[1] "ofn"            "-oTCOADREAD-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/COADREAD-TP/15076882/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/15117685/COADREAD-TP.mergedcluster.txt"

nPatients in clinical file=624, in cluster file=628, common to both=621
[1]  12 621
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
46 62 72 42 
 1  2  3  4 
46 62 72 42 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
52 41 77 52 
 1  2  3  4 
52 41 77 52 
[1] "CN_CNMF"
[1] 3
  1   2   3 
252 205 151 
  1   2   3 
252 205 151 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 94 164 128 
  1   2   3 
 94 164 128 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
100 179  42 140 
  1   2   3   4 
100 179  42 140 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 54 307 100 
  1   2   3 
 54 307 100 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
145 142 130 199 
  1   2   3   4 
145 142 130 199 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 79  84  63  57  90 140 103 
  1   2   3   4   5   6   7 
 79  84  63  57  90 140 103 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
212  96 241 
  1   2   3 
212  96 241 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
229 144 176 
  1   2   3 
229 144 176 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
24 20 29 28 18 17 
 1  2  3  4  5  6 
24 20 29 28 18 17 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
55 15 34 32 
 1  2  3  4 
55 15 34 32 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 621 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=100,	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=352,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM_DISEASESTAGE':	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "350"                 
freq.contrast "350"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=38,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 621 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"                        
 [2] "PRIMARY_SITE_OF_DISEASE"               
 [3] "NEOPLASM_DISEASESTAGE"                 
 [4] "PATHOLOGY_T_STAGE"                     
 [5] "PATHOLOGY_N_STAGE"                     
 [6] "PATHOLOGY_M_STAGE"                     
 [7] "GENDER"                                
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "COMPLETENESS_OF_RESECTION"             
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_DISEASESTAGE, 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 
 20 109 422  68 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 109 422  68 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 109 422  68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 109 422  68 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
351 149 117 
[1] "table(vv)"
vv
 N0  N1  N2 
351 149 117 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
351 149 117 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
351 149 117 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 32  9
  subtype2 43 15
  subtype3 58 10
  subtype4 35  6
subtype1 subtype2 subtype3 subtype4 
      41       58       68       41 
subtype1 subtype2 subtype3 subtype4 
       9       15       10        6 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       46.65        43.76        42.90        33.34        32.75        36.53 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 
        1.02        13.02        24.03         0.99        17.95         0.92 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3842 
       26.99        19.04        10.06        33.04        15.95        37.02 
TCGA-AA-3845 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
        0.00        31.07        17.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A02R 
       38.04        19.00        30.02         0.99        10.98        22.03 
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3600 TCGA-AG-3878 TCGA-AG-3883 
       12.72        12.00         6.05         0.99         1.02 

$subtype2
TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 
       24.33        16.57        34.65        38.99         9.07        34.03 
TCGA-AA-3534 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-3560 TCGA-AA-3666 TCGA-AA-3696 TCGA-AA-3837 TCGA-AA-3875 
       24.00        19.99         2.01         5.03        38.99        18.05 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-A00L TCGA-AA-A00O 
        2.01        50.99        13.05        26.01        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A02E 
       42.02        21.99        15.02        15.02        31.00         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 TCGA-AF-3913 
       39.98         2.01         5.03        41.00        16.31        10.39 
TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3890 
       36.03        24.00        19.99        19.99         7.99        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
        1.02        17.03        15.95         9.07         1.02        31.00 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       51.98         1.94        38.96        38.04 

$subtype3
TCGA-A6-2678 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3552 
       42.28        36.03         0.00        19.07        29.00        13.02 
TCGA-AA-3562 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 
       19.99        14.01        50.04        47.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.00        36.00        35.05         0.99        25.02        17.98 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3862 TCGA-AA-3867 TCGA-AA-3939 
       32.05         0.99        31.07        30.05        24.03        12.99 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03        21.99        36.03        16.08        34.06 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00F 
       24.00        27.02        27.02        19.07         7.96        34.03 
TCGA-AA-A00W TCGA-AY-4071 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3578 TCGA-AG-3580 
       14.99         0.95        43.04        13.55        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        36.03        20.05         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3727 TCGA-AG-3728 
       50.04        12.03         0.99        15.95         0.99        29.98 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       19.99         1.02        19.99         6.02        23.01        37.02 
TCGA-AG-A01L TCGA-AG-A025 
       12.00        49.97 

$subtype4
TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3556 
        1.02        37.05         8.05        19.07        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
       20.98        13.94        54.02        47.05        11.01         5.98 
TCGA-AA-3821 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3941 
        1.02         0.00        36.03        30.05        53.00        24.00 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U 
       27.02        13.94        18.05        18.05         4.01        17.03 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01Q TCGA-AA-A024 
       34.98        32.02        12.00        31.00         1.02        39.06 
TCGA-AA-A029 TCGA-AF-2689 TCGA-AG-3594 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3902 
       51.98        39.48         2.01        36.95        13.02        32.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A02X 
       20.98        13.94        25.97        36.03        41.00 

subtype1 subtype2 subtype3 subtype4 
    0.00     1.02     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 
   46.65    51.98    50.04    54.02 
subtype1 subtype2 subtype3 subtype4 
  22.030   20.500   20.515   23.010 
[1] "0.0 - 46.6 (22.0)" "1.0 - 52.0 (20.5)" "0.0 - 50.0 (20.5)"
[4] "0.0 - 54.0 (23.0)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 39  7
  subtype2 37 25
  subtype3 45 25
  subtype4 31 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    7
  subtype2   37   25
  subtype3   45   25
  subtype4   31   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        39       37       45       31
  RECTUM        7       25       25       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       8        3        15         3         3          1          4
  subtype2       9        2        14         0         2          2          5
  subtype3      19        4        23         0         4          0          7
  subtype4      11        6        13         2         1          0          6
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        6         0
  subtype2         11       17         0
  subtype3          7        8         0
  subtype4          0        2         1
D1V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           8        9       19       11
  STAGE II          3        2        4        6
  STAGE IIA        15       14       23       13
  STAGE IIB         3        0        0        2
  STAGE III         3        2        4        1
  STAGE IIIA        1        2        0        0
  STAGE IIIB        4        5        7        6
  STAGE IIIC        2       11        7        0
  STAGE IV          6       17        8        2
  STAGE IVA         0        0        0        1
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  9 30  6
  subtype2  1 12 41  8
  subtype3  5 16 51  0
  subtype4  2  9 26  5
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        1        5        2
  T2        9       12       16        9
  T3       30       41       51       26
  T4        6        8        0        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 30  6 10
  subtype2 28 17 17
  subtype3 46 12 14
  subtype4 32  8  2
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       30       28       46       32
  N1        6       17       12        8
  N2       10       17       14        2
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 39  6
  subtype2 45 17
  subtype3 63  8
  subtype4 39  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    6
  subtype2   45   17
  subtype3   63    8
  subtype4   39    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       39       45       63       39
  1        6       17        8        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1 28 18
  subtype2 33 29
  subtype3 30 42
  subtype4 15 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   18
  subtype2   33   29
  subtype3   30   42
  subtype4   15   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28       33       30       15
  MALE         18       29       42       27
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   28                            11
  subtype2                   36                             1
  subtype3                   44                             1
  subtype4                   21                             9
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     4                              2
  subtype2                    25                              0
  subtype3                    21                              2
  subtype4                     8                              3
D1V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 28       36       44       21
  COLON MUCINOUS ADENOCARCINOMA        11        1        1        9
  RECTAL ADENOCARCINOMA                 4       25       21        8
  RECTAL MUCINOUS ADENOCARCINOMA        2        0        2        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus        0  1
  subtype1  1 45
  subtype2  0 62
  subtype3  0 72
  subtype4  0 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    0   62
  subtype3    0   72
  subtype4    0   42
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        0        0
  YES       45       62       72       42
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 38  0  4
  subtype2 45  2 15
  subtype3 62  0  8
  subtype4 40  0  2
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       38       45       62       40
  R1        0        2        0        0
  R2        4       15        8        2
[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"
D1V12, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     7
  subtype2                         2     3
  subtype3                         0     4
  subtype4                         0     1
D1V13, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       7        5        4        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                            7        3        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 37 11
  subtype2 28 11
  subtype3 61 13
  subtype4 42  5
subtype1 subtype2 subtype3 subtype4 
      48       39       74       47 
subtype1 subtype2 subtype3 subtype4 
      11       11       13        5 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3514 
       46.65        43.76        42.90        33.34        32.75         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3543 TCGA-AA-3554 
       13.02         1.02         8.05        19.07         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       29.95        23.01         0.92        26.99        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3852 
       33.04         1.02        15.95        37.02         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       36.03        53.00        29.98        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01D 
       38.04        30.02        18.05         4.01         0.99        10.98 
TCGA-AA-A01Q TCGA-AA-A02R TCGA-AF-3400 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-A02X 
        1.02        22.03        12.72         2.01         6.05        41.00 

$subtype2
TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3544 
       24.33        34.65        36.53        34.03        12.99        14.01 
TCGA-AA-3553 TCGA-AA-3696 TCGA-AA-3973 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       24.00         5.03        13.05        38.04        27.02        42.02 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A02E 
       21.99        34.98        15.02        15.02        31.00         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 TCGA-AF-3913 
       39.98         2.01         5.03        41.00        16.31        10.39 
TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3890 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 
       36.03        24.00        17.03        48.03        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       14.04         1.02        17.03         1.02        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
        1.94        38.96        38.04 

