0        0        0        0
  STAGE III         1        5        1        5        8
  STAGE IIIA        0        0        2        5        0
  STAGE IIIB        8       17       14        6        7
  STAGE IIIC        6        7        6        3       12
  STAGE IV          9        4        7       10       12
  STAGE IVA         2        1        7        4        1
  STAGE IVB         0        1        0        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  3 10 41  7
  subtype2  1 12 65  9
  subtype3  1  8 49 14
  subtype4  3 16 56  3
  subtype5  3 22 69 13
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3        1        1        3        3
  T2       10       12        8       16       22
  T3       41       65       49       56       69
  T4        7        9       14        3       13
[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 34 14 13
  subtype2 55 23 10
  subtype3 34 23 15
  subtype4 46 21 11
  subtype5 69 15 23
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       34       55       34       46       69
  N1       14       23       23       21       15
  N2       13       10       15       11       23
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 40 11
  subtype2 63  6
  subtype3 49 14
  subtype4 62 14
  subtype5 93 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   11
  subtype2   63    6
  subtype3   49   14
  subtype4   62   14
  subtype5   93   13
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       40       63       49       62       93
  1       11        6       14       14       13
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 28 33
  subtype2 41 47
  subtype3 32 40
  subtype4 35 43
  subtype5 55 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   33
  subtype2   41   47
  subtype3   32   40
  subtype4   35   43
  subtype5   55   52
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       28       41       32       35       55
  MALE         33       47       40       43       52
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1 51  0
  subtype2 72  2
  subtype3 65  2
  subtype4 58  0
  subtype5 87  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    0
  subtype2   72    2
  subtype3   65    2
  subtype4   58    0
  subtype5   87    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        51       72       65       58       87
  YES        0        2        2        0        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus        0  1
  subtype1 59  2
  subtype2 70 17
  subtype3 61 11
  subtype4 73  2
  subtype5 84 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    2
  subtype2   70   17
  subtype3   61   11
  subtype4   73    2
  subtype5   84   22
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                59       70       61       73       84
  COLON MUCINOUS ADENOCARCINOMA        2       17       11        2       22
[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 36  1  3  6
  subtype2 57  1  1 12
  subtype3 49  0  2  3
  subtype4 52  0 10  0
  subtype5 90  2  9  1
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       36       57       49       52       90
  R1        1        1        0        0        2
  R2        3        1        2       10        9
  RX        6       12        3        0        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         4
  subtype2                                0     6                         8
  subtype3                                1     2                         7
  subtype4                                0     0                         1
  subtype5                                0     0                         3
          vv
clus       WHITE
  subtype1    47
  subtype2    69
  subtype3    52
  subtype4    28
  subtype5    17
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   3        6        2        0        0
  BLACK OR AFRICAN AMERICAN               4        8        7        1        3
  WHITE                                  47       69       52       28       17
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
          cls
clus        0  1
  subtype1  0 51
  subtype2  1 80
  subtype3  0 61
  subtype4  0 29
  subtype5  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   51
  subtype2    1   80
  subtype3    0   61
  subtype4    0   29
  subtype5    0   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        0        0        0
  NOT HISPANIC OR LATINO       51       80       61       29       20
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 60 19
  subtype2 43 12
  subtype3 38  7
  subtype4 11  5
  subtype5 38 16
  subtype6 15  5
  subtype7 18  5
  subtype8 29 13
  subtype9 51  9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      79       55       45       16       54       20       23       42 
subtype9 
      60 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      19       12        7        5       16        5        5       13 
subtype9 
       9 
$subtype1
TCGA-A6-4105 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6294 
       14.53        85.05        19.04        15.52         1.94        28.21 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2675 TCGA-A6-5656 
       22.09        35.80        91.79        79.69        43.43        32.91 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3655 
       24.69        19.66        20.28         7.04         6.97        61.02 
TCGA-AA-A01Z TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-6196 
       37.02        24.53        22.42        27.42        14.50         0.20 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 
       17.82         5.13        12.10         5.23        12.69        12.36 
TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4751 
       12.39        17.56        85.45        82.95       124.27        27.02 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6163 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       32.02        15.02        14.04        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 
       11.08        11.01        10.06        12.03        45.40        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 
       20.42        18.25        15.12         4.80        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       12.39        12.43        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M 
      140.38        14.04        26.47        81.37       119.93        95.18 
TCGA-F4-6806 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6317 
       41.42        47.41        35.31        44.68        39.42        36.00 
TCGA-G4-6626 
       46.75 