$subtype3
TCGA-A6-2678 TCGA-A6-2683 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       42.28        16.57         9.07        24.03        37.05        36.03 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3558 
        0.00        19.07        29.00        33.99        21.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 
       19.99        13.94        54.02         2.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3818 TCGA-AA-3819 
       47.01        11.01         5.98        36.00         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       17.98        38.99        14.93        10.06         0.00        33.07 
TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       30.05        27.02        18.05        12.99        50.99        26.01 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00U 
       19.07         7.96        13.94        19.00        18.05        17.03 
TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A024 TCGA-AA-A029 
       14.99        32.02        12.00        31.00        39.06        51.98 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       39.48        43.04        13.55        12.00        32.02         8.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02        46.03        34.03        12.03         7.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A008 
       36.95        13.02        14.01        32.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A023 TCGA-AG-A025 
       51.98        49.97 

$subtype4
TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3667 
       38.99        29.00        26.01        13.02        19.99        14.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3846 
       15.02        37.05        19.00        35.05        36.95        17.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
       24.03         2.01        20.98        34.03        21.99        36.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-A00F 
       16.08        34.06        24.00        27.02        27.02        34.03 
TCGA-AY-4071 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3605 
        0.95         7.07        36.03        20.05        50.04         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        19.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A011 
        1.02        35.01         1.02        19.99        37.02 

subtype1 subtype2 subtype3 subtype4 
    0.00     1.02     0.00     0.95 
subtype1 subtype2 subtype3 subtype4 
   53.00    48.03    54.02    50.04 
subtype1 subtype2 subtype3 subtype4 
  20.550   24.000   20.485   21.990 
[1] "0.0 - 53.0 (20.6)" "1.0 - 48.0 (24.0)" "0.0 - 54.0 (20.5)"
[4] "0.9 - 50.0 (22.0)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 46  6
  subtype2 24 17
  subtype3 48 28
  subtype4 34 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    6
  subtype2   24   17
  subtype3   48   28
  subtype4   34   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        46       24       48       34
  RECTUM        6       17       28       17
[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       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        17         4         3          1          6
  subtype2       4        2        10         1         0          1          4
  subtype3      20        8        23         0         6          1          5
  subtype4      14        2        15         0         1          0          7
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        5         1
  subtype2          7       12         0
  subtype3          5        9         0
  subtype4          6        7         0
D2V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        4       20       14
  STAGE II          3        2        8        2
  STAGE IIA        17       10       23       15
  STAGE IIB         4        1        0        0
  STAGE III         3        0        6        1
  STAGE IIIA        1        1        1        0
  STAGE IIIB        6        4        5        7
  STAGE IIIC        2        7        5        6
  STAGE IV          5       12        9        7
  STAGE IVA         1        0        0        0
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 10 33  8
  subtype2  0  7 28  6
  subtype3  7 15 51  4
  subtype4  1 14 36  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        7        1
  T2       10        7       15       14
  T3       33       28       51       36
  T4        8        6        4        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 34  9  9
  subtype2 19 11 11
  subtype3 52 12 13
  subtype4 31 11 10
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       34       19       52       31
  N1        9       11       12       11
  N2        9       11       13       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 45  6
  subtype2 29 12
  subtype3 68  9
  subtype4 44  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    6
  subtype2   29   12
  subtype3   68    9
  subtype4   44    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       45       29       68       44
  1        6       12        9        7
[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"
D2V8, binary
          cls
clus        0  1
  subtype1 30 22
  subtype2 22 19
  subtype3 34 43
  subtype4 20 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   22
  subtype2   22   19
  subtype3   34   43
  subtype4   20   32
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30       22       34       20
  MALE         22       19       43       32
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   27                            18
  subtype2                   24                             0
  subtype3                   44                             4
  subtype4                   34                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     2                              3
  subtype2                    17                              0
  subtype3                    23                              3
  subtype4                    16                              1
D2V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 27       24       44       34
  COLON MUCINOUS ADENOCARCINOMA        18        0        4        0
  RECTAL ADENOCARCINOMA                 2       17       23       16
  RECTAL MUCINOUS ADENOCARCINOMA        3        0        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
          cls
clus        0  1
  subtype1  1 51
  subtype2  0 41
  subtype3  0 77
  subtype4  0 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   51
  subtype2    0   41
  subtype3    0   77
  subtype4    0   52
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        0        0
  YES       51       41       77       52
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 45  0  3
  subtype2 28  2 11
  subtype3 69  0  8
  subtype4 43  0  7
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       45       28       69       43
  R1        0        2        0        0
  R2        3       11        8        7
[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"
D2V12, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     6
  subtype2                         2     3
  subtype3                         0     5
  subtype4                         0     1
D2V13, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       6        5        5        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                            6        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 190  53
  subtype2 163  32
  subtype3 115  30
subtype1 subtype2 subtype3 
     243      195      145 
subtype1 subtype2 subtype3 
      53       32       30 
$subtype1
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 
       11.47        46.65        43.76        42.90        42.28        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5664 
       37.05        37.25        37.02        14.53        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.06         8.38        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         7.04         3.02 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       58.03        63.98         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 
       37.05         8.05        19.07        29.00         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 
       29.95        23.01        61.02         6.97         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       11.01         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       38.99        14.93         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       32.05        53.00        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       33.01        26.01        24.00         2.01         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07         7.96        27.02        38.04        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        10.98        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       39.06        51.98        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
       21.37        56.55         0.79         0.72        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.92        27.09         0.20        17.82        17.85        19.33 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6598 
       50.37        58.39         1.41        32.94         5.13        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77        12.10       100.01         3.19         3.06         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 
       20.02        37.02        26.04        22.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       13.05        11.01        12.03        45.40        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 
       17.75        43.27        17.85        12.49        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.26        24.43        92.75        49.91        13.32       140.38 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28M 
      135.65         7.76       139.17        81.37        60.79        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 
       29.59        16.24        35.41        19.43       107.67        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       67.30        53.62        51.75        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV 
       13.78        35.80        26.17        47.15        52.80        19.33 
TCGA-NH-A6GA TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 
        9.93        29.46        31.30        70.03        24.13        43.04 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3599 
       12.72        16.83        12.00         8.02        20.05        12.03 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 
        1.02         0.99        13.02        14.01        20.98        13.94 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
       10.98        49.97        61.97         0.49         1.45        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6160 
        1.81        10.19         6.05         4.73        15.02        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       12.95         5.29        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       18.28         8.61        10.78        17.46         8.45         9.96 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
        0.53         1.12        55.76 

$subtype2
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
        4.80        43.76        44.91        35.11        45.60        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       34.65        36.53        32.45        32.91        30.44        23.61 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       32.71        22.52        24.13        25.08        20.61        24.69 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 
       20.28        61.84        56.25         5.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3560 TCGA-AA-3561 
        9.07        34.03        14.01        21.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       19.99         2.01        14.01        15.02        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 
       85.05        36.95        37.02        17.03        10.06         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       31.07        17.03        27.02        20.98        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00L 
       50.99        13.05        34.06        26.01        34.03        38.04 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        14.99        21.99        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A03J 
       12.00        33.04         2.96        39.98         2.01        40.96 
TCGA-AD-6888 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
        4.21        22.42        27.42        16.44        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-6603 
       15.75        17.26        18.84        75.25        22.36        29.56 
TCGA-AZ-6605 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        5.23         2.14         0.07        49.08        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-5868 
       25.02         8.02        13.02        16.01        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6679 
       14.04        29.03        16.04        15.02        11.08        10.06 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6932 
       19.59        13.51        18.25         1.32        15.12        11.38 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
       12.59       131.51        14.04        26.47       119.93        35.97 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 
        8.61        13.38        33.67        13.25         0.53        28.21 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 
       82.39        65.85        45.11        36.72        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       18.18        19.33        12.79        13.05        12.00        42.77 
TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
        9.70        39.48        13.55        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 
       14.50        15.39        86.63        11.84         7.07        36.03 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       46.03        34.03        50.04        15.95        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98         0.99        19.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04        17.03         0.99         6.02        25.97        23.01 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       36.03         9.07        12.00        38.96        41.00        38.04 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.97         9.37        13.97         7.17        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DE 
       12.99        12.00        15.02        36.00        10.06       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       24.13        51.48         2.40        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       16.41        11.97        31.30         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        0.69         0.76        47.08 

$subtype3
TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5667 
       11.47        43.43        24.33        31.63        29.19        29.16 
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       27.09        25.18         9.63         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 
       35.01        36.03        19.07         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 
       12.99        33.99        13.02        24.00        20.98        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3692 
        6.05        54.02        50.04        47.01         5.98        36.00 
TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3941 TCGA-AA-3956 
       33.07        31.07        24.03        29.98        24.00        34.03 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00U 
       24.00        27.02        13.94        19.00        18.05        17.03 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6899 
        1.02        37.02         5.03         0.92        41.00         5.79 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 
        0.20        16.31        21.44         5.65        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 
       62.79        61.41        11.74         1.94         2.24         3.29 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        1.35        15.62        27.02        29.06        22.98        30.08 
TCGA-CM-5862 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5538 
        5.03        21.99        13.02        11.01        11.08        12.26 
TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       11.51         4.80        17.13        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA 
       12.43         9.04       119.70        38.20       130.65         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6805 TCGA-G4-6295 
       44.32         6.12       117.07        98.24        16.31         8.35 
TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       74.56        44.68        55.04        39.42        35.93        36.00 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2690 
       10.98        15.65        32.98         8.42        30.28        17.23 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3584 
       20.02        10.39        65.98        36.03        32.02        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3732 
        1.02         2.01         6.05         0.99         7.99        32.98 
TCGA-AG-3887 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J 
       36.95        32.02         1.02        37.02        15.95         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AH-6643 
       31.00        70.03        64.01        51.98         1.94         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 
        0.72         6.05        78.12        13.97        10.98        13.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 
      126.44        41.36        57.24         0.49        17.00        15.85 
TCGA-EI-6883 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
       11.51        13.64        37.51        28.57         0.46        18.28 
TCGA-G5-6641 
       26.43 

subtype1 subtype2 subtype3 
    0.00     0.07     0.00 
subtype1 subtype2 subtype3 
  140.38   131.51   130.65 
subtype1 subtype2 subtype3 
   19.04    19.00    20.98 
[1] "0.0 - 140.4 (19.0)" "0.1 - 131.5 (19.0)" "0.0 - 130.7 (21.0)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1 209  43
  subtype2 130  71
  subtype3 103  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  209   43
  subtype2  130   71
  subtype3  103   48
        clus
vv       subtype1 subtype2 subtype3
  COLON       209      130      103
  RECTUM       43       71       48
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      53        1       18        82         6         0        11
  subtype2      33        0        5        54         3         1         9
  subtype3      18        0       13        35         1         2         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         26         19       15         7         1
  subtype2          7         34         14       26        13         1
  subtype3          7         19         21       20         7         0
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          53       33       18
  STAGE IA          1        0        0
  STAGE II         18        5       13
  STAGE IIA        82       54       35
  STAGE IIB         6        3        1
  STAGE IIC         0        1        2
  STAGE III        11        9        6
  STAGE IIIA        7        7        7
  STAGE IIIB       26       34       19
  STAGE IIIC       19       14       21
  STAGE IV         15       26       20
  STAGE IVA         7       13        7
  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  10  50 163  28
  subtype2   8  33 141  22
  subtype3   2  24 109  16
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       10        8        2
  T2       50       33       24
  T3      163      141      109
  T4       28       22       16
[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 166  48  38
  subtype2 103  66  34
  subtype3  73  35  42
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      166      103       73
  N1       48       66       35
  N2       38       34       42
[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"
D3V7, binary
          cls
clus         0   1
  subtype1 197  21
  subtype2 144  39
  subtype3 107  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  197   21
  subtype2  144   39
  subtype3  107   26
   clus
vv  subtype1 subtype2 subtype3
  0      197      144      107
  1       21       39       26
[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 127 125
  subtype2  88 117
  subtype3  71  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127  125
  subtype2   88  117
  subtype3   71   80
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      127       88       71
  MALE        125      117       80
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  161                            47
  subtype2                  125                             5
  subtype3                   95                             8
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    33                              9
  subtype2                    71                              0
  subtype3                    42                              4
D3V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                161      125       95
  COLON MUCINOUS ADENOCARCINOMA        47        5        8
  RECTAL ADENOCARCINOMA                33       71       42
  RECTAL MUCINOUS ADENOCARCINOMA        9        0        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus         0   1
  subtype1   3 249
  subtype2   3 202
  subtype3   3 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  249
  subtype2    3  202
  subtype3    3  148
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        3
  YES      249      202      148
[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 185   3   8  17
  subtype2 153   0  13   6
  subtype3 101   2  15   6
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      185      153      101
  R1        3        0        2
  R2        8       13       15
  RX       17        6        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                        25
  subtype2                                0     2                        23
  subtype3                                0     3                        12
          vv
clus       WHITE
  subtype1   127
  subtype2    93
  subtype3    72
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   7        2        3
  BLACK OR AFRICAN AMERICAN              25       23       12
  WHITE                                 127       93       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"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  78  15
  subtype2 126  35
  subtype3  99  24
subtype1 subtype2 subtype3 
      93      161      123 
subtype1 subtype2 subtype3 
      15       35       24 
$subtype1
TCGA-3L-AA1B TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5664 
       11.47        13.94        37.05        37.25        31.63        22.09 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 
        8.38        25.08        24.16        21.76        23.87        19.66 
TCGA-A6-A565 TCGA-AA-3489 TCGA-AA-3510 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6965 
       16.24         7.04        63.98        56.55        27.42         0.20 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       27.09         0.20        18.84        50.37        58.39         1.41 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 
       62.79        12.10       100.01         5.23         3.19         3.06 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5348 
        0.33         0.10       102.44        23.05        26.04        22.98 
TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6168 
       30.08        15.02        12.00        14.04        14.99        12.99 
TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       12.95        20.19        20.42        17.85        12.49         7.53 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A280 
       14.30         9.04        11.64         1.51        11.38         7.76 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.64        13.45        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6625 
       16.24        13.25        67.30        53.62        51.75        91.79 
TCGA-G4-6627 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6655 
       47.15        70.03        24.13        17.23        14.50        20.02 
TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-A01Y TCGA-AH-6544 TCGA-AH-6547 TCGA-BM-6198 
       10.39        32.98        64.01         0.49         1.45        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-6681 TCGA-DC-6682 TCGA-EI-6507 
        6.05         9.37         4.73        12.95        13.05        19.96 
TCGA-EI-6509 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 
       17.00        10.78        17.46         8.45         9.96        28.57 
TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6235 
        0.66         1.12        55.76 

$subtype2
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-3810 
        4.80        43.76        43.43        24.33        35.11        36.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 
       24.13        25.18        20.61        24.69        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3509 
       56.25         5.03         1.02        37.05         1.02        62.96 
TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3697 TCGA-AD-6888 TCGA-AD-6895 
        6.97        61.02        78.08        85.05         4.21         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        5.79        22.42        10.88        16.44         0.46        14.50 
TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6603 
       15.75        75.25        83.80        22.36        65.00        29.56 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5914 
        1.94         2.14         3.29         0.07        49.08        21.99 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        2.01         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        29.03        16.04        21.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       15.02        11.01        11.08        11.01        10.06        45.40 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       13.51        11.51        18.25         1.32        43.27         4.80 
TCGA-D5-6922 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB 
       10.13        38.20       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-F4-6856 TCGA-G4-6294 TCGA-G4-6295 
       33.67         0.53        35.41        19.43        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        65.85        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       39.42        35.93        36.72        36.00        46.75        18.18 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       12.79        13.05        42.77        32.98         8.42        30.28 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       19.10        37.74        15.39        86.63        65.98        11.84 
TCGA-AG-4022 TCGA-AG-A026 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
        0.99         1.94       117.11        17.49         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       26.43         1.81         6.97        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00        10.98        30.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24       129.27        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       20.55        15.85        16.34        16.31        16.41        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       13.64        11.97        37.51        31.30         0.39        32.19 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76         0.46        47.08        26.43 

$subtype3
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4105 
       11.47        44.91        45.60        37.02        32.75        14.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 
       32.45        30.44        33.53        22.06        22.52        24.39 
TCGA-A6-6780 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       20.12        24.92         9.63         3.02        35.01        58.03 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
        6.05         6.97        19.04         0.07        21.37         0.79 
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-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94         5.13        61.41        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       11.74         2.24         3.25         0.26         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        70.16        15.62        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5860 
      124.27        20.02        37.02        25.02        27.02        16.01 
TCGA-CM-5861 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 
       15.02        13.02        14.04        13.05        11.08        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 
       12.26        19.59        17.75        15.12        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       15.58        12.39        12.43         9.44        13.41        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 
       10.26       119.70        24.43        92.75        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28G 
        7.50       131.51       135.65         6.12        14.04        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6806 
      117.07        98.24        95.18        11.11         6.18        29.59 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
      107.67        74.56        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        52.80        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-QL-A97D 
        9.93        15.65        12.00        29.46        31.30         9.70 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A02N TCGA-CI-6620 
        1.02         0.99        70.03        10.98        61.97         6.05 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        5.29        24.13         0.49        20.91        18.28        17.69 
TCGA-EI-6882 TCGA-F5-6814 TCGA-G5-6233 
        8.61         0.53        18.28 