$subtype2
TCGA-A6-6649 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6310 TCGA-A6-5657 TCGA-A6-5659 
       24.16        25.08       100.01        63.62        31.63        30.44 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6654 TCGA-AD-5900 TCGA-AD-6899 TCGA-AM-5820 
       23.61        29.16        23.87        12.16         5.79         0.46 
TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
       27.09        62.79        29.56         3.19        12.76        10.06 
TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 
       14.30        21.14         2.01        22.03        30.08        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       17.03        12.00        16.04        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       12.95        19.59        17.75        43.27        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       10.13         9.04         9.44        11.64        13.35        11.38 
TCGA-D5-7000 TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       10.26         8.61        11.11        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6320 
       34.42        13.25         0.53        67.30        65.85        26.43 
TCGA-G4-6627 
       74.79 

$subtype3
TCGA-A6-2677 TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3976 
       24.33        58.03        24.03        19.07        34.03        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-G4-6298 TCGA-G4-6314 TCGA-A6-5660 TCGA-A6-5664 
       19.07        38.04        23.51        35.93        29.19        22.09 
TCGA-A6-6651 TCGA-AA-3509 TCGA-AA-3519 TCGA-AA-3534 TCGA-AA-3561 TCGA-AA-3678 
       21.76        62.96         9.07        29.00        13.94        47.01 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3875 TCGA-AA-3989 TCGA-AA-A00U TCGA-AA-A01S 
       25.02        17.98        18.05         7.96        17.03         1.02 
TCGA-AA-A01X TCGA-AA-A02J TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 
       26.01         5.03        12.46        12.59        12.20        21.99 
TCGA-CM-4750 TCGA-CM-6161 TCGA-CM-6166 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6538 
        8.02        15.02        21.99        56.09        25.48        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6460 
       14.30        13.41        38.20       139.17        60.79        31.96 
TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6315 
       35.74         8.35        61.91 

$subtype4
TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3663 TCGA-AD-6889 TCGA-AZ-6598 
       26.17        33.53        24.39         6.97        83.24        49.41 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6540 TCGA-DM-A1DA 
       15.62        51.32        23.05        14.04        16.14         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-F4-6570 TCGA-G4-6309 
      135.65         7.76         6.18        85.48 

$subtype5
TCGA-AA-3496 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3867 
        1.02        23.01        19.99         6.05        36.00        24.03 
TCGA-AD-6548 TCGA-AD-6964 TCGA-DM-A285 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-5666 
       21.37        10.88         5.88        43.76        42.28        32.71 
TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3494 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3538 
       25.08        20.12         1.02        38.99         0.00        26.01 
TCGA-AA-3542 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3837 
       12.99        11.01         5.03        10.06        35.05        38.99 
TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-A00D TCGA-AA-A01V TCGA-AA-A02K TCGA-AD-6965 
        0.00         0.00        19.00         1.02        14.01        26.47 
TCGA-AM-5821 TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-CA-5797 
        0.92        16.31        21.44         1.41         6.77        12.59 
TCGA-CK-4948 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6164 
      148.01        13.02        22.98         5.03        15.02        29.03 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6931 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28F 
       54.61        55.92        12.00       130.65       131.51        35.97 
TCGA-DM-A28H TCGA-F4-6807 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6323 
      117.07        43.04        82.39        74.56        55.04        13.78 

$subtype6
TCGA-CK-5912 TCGA-A6-6137 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3660 TCGA-AA-3861 
       49.08        27.09        35.01         1.02        78.08        30.05 
TCGA-AA-A010 TCGA-AA-A02H TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6606 TCGA-CM-6172 
       34.98         2.01        33.01        88.21        11.74        11.01 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28K TCGA-F4-6808 TCGA-G4-6293 
      119.70        24.43        44.32        98.24        33.67       133.18 
TCGA-G4-6304 TCGA-G4-6322 
       53.62        26.04 

$subtype7
TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3672 TCGA-AA-3870 TCGA-A6-2671 TCGA-A6-2684 
       45.60        13.94         0.92        29.98        43.76        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3818 
       37.25        37.02        33.34        36.53         1.02         0.99 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3956 
       15.95        37.02        17.03        31.00        26.01        34.03 
TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A00O TCGA-AA-A01P TCGA-CM-4748 
       13.05        27.02        27.02        38.07        26.04 