subtype1 subtype2 subtype3 
    0.10     0.07     0.07 
subtype1 subtype2 subtype3 
  102.44   139.17   140.38 
subtype1 subtype2 subtype3 
   15.02    20.61    17.82 
[1] "0.1 - 102.4 (15.0)" "0.1 - 139.2 (20.6)" "0.1 - 140.4 (17.8)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  68  25
  subtype2 110  53
  subtype3 110  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   25
  subtype2  110   53
  subtype3  110   18
        clus
vv       subtype1 subtype2 subtype3
  COLON        68      110      110
  RECTUM       25       53       18
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      11        0        5        28         1         0         1
  subtype2      19        0        9        44         2         2         4
  subtype3      24        1        6        40         4         1         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         13         11        6         7         0
  subtype2          9         29         13       12        13         1
  subtype3          2         15         11        9         6         1
D4V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          11       19       24
  STAGE IA          0        0        1
  STAGE II          5        9        6
  STAGE IIA        28       44       40
  STAGE IIB         1        2        4
  STAGE IIC         0        2        1
  STAGE III         1        4        6
  STAGE IIIA        7        9        2
  STAGE IIIB       13       29       15
  STAGE IIIC       11       13       11
  STAGE IV          6       12        9
  STAGE IVA         7       13        6
  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   3   9  67  15
  subtype2   4  24 116  19
  subtype3   4  24  84  15
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        4        4
  T2        9       24       24
  T3       67      116       84
  T4       15       19       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 49 27 18
  subtype2 82 50 28
  subtype3 79 25 24
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49       82       79
  N1       27       50       25
  N2       18       28       24
[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"
D4V7, binary
          cls
clus         0   1
  subtype1  67  11
  subtype2 106  26
  subtype3  89  14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   11
  subtype2  106   26
  subtype3   89   14
   clus
vv  subtype1 subtype2 subtype3
  0       67      106       89
  1       11       26       14
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus        0  1
  subtype1 36 58
  subtype2 71 93
  subtype3 70 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   58
  subtype2   71   93
  subtype3   70   58
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       36       71       70
  MALE         58       93       58
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   55                            13
  subtype2                  103                             7
  subtype3                   92                            18
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    24                              1
  subtype2                    51                              2
  subtype3                    15                              3
D4V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 55      103       92
  COLON MUCINOUS ADENOCARCINOMA        13        7       18
  RECTAL ADENOCARCINOMA                24       51       15
  RECTAL MUCINOUS ADENOCARCINOMA        1        2        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus         0   1
  subtype1   4  90
  subtype2   4 160
  subtype3   0 128
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   90
  subtype2    4  160
  subtype3    0  128
     clus
vv    subtype1 subtype2 subtype3
  NO         4        4        0
  YES       90      160      128
[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  64   1   0   5
  subtype2 108   1   2  10
  subtype3  81   2   4  14
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       64      108       81
  R1        1        1        2
  R2        0        2        4
  RX        5       10       14
[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"
D4V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        12
  subtype2                                0     3                        23
  subtype3                                0     5                        23
          vv
clus       WHITE
  subtype1    73
  subtype2   123
  subtype3    86
D4V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        3        5
  BLACK OR AFRICAN AMERICAN              12       23       23
  WHITE                                  73      123       86
[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"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  73  21
  subtype2 130  39
  subtype3  37   5
  subtype4 113  26
subtype1 subtype2 subtype3 subtype4 
      94      169       42      139 
subtype1 subtype2 subtype3 subtype4 
      21       39        5       26 
$subtype1
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 
       43.76        24.33        35.11        37.25        37.02        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6782 
       29.16         8.38        25.08        24.16        21.76        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3655 
        7.04        35.01         1.02        24.03         0.00        61.02 
TCGA-AA-3678 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3852 
       47.01        19.04        35.05         0.99        38.99         0.00 
TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3971 
        0.99        53.00        17.03        33.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00K TCGA-AY-6196 
       50.99        34.06        27.02        18.05        18.05         0.20 
TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       17.82        75.25        32.94         3.19         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5341 
        3.29         0.33         1.35         2.01        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5868 TCGA-CM-6167 TCGA-D5-5538 TCGA-D5-6922 
       22.03        22.98        17.03        14.99        12.26        10.13 
TCGA-D5-6926 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6809 
        9.04        26.47         8.61        13.64         6.18        13.25 
TCGA-F4-6854 TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 
        0.53        45.11        91.79        17.23        12.72        10.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3594 TCGA-AG-3599 
       20.02        36.03         7.07        36.03         2.01        12.03 
TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       19.99         1.02         0.99        36.03         1.02        17.03 
TCGA-AG-A036 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-F5-6464 
      117.11        15.02        12.95        10.06         5.29         9.96 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6572 
       28.57         0.66         0.76        47.08 

$subtype2
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-5662 TCGA-A6-5664 
       46.65        42.90        42.28        16.57        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6652 
       22.06        32.71        27.09        22.52        20.61        24.69 
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       23.87         3.02         1.02        58.03        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3548 TCGA-AA-3555 
       38.99         9.07        19.07        34.03        33.99        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3688 TCGA-AA-3696 
       20.98        19.99        13.94        54.02        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3844 
       85.05        19.04        10.06        25.02        17.98        14.93 
TCGA-AA-3848 TCGA-AA-3861 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3973 TCGA-AA-3989 
       10.06        30.05         2.01        20.98        13.05         7.96 
TCGA-AA-A00E TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C 
       30.02        42.02        17.03        14.99        34.98        15.02 
TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       31.00        35.01         1.02        35.01        26.01        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-6197 TCGA-AZ-4614 
       40.96        56.55         5.79         0.20        21.44         5.65 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6606 
       22.36        65.00        61.41         6.77        29.56        11.74 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 
        1.94         2.14         3.25         0.07         0.26        21.99 
TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6165 TCGA-CM-6166 
        2.93        37.02        15.02        15.02        16.04        21.99 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 
       11.01        13.05        11.08        10.06        12.03        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 TCGA-D5-6923 
       11.51        18.25         4.80        17.13        12.39        12.43 
TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       12.00       119.70        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6806 TCGA-G4-6294 TCGA-G4-6295 
       60.79        95.18        13.38        29.59        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       82.39        65.85        51.75        36.72        26.43        26.04 
TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 
       39.48        16.83        15.39        10.39         8.02        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 
       24.00         1.02        46.03        34.03        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3896 TCGA-AG-A008 
        0.99        19.99         0.99         0.99         1.02        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A026 
        6.02        23.01        36.03         9.07        51.98         1.94 
TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 
       38.96         0.49        26.43        10.98        12.99        13.97 
TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       36.00       126.44        57.24       129.27        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
        0.49         2.40        20.91        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 
        8.61        10.78        13.64         0.39        32.19         1.12 
TCGA-G5-6641 
       26.43 

$subtype3
TCGA-A6-2681 TCGA-A6-6140 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 
       45.60        24.13        37.05         8.05        29.00        29.00 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3854 TCGA-AA-A004 TCGA-AA-A00F 
       13.02        24.00        19.99        36.03        13.94        34.03 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01P 
       38.04        21.99        15.02        10.98        32.02        38.07 
TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-5900 TCGA-AY-5543 
       33.04        51.98        14.01        41.00         0.07        15.75 
TCGA-CM-5863 TCGA-CM-6164 TCGA-D5-6531 TCGA-D5-6898 TCGA-D5-6924 TCGA-DM-A280 
       15.02        29.03        17.75         7.53        14.30         7.76 
TCGA-F4-6855 TCGA-G4-6323 TCGA-AG-3578 TCGA-AG-3891 TCGA-AG-4022 TCGA-AG-A011 
       35.41        13.78        32.02        18.02         0.99        37.02 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6549 TCGA-EI-6509 
       15.95         1.02        61.97        41.00        17.49        17.00 

$subtype4
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-5661 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       37.05        34.65        33.53        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
       19.66        17.95         0.92         5.98        26.99        33.04 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3862 TCGA-AA-3869 
       15.95        36.95         0.00         0.00        30.05        27.02 
TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K 
       24.00        19.07        38.04         4.01         0.99        31.00 
TCGA-AA-A01Q TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6548 TCGA-AM-5820 TCGA-AM-5821 
        1.02        22.03        18.05        21.37         0.46         0.92 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 
       27.09        58.39         1.41         5.13        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
      100.01         5.23         0.10        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6169 
       15.02         5.03        12.00        14.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5539 
       15.02        14.04        12.95        11.08        11.01        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42         1.32        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.49        16.14        15.58         9.44        11.64         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1HB 
       11.38        38.20       130.65        92.75        12.59       135.65 
TCGA-DM-A288 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       14.04        11.11        13.45        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 
       16.24        33.67        19.43       107.67        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 
       67.30        53.62        44.68        55.04        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       36.00        22.09        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-AF-3914 TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3902 
       52.80        37.68        19.99        35.01        48.03        32.02 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       14.04        20.98        25.97        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 
       10.98         1.45         0.69         0.72        10.19         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DC 
       11.01        15.02        10.98        30.05        13.05        41.36 
TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       24.13        20.55        19.96        15.85        16.34        16.41 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 
       17.46        37.51        31.30         0.69         0.46        18.28 
TCGA-G5-6235 
       55.76 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.07     0.07     0.00 
subtype1 subtype2 subtype3 subtype4 
  117.11   140.38    61.97   135.65 
subtype1 subtype2 subtype3 subtype4 
  18.545   19.990   20.990   19.660 
[1] "0.0 - 117.1 (18.5)" "0.1 - 140.4 (20.0)" "0.1 - 62.0 (21.0)" 
[4] "0.0 - 135.7 (19.7)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1  70  30
  subtype2 126  53
  subtype3  32  10
  subtype4 103  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70   30
  subtype2  126   53
  subtype3   32   10
  subtype4  103   37
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        70      126       32      103
  RECTUM       30       53       10       37
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        0        8        26         3         0         3
  subtype2      27        0       11        44         4         1        11
  subtype3       8        1        3        17         0         0         2
  subtype4      25        0        5        52         2         1         8
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         18         10       10         7         0
  subtype2          7         27         10       26         7         1
  subtype3          0          3          5        1         1         0
  subtype4          5         14         14        7         4         0
D5V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          10       27        8       25
  STAGE IA          0        0        1        0
  STAGE II          8       11        3        5
  STAGE IIA        26       44       17       52
  STAGE IIB         3        4        0        2
  STAGE IIC         0        1        0        1
  STAGE III         3       11        2        8
  STAGE IIIA        4        7        0        5
  STAGE IIIB       18       27        3       14
  STAGE IIIC       10       10        5       14
  STAGE IV         10       26        1        7
  STAGE IVA         7        7        1        4
  STAGE IVB         0        1        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   0  13  72  14
  subtype2   6  31 123  19
  subtype3   0   8  32   1
  subtype4   5  24  97  14
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        6        0        5
  T2       13       31        8       24
  T3       72      123       32       97
  T4       14       19        1       14
[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 47 33 19
  subtype2 95 50 34
  subtype3 29  6  6
  subtype4 89 28 22
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       47       95       29       89
  N1       33       50        6       28
  N2       19       34        6       22
[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"
D5V7, binary
          cls
clus         0   1
  subtype1  78  17
  subtype2 130  33
  subtype3  37   2
  subtype4 112  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78   17
  subtype2  130   33
  subtype3   37    2
  subtype4  112   11
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       78      130       37      112
  1       17       33        2       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 42 58
  subtype2 88 91
  subtype3 19 23
  subtype4 66 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   58
  subtype2   88   91
  subtype3   19   23
  subtype4   66   74
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       88       19       66
  MALE         58       91       23       74
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   61                             9
  subtype2                  119                             7
  subtype3                   27                             5
  subtype4                   86                            17
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    24                              4
  subtype2                    48                              4
  subtype3                     9                              1
  subtype4                    36                              1
D5V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 61      119       27       86
  COLON MUCINOUS ADENOCARCINOMA         9        7        5       17
  RECTAL ADENOCARCINOMA                24       48        9       36
  RECTAL MUCINOUS ADENOCARCINOMA        4        4        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus         0   1
  subtype1   3  97
  subtype2   3 176
  subtype3   0  42
  subtype4   2 138
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   97
  subtype2    3  176
  subtype3    0   42
  subtype4    2  138
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        3        0        2
  YES       97      176       42      138
[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  74   0   7   7
  subtype2 114   1  18   6
  subtype3  38   0   1   1
  subtype4 112   1   2   5
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       74      114       38      112
  R1        0        1        0        1
  R2        7       18        1        2
  RX        7        6        1        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                         8
  subtype2                                0     5                         8
  subtype3                                0     0                         2
  subtype4                                1     1                         6
          vv
clus       WHITE
  subtype1    45
  subtype2    88
  subtype3    12
  subtype4   101
D5V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   6        5        0        1
  BLACK OR AFRICAN AMERICAN               8        8        2        6
  WHITE                                  45       88       12      101
[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"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  45   8
  subtype2 224  68
  subtype3  84  15
subtype1 subtype2 subtype3 
      53      292       99 
subtype1 subtype2 subtype3 
       8       68       15 
$subtype1
TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5660 TCGA-A6-6142 
       43.76        37.05        37.25        33.34        29.19        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3812 TCGA-AA-3866 TCGA-AA-3950 
       24.16        21.76        20.28        35.05        17.03        24.00 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A02W TCGA-AD-5900 TCGA-AM-5820 TCGA-AY-6196 
       18.05        18.05        41.00         0.07         0.46         0.20 
TCGA-AZ-4308 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CM-4747 TCGA-CM-5868 TCGA-CM-6167 
       75.25         3.19         3.29        25.02        17.03        14.99 
TCGA-D5-5538 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-DM-A1D0 TCGA-F4-6459 
       12.26        10.13        14.30         9.04       130.65         8.61 
TCGA-F4-6463 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6310 
       13.64        16.31        13.25         0.53        67.30        45.11 
TCGA-G4-6314 TCGA-G4-6625 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3581 
       35.93        91.79        17.23        12.72        20.02         7.07 
TCGA-AG-A014 TCGA-AG-A036 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.95       117.11        15.02        12.95        10.06         5.29 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6863 TCGA-G5-6235 
        9.96        31.30        28.57         0.76        55.76 

$subtype2
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
       46.65        42.90        24.33        42.28        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
       16.57        37.02        32.75        36.53        32.91        30.44 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       22.52        24.13         8.38        20.61        24.69        23.87 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        7.04         3.02         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        38.99         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       33.99        13.02        24.00        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       13.94        19.99        61.02        54.02         0.92        47.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        10.06        33.04         0.99        25.02        17.98 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3854 
       38.99        14.93         0.00        10.06         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3947 
        0.99        30.05        53.00        27.02         2.01        33.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L 
       27.02         7.96        13.94        30.02        34.03        38.04 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        10.98        32.02        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
        2.96        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 
       22.03        39.98        40.96        56.55         5.79         0.20 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       15.75        21.44        17.82        58.39         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56        11.74         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-5914 
        3.25         0.07         0.26         0.33         1.35        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5344 
        2.93         2.01        37.02        26.04        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6172 
       15.02        12.00        29.03        16.04        21.99        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 
       13.05        11.08        11.08        10.06        12.03        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6931 
        4.80        17.13         7.53        12.39        12.43        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.38       119.70        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50        44.32       131.51         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 
       95.18        13.38        11.11         6.18         1.55        29.59 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       35.41       107.67        28.21         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       65.85        53.62        51.75        36.72        26.43        26.04 
TCGA-G4-6323 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       13.78        39.48        10.39        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        32.02         8.02        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 
        6.05         0.99        19.99        19.99         0.99         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         0.99         1.02        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       36.03         9.07         1.02        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-4745 
       38.96        61.97         0.49        17.49        26.43        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        12.99        13.97        36.00       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       20.91        17.00        18.28        17.69        16.31         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        13.64        17.46         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.46        47.08        26.43 

$subtype3
TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       34.65        31.63        33.53        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3862 
       19.66        17.95        15.95        36.95         0.00        30.05 
TCGA-AA-3986 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q 
       19.07        38.04         4.01         0.99        31.00         1.02 
TCGA-AA-A03F TCGA-AD-6548 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4323 TCGA-AZ-4616 
       18.05        21.37         0.92        27.09         1.41         5.13 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
      100.01         5.23         0.10        21.14       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6168 
       20.02         8.02        13.02         5.03        14.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5539 
       13.02        15.02        14.04        12.95        11.01        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       20.19        20.42         1.32        12.49        16.14        15.58 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6569 
        9.44        11.64         1.51        38.20       135.65        13.45 
TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6298 TCGA-G4-6306 
       35.87        16.24        33.67        19.43        23.51        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       55.04        39.42        36.00        22.09        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-AF-3914 TCGA-AG-3882 TCGA-AG-3891 
       46.75        47.15        52.80        37.68        19.99        18.02 
TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A01N 
       35.01        48.03        32.02        14.04        25.97        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       70.03        64.01        41.00         1.45         0.69         0.72 
TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       10.19         7.17        11.01        10.98        30.05        13.05 
TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       41.36        20.55        19.96        15.85        16.34        16.41 
TCGA-F5-6465 TCGA-F5-6861 TCGA-G5-6233 
       37.51         1.12        18.28 