$subtype8
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 
       13.02        37.05         8.05         0.99        17.95        19.99 
TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-4313 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2683 
       19.04        24.00        75.95        46.65        42.90        16.57 
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3555 
       32.75         3.02        19.07        14.01        33.99        29.95 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3821 
       54.02         2.01         5.98        26.99        33.04         1.02 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3966 
       10.06        36.03        53.00         2.01        33.01         2.01 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A02R 
       25.02        18.05        10.98        35.01        51.98        22.03 
TCGA-AA-A03F TCGA-AZ-4614 TCGA-AZ-4615 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 
       18.05         5.65        32.94        70.16        20.02        37.02 

$subtype9
TCGA-AA-3524 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3862 
       36.03        13.02        19.00        14.93        31.07        30.05 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A024 TCGA-AZ-4681 
       12.99         2.01        50.99        24.00        39.06       106.75 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-3807 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3495 
       44.91        35.11        34.65        32.45         5.03        37.05 
TCGA-AA-3510 TCGA-AA-3532 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3667 
       63.98        29.00        21.01        24.00        20.98        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3846 TCGA-AA-3850 
       50.04        47.05        15.02        37.05        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 
       33.07        32.05         0.99        31.07        27.02        24.00 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 
       20.98        21.99        36.03        16.08        34.06        27.02 
TCGA-AA-3982 TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01T 
       27.02        42.02        14.99        32.02        12.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AY-4071 
        2.96        39.98         0.92        39.98        40.96         0.95 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CM-4747 TCGA-CM-5341 
      109.28        58.39        22.36        65.00        25.02        29.06 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.20     0.46     1.02     6.18     0.00     1.02     0.92     0.99 
subtype9 
    0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  140.38   100.01   139.17   135.65   148.01   133.18    45.60    75.95 
subtype9 
  109.28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  20.420   16.040   22.090   23.720   20.745   34.325   29.980   21.025 
subtype9 
  29.030 
[1] "0.2 - 140.4 (20.4)" "0.5 - 100.0 (16.0)" "1.0 - 139.2 (22.1)"
[4] "6.2 - 135.7 (23.7)" "0.0 - 148.0 (20.7)" "1.0 - 133.2 (34.3)"
[7] "0.9 - 45.6 (30.0)"  "1.0 - 76.0 (21.0)"  "0.0 - 109.3 (29.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      11        0        5        30         1         0         2
  subtype2       7        0        2        21         0         0         1
  subtype3       7        0        3        13         0         0         4
  subtype4       3        0        2         7         1         0         0
  subtype5       7        1        1        13         0         1         2
  subtype6       4        0        1         6         2         0         2
  subtype7       4        0        0        10         0         0         2
  subtype8       8        0        6         9         3         0         5
  subtype9      15        0        9        11         1         0         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1         10          5        4         3         1
  subtype2          2         10          4        3         4         0
  subtype3          2          7          4        6         0         0
  subtype4          0          2          2        0         0         0
  subtype5          0          6         10       12         2         0
  subtype6          0          3          0        2         1         0
  subtype7          1          3          1        6         0         0
  subtype8          0          4          4        2         1         0
  subtype9          1          7          4        7         4         0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          11        7        7        3        7        4        4
  STAGE IA          0        0        0        0        1        0        0
  STAGE II          5        2        3        2        1        1        0
  STAGE IIA        30       21       13        7       13        6       10
  STAGE IIB         1        0        0        1        0        2        0
  STAGE IIC         0        0        0        0        1        0        0
  STAGE III         2        1        4        0        2        2        2
  STAGE IIIA        1        2        2        0        0        0        1
  STAGE IIIB       10       10        7        2        6        3        3
  STAGE IIIC        5        4        4        2       10        0        1
  STAGE IV          4        3        6        0       12        2        6
  STAGE IVA         3        4        0        0        2        1        0
  STAGE IVB         1        0        0        0        0        0        0
            clus
vv           subtype8 subtype9
  STAGE I           8       15
  STAGE IA          0        0
  STAGE II          6        9
  STAGE IIA         9       11
  STAGE IIB         3        1
  STAGE IIC         0        0
  STAGE III         5        2
  STAGE IIIA        0        1
  STAGE IIIB        4        7
  STAGE IIIC        4        4
  STAGE IV          2        7
  STAGE IVA         1        4
  STAGE IVB         0        0
[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  2 13 57  7
  subtype2  1  7 41  6
  subtype3  2  9 33  3
  subtype4  0  3 12  2
  subtype5  0  7 39  9
  subtype6  2  2 14  3
  subtype7  1  4 17  5
  subtype8  1  8 27  7
  subtype9  2 15 40  4
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        2        1        2        0        0        2        1        1
  T2       13        7        9        3        7        2        4        8
  T3       57       41       33       12       39       14       17       27
  T4        7        6        3        2        9        3        5        7
    clus
vv   subtype9
  T1        2
  T2       15
  T3       40
  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 54 17  8
  subtype2 30 17  8
  subtype3 25 14  8
  subtype4 13  2  2
  subtype5 24 10 22
  subtype6 13  5  3
  subtype7 14  9  4
  subtype8 28  7  8
  subtype9 37 15  9
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       54       30       25       13       24       13       14       28
  N1       17       17       14        2       10        5        9        7
  N2        8        8        8        2       22        3        4        8
    clus
vv   subtype9
  N0       37
  N1       15
  N2        9
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 55  8
  subtype2 41  7
  subtype3 36  6
  subtype4 14  0
  subtype5 37 14
  subtype6 16  3
  subtype7 21  6
  subtype8 39  3
  subtype9 48 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    8
  subtype2   41    7
  subtype3   36    6
  subtype4   14    0
  subtype5   37   14
  subtype6   16    3
  subtype7   21    6
  subtype8   39    3
  subtype9   48   11
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       55       41       36       14       37       16       21       39
  1        8        7        6        0       14        3        6        3
   clus
vv  subtype9
  0       48
  1       11
[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"
D10V7, binary
          cls
clus        0  1
  subtype1 29 50
  subtype2 24 31
  subtype3 25 22
  subtype4 11  6
  subtype5 24 32
  subtype6 11 10
  subtype7 18  9
  subtype8 27 16
  subtype9 22 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   50
  subtype2   24   31
  subtype3   25   22
  subtype4   11    6
  subtype5   24   32
  subtype6   11   10
  subtype7   18    9
  subtype8   27   16
  subtype9   22   39
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       29       24       25       11       24       11       18
  MALE         50       31       22        6       32       10        9
        clus
vv       subtype8 subtype9
  FEMALE       27       22
  MALE         16       39
[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"
D10V8, binary
          cls
clus        0  1
  subtype1 66  2
  subtype2 50  2
  subtype3 39  0
  subtype4 12  0
  subtype5 41  1
  subtype6 14  0
  subtype7 21  0
  subtype8 38  1
  subtype9 52  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    2
  subtype2   50    2
  subtype3   39    0
  subtype4   12    0
  subtype5   41    1
  subtype6   14    0
  subtype7   21    0
  subtype8   38    1
  subtype9   52    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        66       50       39       12       41       14       21       38
  YES        2        2        0        0        1        0        0        1
     clus
vv    subtype9
  NO        52
  YES        2
[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"
D10V9, binary
          cls
clus        0  1
  subtype1 69  9
  subtype2 43 12
  subtype3 45  1
  subtype4 13  3
  subtype5 49  6
  subtype6 19  2
  subtype7 22  5
  subtype8 29 14
  subtype9 58  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69    9
  subtype2   43   12
  subtype3   45    1
  subtype4   13    3
  subtype5   49    6
  subtype6   19    2
  subtype7   22    5
  subtype8   29   14
  subtype9   58    2
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                69       43       45       13       49
  COLON MUCINOUS ADENOCARCINOMA        9       12        1        3        6
                               clus
vv                              subtype6 subtype7 subtype8 subtype9
  COLON ADENOCARCINOMA                19       22       29       58
  COLON MUCINOUS ADENOCARCINOMA        2        5       14        2
[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 R1 R2 RX
  subtype1 44  1  1  7
  subtype2 42  0  0  5
  subtype3 32  0  3  5
  subtype4  9  0  0  3
  subtype5 35  2  8  0
  subtype6 12  0  1  1
  subtype7 24  0  3  0
  subtype8 36  1  1  1
  subtype9 50  0  8  0
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       44       42       32        9       35       12       24       36
  R1        1        0        0        0        2        0        0        1
  R2        1        0        3        0        8        1        3        1
  RX        7        5        5        3        0        1        0        1
    clus
vv   subtype9
  R0       50
  R1        0
  R2        8
  RX        0
[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"
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         7
  subtype2                                1     3                         4
  subtype3                                0     3                         3
  subtype4                                0     1                         2
  subtype5                                0     1                         3
  subtype6                                0     0                         1
  subtype7                                0     0                         1
  subtype8                                0     0                         1
  subtype9                                0     0                         1
          vv
clus       WHITE
  subtype1    63
  subtype2    47
  subtype3    20
  subtype4    13
  subtype5    29
  subtype6    13
  subtype7     8
  subtype8     9
  subtype9    11
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   3        3        3        1        1
  BLACK OR AFRICAN AMERICAN               7        4        3        2        3
  WHITE                                  63       47       20       13       29
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0
  ASIAN                                   0        0        0        0
  BLACK OR AFRICAN AMERICAN               1        1        1        1
  WHITE                                  13        8        9       11
[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"
D10V13, binary
          cls
clus        0  1
  subtype1  0 70
  subtype2  1 53
  subtype3  0 25
  subtype4  0 15
  subtype5  0 33
  subtype6  0 14
  subtype7  0  9
  subtype8  0 10
  subtype9  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   70
  subtype2    1   53
  subtype3    0   25
  subtype4    0   15
  subtype5    0   33
  subtype6    0   14
  subtype7    0    9
  subtype8    0   10
  subtype9    0   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        0        0        0
  NOT HISPANIC OR LATINO       70       53       25       15       33       14
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            0        0        0
  NOT HISPANIC OR LATINO        9       10       12
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 12  6
  subtype2 14  6
  subtype3 10  6
  subtype4  8  3
  subtype5  5  6
  subtype6  5  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       20       16       11       11        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        6        6        3        6        4 
$subtype1
TCGA-G4-6294 TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-AD-6965 
       28.21        43.43        27.09        24.13        20.61        26.47 
TCGA-AZ-6603 TCGA-D5-5537 TCGA-D5-6533 TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 
       29.56        45.40        25.48       130.65        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6306 
        7.50       139.17        35.97        33.67         8.35        44.68 