subtype1 subtype2 subtype3 
    0.07     0.00     0.00 
subtype1 subtype2 subtype3 
  130.65   140.38   135.65 
subtype1 subtype2 subtype3 
   17.23    19.99    19.66 
[1] "0.1 - 130.7 (17.2)" "0.0 - 140.4 (20.0)" "0.0 - 135.7 (19.7)"
D6V2, continuous
D6V3, binary
          cls
clus         0   1
  subtype1  39  15
  subtype2 223  84
  subtype3  69  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   15
  subtype2  223   84
  subtype3   69   31
        clus
vv       subtype1 subtype2 subtype3
  COLON        39      223       69
  RECTUM       15       84       31
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       6        0        1        15         1         0         1
  subtype2      40        1       22        90         7         1        19
  subtype3      24        0        4        34         1         1         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         10          5        4         8         0
  subtype2          8         41         27       36         8         1
  subtype3          5         11          7        4         3         0
D6V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           6       40       24
  STAGE IA          0        1        0
  STAGE II          1       22        4
  STAGE IIA        15       90       34
  STAGE IIB         1        7        1
  STAGE IIC         0        1        1
  STAGE III         1       19        4
  STAGE IIIA        3        8        5
  STAGE IIIB       10       41       11
  STAGE IIIC        5       27        7
  STAGE IV          4       36        4
  STAGE IVA         8        8        3
  STAGE IVB         0        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   7  36  11
  subtype2   7  45 223  30
  subtype3   4  24  65   7
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        7        4
  T2        7       45       24
  T3       36      223       65
  T4       11       30        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  23  17  14
  subtype2 168  82  55
  subtype3  69  18  12
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       23      168       69
  N1       17       82       18
  N2       14       55       12
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  37  12
  subtype2 239  44
  subtype3  81   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   12
  subtype2  239   44
  subtype3   81    7
   clus
vv  subtype1 subtype2 subtype3
  0       37      239       81
  1       12       44        7
[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"
D6V8, binary
          cls
clus         0   1
  subtype1  26  28
  subtype2 149 158
  subtype3  40  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   28
  subtype2  149  158
  subtype3   40   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26      149       40
  MALE         28      158       60
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   33                             6
  subtype2                  202                            21
  subtype3                   58                            11
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    13                              2
  subtype2                    73                              8
  subtype3                    31                              0
D6V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 33      202       58
  COLON MUCINOUS ADENOCARCINOMA         6       21       11
  RECTAL ADENOCARCINOMA                13       73       31
  RECTAL MUCINOUS ADENOCARCINOMA        2        8        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
          cls
clus         0   1
  subtype1   3  51
  subtype2   3 304
  subtype3   2  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    3  304
  subtype3    2   98
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        2
  YES       51      304       98
[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  44   1   1   1
  subtype2 212   1  26  14
  subtype3  82   0   1   4
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       44      212       82
  R1        1        1        0
  R2        1       26        1
  RX        1       14        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"
D6V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         3
  subtype2                                1     9                        15
  subtype3                                0     1                         6
          vv
clus       WHITE
  subtype1    39
  subtype2   137
  subtype3    70
D6V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   2        9        1
  BLACK OR AFRICAN AMERICAN               3       15        6
  WHITE                                  39      137       70
[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"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 106  34
  subtype2 115  23
  subtype3  97  29
  subtype4 159  29
subtype1 subtype2 subtype3 subtype4 
     140      138      126      188 
subtype1 subtype2 subtype3 subtype4 
      34       23       29       29 
$subtype1
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2677 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       11.47         4.80        24.33        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       23.61        32.71        29.16        24.13        25.18        20.61 
TCGA-A6-6652 TCGA-A6-A567 TCGA-AA-3494 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3517 
       24.69        61.84         1.02        62.96         6.97        38.99 
TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3955 
       19.07        29.00        26.01        78.08        85.05        20.98 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       38.04        27.02        26.01        39.98         5.03        14.01 
TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00         4.21         0.79        27.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 
       14.50        18.84        22.36        62.79        29.56         1.94 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 
        2.14         3.29         0.07         0.26        49.08        21.99 
TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       25.02        22.03         5.03        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 
       14.04        29.03        21.99        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       45.40        13.51        18.25         1.32         4.80        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
       14.30        13.41        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C 
      140.38        44.32       139.17         6.12        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6808 
      119.93        35.97        60.79       117.07        13.38        33.67 
TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
        0.53        28.21        55.04        45.11        36.72        36.00 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z1 
       46.75        18.18        10.98        13.05        42.77         8.42 
TCGA-RU-A8FL TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       30.28        37.74        16.83        86.63        11.84        36.03 
TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6549 
        0.99         0.99        31.00         1.94        38.96        17.49 
TCGA-AH-6897 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       26.43         6.97         9.37        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       10.98        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
       51.48        32.61         0.49        20.91        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6810 TCGA-F5-6861 
       16.34        16.31        11.51        11.97         0.39         1.12 
TCGA-F5-6863 TCGA-G5-6572 
        0.76        47.08 

$subtype2
TCGA-4T-AA8H TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 
       11.47        14.53        33.53        22.06        27.09         8.38 
TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-A565 TCGA-AA-3492 TCGA-AA-3495 
       24.16        24.39        20.12        16.24         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 
       35.01        58.03        13.02        37.05         8.05        23.01 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 
       61.02         6.05         6.97        54.02        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3851 
        5.98        37.05        19.04        15.95         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A01Z 
        0.00        36.03        30.05        53.00         4.01        37.02 
TCGA-AA-A024 TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 TCGA-AY-5543 TCGA-AY-6197 
       39.06        39.98        18.05        56.55        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.26        17.85        19.33        50.37        58.39 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.65        65.00        61.41        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         2.24         3.06         3.25        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       15.62        51.32         2.93       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-A1D4 
       16.14        12.39        12.00       119.70        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K 
       49.91         7.50       135.65         7.76        14.04        98.24 
TCGA-DM-A28M TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 
       95.18        29.59        19.43       107.67        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       51.75        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.17        15.65        12.79        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3594 
        9.70        19.10        14.50        15.39        10.39         2.01 
TCGA-AG-3599 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A008 TCGA-AG-A02N 
       12.03        32.98        13.02        32.02        13.94        61.97 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.49         1.45         1.81        10.19         6.05         6.05 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6512 
        4.73        13.97        30.05        20.55        18.28        17.69 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       16.41         8.61        10.78        18.28        55.76        26.43 

$subtype3
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       43.76        43.43        13.94        37.05        37.25        37.02 
TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       33.34        31.63        22.09        22.52        25.08        21.76 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       23.87        19.66        20.28        24.92        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3870 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6548 
        7.04         1.02        29.98        38.07         0.07        21.37 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         5.79        22.42        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6601 
       27.09         0.20         1.41        32.94         5.13       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        5.23         3.19         0.33         0.10         1.35       102.44 
TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       70.16        21.14         2.01        22.98        30.08        16.01 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6674 
       12.00        16.04        14.99        12.99        13.02        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       11.08        10.06        12.26        11.51        20.19        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       43.27        17.85        15.58         7.53        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        11.38        10.26 
TCGA-DM-A1HA TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
      131.51         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6855 
       35.87         1.55        16.31        16.24        13.25        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       39.42        35.93        91.79        47.15        52.80        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       19.33         9.93        12.00        70.03        24.13        17.23 
TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3731 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6156 
       20.02        65.98         1.02         0.69         0.72        15.02 
TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6507 
       10.98         5.29       129.27        24.13         2.40        19.96 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6864 
       28.57        32.19         0.66         0.69         0.53         0.46 

$subtype4
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        46.65        42.90        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       45.60        16.57        34.65        32.75        36.53        32.45 
TCGA-AA-3488 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        5.03        63.98         1.02         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 
       36.03         0.00        19.07        34.03        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       17.95        29.95        19.99        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 
       14.01         0.92        50.04        47.01        15.02        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        21.99        36.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        18.05        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E 
       35.01         1.02        33.04        35.01        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
        2.01         0.92        22.03        40.96        16.31         0.95 
TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       75.25        83.80        26.04         8.02        13.02        29.06 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3578 
       43.04        13.55        12.72        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       46.03        34.03        50.04         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
       19.99        19.99         7.99         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02X 
       70.03        64.01        10.98        51.98        49.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.00     0.07     0.00 
subtype1 subtype2 subtype3 subtype4 
  140.38   135.65   131.51   117.11 
subtype1 subtype2 subtype3 subtype4 
  19.840   18.660   16.025   21.500 
[1] "0.1 - 140.4 (19.8)" "0.0 - 135.7 (18.7)" "0.1 - 131.5 (16.0)"
[4] "0.0 - 117.1 (21.5)"
D7V2, continuous
D7V3, binary
          cls
clus         0   1
  subtype1 100  45
  subtype2 110  30
  subtype3 102  28
  subtype4 137  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  100   45
  subtype2  110   30
  subtype3  102   28
  subtype4  137   60
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       100      110      102      137
  RECTUM       45       30       28       60
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      23        0        7        35         2         2         4
  subtype2      29        1       11        42         2         1         8
  subtype3      12        0        5        44         2         0         2
  subtype4      40        0       14        55         5         0        13
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         24         11       13        13         0
  subtype2          7         17          6        7         7         2
  subtype3          5         16         19       15         6         0
  subtype4          5         22         18       25         1         0
D7V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          23       29       12       40
  STAGE IA          0        1        0        0
  STAGE II          7       11        5       14
  STAGE IIA        35       42       44       55
  STAGE IIB         2        2        2        5
  STAGE IIC         2        1        0        0
  STAGE III         4        8        2       13
  STAGE IIIA        4        7        5        5
  STAGE IIIB       24       17       16       22
  STAGE IIIC       11        6       19       18
  STAGE IV         13        7       15       25
  STAGE IVA        13        7        6        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   6  26  95  17
  subtype2   4  30  94  13
  subtype3   1  13  94  22
  subtype4   9  38 136  16
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        6        4        1        9
  T2       26       30       13       38
  T3       95       94       94      136
  T4       17       13       22       16
[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  80  39  23
  subtype2  89  34  19
  subtype3  64  31  34
  subtype4 116  45  38
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       80       89       64      116
  N1       39       34       31       45
  N2       23       19       34       38
[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"
D7V7, binary
          cls
clus         0   1
  subtype1  94  26
  subtype2 101  13
  subtype3  91  20
  subtype4 170  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94   26
  subtype2  101   13
  subtype3   91   20
  subtype4  170   26
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       94      101       91      170
  1       26       13       20       26
[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  64  81
  subtype2  68  74
  subtype3  57  73
  subtype4  99 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64   81
  subtype2   68   74
  subtype3   57   73
  subtype4   99  100
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       64       68       57       99
  MALE         81       74       73      100
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   97                             3
  subtype2                   86                            23
  subtype3                   84                            18
  subtype4                  120                            17
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    45                              0
  subtype2                    24                              5
  subtype3                    25                              3
  subtype4                    53                              5
D7V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 97       86       84      120
  COLON MUCINOUS ADENOCARCINOMA         3       23       18       17
  RECTAL ADENOCARCINOMA                45       24       25       53
  RECTAL MUCINOUS ADENOCARCINOMA        0        5        3        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
          cls
clus         0   1
  subtype1   2 143
  subtype2   4 138
  subtype3   2 128
  subtype4   1 198
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  143
  subtype2    4  138
  subtype3    2  128
  subtype4    1  198
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        4        2        1
  YES      143      138      128      198
[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  87   1   7  10
  subtype2  94   2   3   9
  subtype3  94   1   3  11
  subtype4 171   1  22   0
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       87       94       94      171
  R1        1        2        1        1
  R2        7        3        3       22
  RX       10        9       11        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"
D7V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        18
  subtype2                                0     4                        22
  subtype3                                1     4                        16
  subtype4                                0     0                         4
          vv
clus       WHITE
  subtype1    96
  subtype2    77
  subtype3   101
  subtype4    20
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   4        4        4        0
  BLACK OR AFRICAN AMERICAN              18       22       16        4
  WHITE                                  96       77      101       20
[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"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  58  19
  subtype2  67  14
  subtype3  47  14
  subtype4  48   7
  subtype5  71  19
  subtype6 110  20
  subtype7  76  22
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      77       81       61       55       90      130       98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      19       14       14        7       19       20       22 
$subtype1
TCGA-3L-AA1B TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6652 
       11.47        32.91        29.19        22.09        32.71        24.69 
TCGA-A6-A5ZU TCGA-AA-3675 TCGA-AA-A02K TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        9.63        47.05        14.01         0.20        16.44        14.50 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 
        1.94         2.14         0.07         0.26       102.44        49.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6677 TCGA-CM-6678 
        5.03        15.02        15.02        21.99        11.08        11.01 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       45.40        12.26        13.51        18.25         1.32        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
        4.80        17.13        13.41        11.38        38.20       130.65 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38        44.32       131.51       139.17         6.12 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 
       26.47        81.37       119.93        60.79       117.07        13.64 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6317 
       33.67        35.41        28.21        23.51        55.04        36.00 
TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-5654 TCGA-AF-A56N TCGA-AG-3742 TCGA-AG-A002 
       13.05        30.28        16.83        11.84         0.99        20.98 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6897 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 
       17.49         0.69        26.43         7.17        12.99        12.00 
TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       36.00       126.44        41.36        51.48        32.61         0.49 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-F5-6811 TCGA-F5-6861 
       17.00        15.85        16.34        32.19         1.12 