$subtype2
TCGA-G4-6314 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3489 
       35.93        31.63        29.16        21.76        23.87         7.04 
TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6719 
       12.16         0.20        62.79        12.10         3.19        14.30 
TCGA-CM-6167 TCGA-D5-6534 TCGA-F4-6569 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
       14.99        43.27        35.74        34.42        43.04        13.25 
TCGA-G4-6302 TCGA-G4-6627 
       67.30        74.79 

$subtype3
TCGA-AD-6964 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-6138 TCGA-A6-6141 TCGA-AD-6963 
       10.88        91.79        79.69        22.52         8.38        27.42 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6605 TCGA-CM-4751 TCGA-CM-6674 TCGA-CM-6677 
        1.41         5.13         5.23        27.02        12.95        11.08 
TCGA-CM-6680 TCGA-DM-A0XD TCGA-DM-A280 TCGA-G4-6299 
       12.03        24.43         7.76        74.56 

$subtype4
TCGA-A6-6649 TCGA-A6-6142 TCGA-CK-6748 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-6536 
       24.16        25.08         2.01        11.08        11.01        17.85 
TCGA-D5-6922 TCGA-D5-6924 TCGA-F4-6459 TCGA-F4-6460 TCGA-G4-6303 
       10.13        14.30         8.61        31.96        65.85 

$subtype5
TCGA-AD-6548 TCGA-AZ-6601 TCGA-A6-6653 TCGA-A6-6781 TCGA-AD-6889 TCGA-AZ-6598 
       21.37       100.01        24.39        19.66        83.24        49.41 
TCGA-CA-6718 TCGA-CK-5916 TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6309 
       10.06        21.14       131.51         6.18        85.48 

$subtype6
TCGA-DM-A285 TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-CM-5860 TCGA-CM-6679 
        5.88        20.28         6.97        22.42        32.02        10.06 
TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-F4-6704 
       38.20        13.32         1.55 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    7.50     0.20     1.41     2.01     6.18     1.55 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  140.38    74.79    91.79    65.85   131.51    38.20 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  28.885   26.515   12.490   14.300   24.390   13.320 
[1] "7.5 - 140.4 (28.9)" "0.2 - 74.8 (26.5)"  "1.4 - 91.8 (12.5)" 
[4] "2.0 - 65.8 (14.3)"  "6.2 - 131.5 (24.4)" "1.6 - 38.2 (13.3)" 
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        1         7         0          0          2
  subtype2       2        2         5         0          0          4
  subtype3       2        0         6         0          0          3
  subtype4       1        0         2         0          1          3
  subtype5       3        2         3         0          0          1
  subtype6       0        1         3         1          0          0
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        1         0
  subtype2          3        3         1
  subtype3          1        2         0
  subtype4          0        2         2
  subtype5          2        0         0
  subtype6          2        1         0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        2        2        1        3        0
  STAGE II          1        2        0        0        2        1
  STAGE IIA         7        5        6        2        3        3
  STAGE IIB         0        0        0        0        0        1
  STAGE IIIA        0        0        0        1        0        0
  STAGE IIIB        2        4        3        3        1        0
  STAGE IIIC        2        3        1        0        2        2
  STAGE IV          1        3        2        2        0        1
  STAGE IVA         0        1        0        2        0        0
[1] 9 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  2 13  2
  subtype2  0  2 16  2
  subtype3  0  2 11  3
  subtype4  0  1  9  1
  subtype5  1  2  7  1
  subtype6  0  0  7  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        0        0        0        1        0
  T2        2        2        2        1        2        0
  T3       13       16       11        9        7        7
  T4        2        2        3        1        1        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 10  5  3
  subtype2  9  6  5
  subtype3  9  2  5
  subtype4  3  7  1
  subtype5  8  2  1
  subtype6  6  0  3
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       10        9        9        3        8        6
  N1        5        6        2        7        2        0
  N2        3        5        5        1        1        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 13  1
  subtype2 11  4
  subtype3 12  2
  subtype4  7  4
  subtype5  9  0
  subtype6  5  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   11    4
  subtype3   12    2
  subtype4    7    4
  subtype5    9    0
  subtype6    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       13       11       12        7        9        5
  1        1        4        2        4        0        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1 10  8
  subtype2 10 10
  subtype3  5 11
  subtype4  6  5
  subtype5  5  6
  subtype6  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    8
  subtype2   10   10
  subtype3    5   11
  subtype4    6    5
  subtype5    5    6
  subtype6    2    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       10       10        5        6        5        2
  MALE          8       10       11        5        6        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0
  subtype1 12
  subtype2 19
  subtype3 14
  subtype4 11
  subtype5 10
  subtype6  5
[1] "NOT AVAILABLE: table only has an event [0]"
D11V9, binary
          cls
clus        0  1
  subtype1 18  0
  subtype2 16  4
  subtype3 15  1
  subtype4 10  1
  subtype5 10  1
  subtype6  5  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    0
  subtype2   16    4
  subtype3   15    1
  subtype4   10    1
  subtype5   10    1
  subtype6    5    2
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                18       16       15       10       10
  COLON MUCINOUS ADENOCARCINOMA        0        4        1        1        1
                               clus
vv                              subtype6
  COLON ADENOCARCINOMA                 5
  COLON MUCINOUS ADENOCARCINOMA        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 RX
  subtype1  5  1  1
  subtype2 14  0  1
  subtype3  7  0  0
  subtype4  8  0  1
  subtype5  5  0  2
  subtype6  4  0  0
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        5       14        7        8        5        4
  R1        1        0        0        0        0        0
  RX        1        1        0        1        2        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                0     1                         3
  subtype3                                0     0                         1
  subtype4                                0     0                         0
  subtype5                                0     2                         1
  subtype6                                1     0                         0
          vv
clus       WHITE
  subtype1    17
  subtype2    15
  subtype3    15
  subtype4    11
  subtype5     8
  subtype6     7
D11V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   0        1        0        0        2
  BLACK OR AFRICAN AMERICAN               1        3        1        0        1
  WHITE                                  17       15       15       11        8
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                   0
  BLACK OR AFRICAN AMERICAN               0
  WHITE                                   7
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
          cls
clus        0
  subtype1 18
  subtype2 19
  subtype3 15
  subtype4 11
  subtype5 10
  subtype6  7
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2      0 1
  subtype1 7 5
  subtype2 7 2
  subtype3 5 3
  subtype4 8 4
  subtype5 5 4
  subtype6 5 2
  subtype7 8 5
  subtype8 6 3
  subtype9 3 3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12        9        8       12        9        7       13        9 
subtype9 
       6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       5        2        3        4        4        2        5        3 
subtype9 
       3 
$subtype1
TCGA-A6-2675 TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-5403 
       43.43        20.28         7.04        22.42         0.20        62.79 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CM-5860 TCGA-CM-6677 TCGA-CM-6679 TCGA-F4-6569 
       12.10         5.23        32.02        11.08        10.06        35.74 

$subtype2
TCGA-A6-5657 TCGA-A6-6651 TCGA-A6-6654 TCGA-CM-6167 TCGA-F4-6805 TCGA-F4-6807 
       31.63        21.76        23.87        14.99        34.42        43.04 
TCGA-F4-6809 TCGA-G4-6302 TCGA-G4-6627 
       13.25        67.30        74.79 