$subtype2
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6650 
        4.80        11.47        13.94        14.53         8.38        20.61 
TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 
       20.12        24.92         1.02        35.01        58.03        62.96 
TCGA-AA-3526 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-A01Z TCGA-AA-A02Y 
       19.07        61.02        78.08         6.05        37.02        39.98 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L 
        4.21         0.79        27.42        15.75        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 
       17.85        19.33        58.39        61.41         6.77        11.74 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6162 
       21.99         2.93       124.27        16.01        15.02        12.00 
TCGA-CM-6172 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6541 
       11.01        12.03        19.59        20.19        15.12        15.58 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A280 TCGA-DM-A288 
      119.70        92.75        49.91        13.32         7.76        14.04 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6295 
       35.97        95.18        11.11        29.59       107.67         8.35 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       53.62        44.68        26.43        26.04        13.78        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
       18.18        10.98        19.33        15.65        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-6672 TCGA-CI-6620 
       29.46        32.98        31.30         9.70        10.39         6.05 
TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-EI-6510 
        9.37        13.97        11.01        15.02        13.97        18.28 
TCGA-EI-6512 TCGA-EI-7004 TCGA-G5-6641 
       17.69         8.45        26.43 

$subtype3
TCGA-A6-2686 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 
       37.02        33.53        22.06        24.39        19.66         3.02 
TCGA-AA-3663 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
        6.97        38.07         0.07        56.55         0.72        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4313 TCGA-AZ-4614 
        0.92        27.09         0.20        21.44        50.37         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 
       32.94         5.13        49.41       100.01         2.24         3.06 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
        0.10        70.16        15.62        51.32        21.14        23.05 
TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 
       20.02        15.02        14.04        12.95        13.05        20.42 
TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD 
       16.14         9.44        11.64         1.51        10.26        24.43 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        7.50       135.65        98.24        13.45         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       19.43        74.56        51.75        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-WS-AB45 TCGA-BM-6198 TCGA-EI-6507 TCGA-EI-6882 
       19.33         9.93        70.03        10.19        19.96         8.61 
TCGA-EI-6917 
       17.46 

$subtype4
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-A565 
       43.43        27.09        24.13        25.18        24.16        16.24 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6548 
       37.05         6.97        37.05        85.05        19.04        21.37 
TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6605 
       18.84        22.36        65.00        62.79        12.10         5.23 
TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CM-4751 TCGA-CM-6163 TCGA-D5-6539 
        3.25        17.56        40.34        27.02        14.04        12.49 
TCGA-D5-6920 TCGA-D5-6931 TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6321 
       12.39        12.00        82.39        39.42        36.72        22.09 
TCGA-G4-6625 TCGA-G4-6627 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       91.79        47.15        19.10        37.74        14.50        15.39 
TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3902 TCGA-AH-6544 TCGA-AH-6547 
       20.02         1.02        32.98        32.02         0.49         1.45 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6158 
        1.81         6.05         6.97         4.73        10.98        10.98 
TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6881 TCGA-EI-6884 TCGA-G5-6233 
       30.05        20.55        20.91        16.41        10.78        18.28 
TCGA-G5-6235 
       55.76 

$subtype5
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5667 
       37.05        37.25        31.63        30.44        23.61        29.16 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       22.52        25.08        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-A01X TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 
       56.25         7.04        26.01         5.79        22.42         0.46 
TCGA-AZ-4323 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 
        1.41        29.56         3.19         3.29         0.33         1.35 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5868 
        2.01        25.02        22.03        22.98        30.08        17.03 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6898 
       11.08        10.06        11.51        17.75        43.27         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-F4-6459 TCGA-F4-6460 
       10.13        12.43        14.30         9.04         8.61        13.38 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 
        1.55        16.31        16.24        13.25         0.53        67.30 
TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6314 TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-AF-2687 
       65.85        45.11        35.93        12.00         8.42        24.13 
TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-4022 TCGA-AH-6644 TCGA-CL-5917 
       17.23        86.63        65.98         0.99         0.72        78.12 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD 
       15.02        12.95        13.05        10.06         5.29        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 
      129.27        24.13         2.40        16.31        11.51        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.66         0.69         0.53         0.76         0.46        47.08 

$subtype6
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       43.76        24.33        44.91        35.11        45.60        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3514 TCGA-AA-3517 
       34.65        36.53         5.03         1.02         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        9.07        36.03         0.00        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3562 
       26.01        12.99        21.01        24.00        13.94        19.99 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3819 
       14.01        47.01        15.02        19.00        35.05        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        38.99        36.95        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.03        18.05         2.01        20.98        34.03        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       36.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00K 
       27.02        19.07         7.96        13.94        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       38.04        27.02        42.02        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02F TCGA-AA-A02H 
       15.02        32.02         1.02        33.04        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 
        5.03        41.00        40.96        16.31         0.95        75.25 
TCGA-AZ-4681 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AF-3913 
       83.80        26.04         8.02        13.02        29.06        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       36.03         8.02         7.07        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       46.03        34.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        7.99         0.99        29.98         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        38.04       117.11 