$subtype3
TCGA-AD-6548 TCGA-A6-5667 TCGA-AZ-6603 TCGA-CA-6719 TCGA-CK-6748 TCGA-D5-6922 
       21.37        29.16        29.56        14.30         2.01        10.13 
TCGA-F4-6459 TCGA-G4-6303 
        8.61        65.85 

$subtype4
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AZ-6598 
       27.09        24.13        20.61        24.39        83.24        49.41 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 
        7.50       131.51        35.97         8.35        44.68        85.48 

$subtype5
TCGA-AD-6964 TCGA-G4-6625 TCGA-A6-6138 TCGA-A6-6141 TCGA-AD-6963 TCGA-AZ-4616 
       10.88        91.79        22.52         8.38        27.42         5.13 
TCGA-DM-A280 TCGA-F4-6570 TCGA-G4-6299 
        7.76         6.18        74.56 

$subtype6
TCGA-DM-A285 TCGA-A6-6142 TCGA-A6-6781 TCGA-AZ-6607 TCGA-CM-6674 TCGA-D5-6534 
        5.88        25.08        19.66         3.19        12.95        43.27 
TCGA-F4-6704 
        1.55 

$subtype7
TCGA-A6-6649 TCGA-AZ-6601 TCGA-G4-6314 TCGA-G4-6628 TCGA-AD-5900 TCGA-AZ-4323 
       24.16       100.01        35.93        79.69        12.16         1.41 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4751 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6536 
       10.06        21.14        27.02        11.01        12.03        17.85 
TCGA-F4-6460 
       31.96 

$subtype8
TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF TCGA-DM-A1D7 
        6.97        11.08        25.48        14.30        38.20        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 
       12.59       140.38       139.17 

$subtype9
TCGA-G4-6294 TCGA-AD-6965 TCGA-D5-5537 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-F4-6808 
       28.21        26.47        45.40        24.43       130.65        33.67 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.20    13.25     2.01     7.50     5.13     1.55     1.41     6.97 
subtype9 
   24.43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   62.79    74.79    65.85   131.51    91.79    43.27   100.01   140.38 
subtype9 
  130.65 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  16.190   31.630   17.835   31.530   10.880   12.950   21.140   14.300 
subtype9 
  30.940 
[1] "0.2 - 62.8 (16.2)"   "13.2 - 74.8 (31.6)"  "2.0 - 65.8 (17.8)"  
[4] "7.5 - 131.5 (31.5)"  "5.1 - 91.8 (10.9)"   "1.6 - 43.3 (12.9)"  
[7] "1.4 - 100.0 (21.1)"  "7.0 - 140.4 (14.3)"  "24.4 - 130.7 (30.9)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        2         4         1          0          1
  subtype2       0        0         3         0          0          3
  subtype3       1        0         1         0          1          2
  subtype4       1        2         3         0          0          3
  subtype5       1        0         4         0          0          0
  subtype6       0        0         2         0          0          0
  subtype7       3        1         2         0          0          4
  subtype8       1        1         4         0          0          0
  subtype9       1        0         3         0          0          0
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        1         0
  subtype2          2        0         1
  subtype3          0        2         0
  subtype4          2        0         0
  subtype5          1        1         0
  subtype6          2        2         1
  subtype7          0        2         1
  subtype8          1        0         0
  subtype9          1        1         0
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        0        1        1        1        0        3
  STAGE II          2        0        0        2        0        0        1
  STAGE IIA         4        3        1        3        4        2        2
  STAGE IIB         1        0        0        0        0        0        0
  STAGE IIIA        0        0        1        0        0        0        0
  STAGE IIIB        1        3        2        3        0        0        4
  STAGE IIIC        1        2        0        2        1        2        0
  STAGE IV          1        0        2        0        1        2        2
  STAGE IVA         0        1        0        0        0        1        1
            clus
vv           subtype8 subtype9
  STAGE I           1        1
  STAGE II          1        0
  STAGE IIA         4        3
  STAGE IIB         0        0
  STAGE IIIA        0        0
  STAGE IIIB        0        0
  STAGE IIIC        1        1
  STAGE IV          0        1
  STAGE IVA         0        0
[1] 9 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  1  8  3
  subtype2  0  0  9  0
  subtype3  0  2  6  0
  subtype4  0  2 10  0
  subtype5  0  1  7  1
  subtype6  0  0  5  2
  subtype7  1  2  8  2
  subtype8  0  1  6  2
  subtype9  1  0  4  1
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        0        0        0        0        0        0        1        0
  T2        1        0        2        2        1        0        2        1
  T3        8        9        6       10        7        5        8        6
  T4        3        0        0        0        1        2        2        2
    clus
vv   subtype9
  T1        1
  T2        0
  T3        4
  T4        1
[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  9  2  1
  subtype2  3  4  2
  subtype3  2  5  1
  subtype4  7  3  2
  subtype5  6  0  3
  subtype6  2  2  3
  subtype7  6  4  3
  subtype8  7  1  1
  subtype9  3  1  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        9        3        2        7        6        2        6        7
  N1        2        4        5        3        0        2        4        1
  N2        1        2        1        2        3        3        3        1
    clus
vv   subtype9
  N0        3
  N1        1
  N2        2
[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"
D12V6, binary
          cls
clus        0  1
  subtype1  6  1
  subtype2  7  1
  subtype3  4  2
  subtype4 11  0
  subtype5  6  1
  subtype6  2  3
  subtype7  9  3
  subtype8  8  0
  subtype9  4  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    7    1
  subtype3    4    2
  subtype4   11    0
  subtype5    6    1
  subtype6    2    3
  subtype7    9    3
  subtype8    8    0
  subtype9    4    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0        6        7        4       11        6        2        9        8
  1        1        1        2        0        1        3        3        0
   clus
vv  subtype9
  0        4
  1        1
[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"
D12V7, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2  7  2
  subtype3  6  2
  subtype4  5  7
  subtype5  4  5
  subtype6  3  4
  subtype7  5  8
  subtype8  5  4
  subtype9  2  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2    7    2
  subtype3    6    2
  subtype4    5    7
  subtype5    4    5
  subtype6    3    4
  subtype7    5    8
  subtype8    5    4
  subtype9    2    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        1        7        6        5        4        3        5
  MALE         11        2        2        7        5        4        8
        clus
vv       subtype8 subtype9
  FEMALE        5        2
  MALE          4        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"
D12V8, binary
          cls
clus        0
  subtype1 11
  subtype2  9
  subtype3  8
  subtype4  9
  subtype5  8
  subtype6  5
  subtype7 13
  subtype8  4
  subtype9  4
[1] "NOT AVAILABLE: table only has an event [0]"
D12V9, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2  8  1
  subtype3  7  1
  subtype4 12  0
  subtype5  8  1
  subtype6  3  4
  subtype7 12  1
  subtype8  7  0
  subtype9  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2    8    1
  subtype3    7    1
  subtype4   12    0
  subtype5    8    1
  subtype6    3    4
  subtype7   12    1
  subtype8    7    0
  subtype9    6    0
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                11        8        7       12        8
  COLON MUCINOUS ADENOCARCINOMA        1        1        1        0        1
                               clus
vv                              subtype6 subtype7 subtype8 subtype9
  COLON ADENOCARCINOMA                 3       12        7        6
  COLON MUCINOUS ADENOCARCINOMA        4        1        0        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"
          vv
clus       R0 R1 RX
  subtype1  7  0  0
  subtype2  7  0  0
  subtype3  5  0  2
  subtype4  3  0  0
  subtype5  3  0  0
  subtype6  4  0  0
  subtype7  8  0  2
  subtype8  4  0  0
  subtype9  2  1  1
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0        7        7        5        3        3        4        8        4
  R1        0        0        0        0        0        0        0        0
  RX        0        0        2        0        0        0        2        0
    clus
vv   subtype9
  R0        2
  R1        1
  RX        1
[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"
D12V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                0     0                         2
  subtype3                                0     1                         0
  subtype4                                0     1                         2
  subtype5                                0     0                         1
  subtype6                                1     0                         0
  subtype7                                0     1                         0
  subtype8                                0     0                         0
  subtype9                                0     0                         0
          vv
clus       WHITE
  subtype1    10
  subtype2     7
  subtype3     7
  subtype4     9
  subtype5     8
  subtype6     6
  subtype7    12
  subtype8     8
  subtype9     6
D12V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   0        0        1        1        0
  BLACK OR AFRICAN AMERICAN               1        2        0        2        1
  WHITE                                  10        7        7        9        8
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   0        1        0        0
  BLACK OR AFRICAN AMERICAN               0        0        0        0
  WHITE                                   6       12        8        6
[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"
D12V13, binary
          cls
clus        0
  subtype1 10
  subtype2  9
  subtype3  8
  subtype4 11
  subtype5  8
  subtype6  7
  subtype7 13
  subtype8  8
  subtype9  6
[1] "NOT AVAILABLE: table only has an event [0]"