$subtype7
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3808 TCGA-A6-3809 
       46.65        43.76        42.90        42.28        33.34        32.75 
TCGA-A6-4107 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       32.45        63.98        13.02         1.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
        8.05        19.07         0.99        14.01        33.99        13.02 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 
       17.95        29.95        23.01        19.99        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
        0.92        50.04        11.01         5.98        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        19.04        10.06        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       15.95        37.02         0.00        33.07         0.00        36.03 
TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       30.05        30.05        53.00        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3994 TCGA-AA-A00A 
        2.01        25.02        24.00        27.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       19.00        30.02        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       34.98        10.98        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02O 
       35.01        35.01        39.06        51.98         2.96         0.92 
TCGA-AA-A02R TCGA-AA-A03F TCGA-CM-4746 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       22.03        18.05        37.02        43.04        13.55        12.72 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       12.00        32.02        20.05         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-A008 TCGA-AG-A015 TCGA-AG-A020 
        6.05        36.95        13.02        13.94        36.03        10.98 
TCGA-AG-A02N TCGA-AG-A02X 
       61.97        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.79     0.07     0.49     0.33     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  140.38   124.27   135.65    91.79   129.27   117.11    63.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   17.49    17.82    19.43    20.02    15.02    21.50    24.00 
[1] "0.1 - 140.4 (17.5)" "0.8 - 124.3 (17.8)" "0.1 - 135.7 (19.4)"
[4] "0.5 - 91.8 (20.0)"  "0.3 - 129.3 (15.0)" "0.0 - 117.1 (21.5)"
[7] "0.0 - 64.0 (24.0)" 
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 57 22
  subtype2 71 13
  subtype3 59  4
  subtype4 32 23
  subtype5 59 31
  subtype6 88 51
  subtype7 83 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   22
  subtype2   71   13
  subtype3   59    4
  subtype4   32   23
  subtype5   59   31
  subtype6   88   51
  subtype7   83   19
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COLON        57       71       59       32       59       88       83
  RECTUM       22       13        4       23       31       51       19
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      14        0        1        24         1         1         0
  subtype2      15        1        6        23         1         0         3
  subtype3      13        0        4        28         1         0         2
  subtype4       8        0        3         8         1         1         5
  subtype5       7        0        3        26         1         1         1
  subtype6      28        0        7        37         1         0         8
  subtype7      19        0       13        30         5         0         8
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         12          9        5         5         0
  subtype2          4         14          5        4         5         1
  subtype3          1          4          5        1         1         1
  subtype4          5          9          3        6         6         0
  subtype5          2         15         12        9         9         0
  subtype6          4         16         14       25         0         0
  subtype7          1          9          6       10         1         0
D8V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          14       15       13        8        7       28       19
  STAGE IA          0        1        0        0        0        0        0
  STAGE II          1        6        4        3        3        7       13
  STAGE IIA        24       23       28        8       26       37       30
  STAGE IIB         1        1        1        1        1        1        5
  STAGE IIC         1        0        0        1        1        0        0
  STAGE III         0        3        2        5        1        8        8
  STAGE IIIA        4        4        1        5        2        4        1
  STAGE IIIB       12       14        4        9       15       16        9
  STAGE IIIC        9        5        5        3       12       14        6
  STAGE IV          5        4        1        6        9       25       10
  STAGE IVA         5        5        1        6        9        0        1
  STAGE IVB         0        1        1        0        0        0        0
[1] 13  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 14 54  9
  subtype2  5 16 50 12
  subtype3  2 11 44  6
  subtype4  1  9 40  7
  subtype5  0 10 66 13
  subtype6  6 30 94 10
  subtype7  4 17 71 11
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        2        5        2        1        0        6        4
  T2       14       16       11        9       10       30       17
  T3       54       50       44       40       66       94       71
  T4        9       12        6        7       13       10       11
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 43 18 17
  subtype2 50 22 11
  subtype3 46  9  8
  subtype4 26 22  9
  subtype5 39 27 22
  subtype6 77 34 29
  subtype7 68 17 18
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       43       50       46       26       39       77       68
  N1       18       22        9       22       27       34       17
  N2       17       11        8        9       22       29       18
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  55  10
  subtype2  56   7
  subtype3  46   3
  subtype4  34  11
  subtype5  61  18
  subtype6 113  25
  subtype7  91  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55   10
  subtype2   56    7
  subtype3   46    3
  subtype4   34   11
  subtype5   61   18
  subtype6  113   25
  subtype7   91   11
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       55       56       46       34       61      113       91
  1       10        7        3       11       18       25       11
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 37 42
  subtype2 41 43
  subtype3 28 35
  subtype4 18 39
  subtype5 43 47
  subtype6 68 72
  subtype7 53 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   42
  subtype2   41   43
  subtype3   28   35
  subtype4   18   39
  subtype5   43   47
  subtype6   68   72
  subtype7   53   50
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       37       41       28       18       43       68       53
  MALE         42       43       35       39       47       72       50
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   54                             3
  subtype2                   57                            14
  subtype3                   47                            12
  subtype4                   30                             2
  subtype5                   53                             6
  subtype6                   86                             2
  subtype7                   60                            22
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    22                              0
  subtype2                    11                              2
  subtype3                     3                              1
  subtype4                    22                              1
  subtype5                    30                              1
  subtype6                    50                              0
  subtype7                     9                              8
D8V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 54       57       47       30       53
  COLON MUCINOUS ADENOCARCINOMA         3       14       12        2        6
  RECTAL ADENOCARCINOMA                22       11        3       22       30
  RECTAL MUCINOUS ADENOCARCINOMA        0        2        1        1        1
                                clus
vv                               subtype6 subtype7
  COLON ADENOCARCINOMA                 86       60
  COLON MUCINOUS ADENOCARCINOMA         2       22
  RECTAL ADENOCARCINOMA                50        9
  RECTAL MUCINOUS ADENOCARCINOMA        0        8
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus         0   1
  subtype1   0  79
  subtype2   1  83
  subtype3   1  62
  subtype4   3  54
  subtype5   3  87
  subtype6   0 140
  subtype7   1 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   79
  subtype2    1   83
  subtype3    1   62
  subtype4    3   54
  subtype5    3   87
  subtype6    0  140
  subtype7    1  102
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        1        1        3        3        0        1
  YES       79       83       62       54       87      140      102
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  44   0   2   8
  subtype2  56   0   1   4
  subtype3  41   1   0   9
  subtype4  34   2   2   2
  subtype5  66   0   0   7
  subtype6 115   2  22   0
  subtype7  90   0   8   0
D8V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       44       56       41       34       66      115       90
  R1        0        0        1        2        0        2        0
  R2        2        1        0        2        0       22        8
  RX        8        4        9        2        7        0        0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        12
  subtype2                                0     0                        21
  subtype3                                0     4                         7
  subtype4                                0     1                         4
  subtype5                                1     4                        11
  subtype6                                0     0                         4
  subtype7                                0     0                         1
          vv
clus       WHITE
  subtype1    59
  subtype2    49
  subtype3    49
  subtype4    43
  subtype5    71
  subtype6    13
  subtype7    10
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   3        0        4        1        4
  BLACK OR AFRICAN AMERICAN              12       21        7        4       11
  WHITE                                  59       49       49       43       71
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        0
  BLACK OR AFRICAN AMERICAN               4        1
  WHITE                                  13       10
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 165  40
  subtype2  72  23
  subtype3 181  44
subtype1 subtype2 subtype3 
     205       95      225 
subtype1 subtype2 subtype3 
      40       23       44 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       43.43        14.53        32.91        30.44        29.19        33.53 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3511 
       25.08        25.18        20.61        20.28         1.02         6.97 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 
       61.02        78.08         6.05         6.97        85.05        19.04 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       39.98         2.01        21.37         4.21        56.55         0.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6197 
       27.42         0.20         0.92        14.50        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       17.82         5.13        61.41        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         1.94         2.24         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.99         2.93       124.27        23.05 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       27.02        22.03        30.08        16.01         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 
       17.03        15.02        14.04        29.03        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        45.40        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       20.19        17.75        18.25         1.32        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14        15.58        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30        13.41        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6808 
      117.07        98.24        95.18         6.18        29.59        33.67 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        36.72        36.00        26.43        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-5654 
       35.80        91.79        46.75        52.80        19.10        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-4001 
       15.39        20.02        10.39        32.98         0.99        36.03 
TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
        0.99         0.49        17.49         0.69        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        10.98        30.05        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-F5-6465 
       18.28        15.85        17.69        16.34        16.31        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       31.30         0.39        32.19        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$subtype2
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 
       43.76        45.60        37.05        37.25        33.34        31.63 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       23.61        22.09         8.38        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3818 TCGA-AA-3994 TCGA-AA-A00O 
       23.87        19.66         7.04         0.99        27.02        27.02 
TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6899 
       38.07        26.01         2.96         0.07         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4308 
       22.42        10.88         0.46        27.09         0.20        75.25 
TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        1.41        62.79       100.01        29.56         5.23         3.19 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4747 
        3.06         0.33         0.10        21.14         2.01        25.02 
TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6165 
       26.04        22.98        15.02        15.02        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 
       14.99        12.99        12.95        10.06        19.59        43.27 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       17.85         7.53        10.13         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A1D6 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
        1.51        10.26        49.91         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.64        13.45        35.87         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6310 TCGA-G4-6314 
       13.25         0.53        19.43        67.30        45.11        35.93 
TCGA-G4-6321 TCGA-G4-6627 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 
       22.09        47.15        24.13        17.23        37.74        14.50 
TCGA-AG-3575 TCGA-AG-3731 TCGA-AG-A015 TCGA-AH-6547 TCGA-AH-6644 TCGA-DC-6681 
       12.00         1.02        36.03         1.45         0.72        12.95 
TCGA-DT-5265 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        5.29         9.96        28.57         0.66         0.69 

$subtype3
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       35.11        13.94        16.57        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3488 TCGA-AA-3492 
       36.53        32.45        24.39        20.12         5.03         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 
        1.02        37.05        35.01        58.03        62.96        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        30.05        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 
       34.03         2.01        21.99        36.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A00L 
       27.02        19.07         7.96        19.00        18.05        38.04 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
       42.02        17.03        14.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       12.00        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         5.03        14.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4313 
       39.98        18.05        40.96        16.31         0.95        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         5.65        32.94        83.80        22.36        65.00 
TCGA-CA-5256 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4750 TCGA-CM-4752 
        2.14        70.16        20.02        37.02         8.02        13.02 
TCGA-CM-5341 TCGA-D5-6530 TCGA-D5-6931 TCGA-G4-6588 TCGA-AF-2689 TCGA-AF-2691 
       29.06        20.42        12.00        26.17        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       13.55        12.72        10.39        36.03        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
        6.02        37.02         9.07        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-EI-6507 
       41.00       117.11        19.96 

subtype1 subtype2 subtype3 
    0.07     0.07     0.00 
subtype1 subtype2 subtype3 
  140.38   100.01   117.11 
subtype1 subtype2 subtype3 
   18.28    15.02    22.36 
[1] "0.1 - 140.4 (18.3)" "0.1 - 100.0 (15.0)" "0.0 - 117.1 (22.4)"
D9V2, continuous
D9V3, binary
          cls
clus         0   1
  subtype1 150  61
  subtype2  80  15
  subtype3 175  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  150   61
  subtype2   80   15
  subtype3  175   64
        clus
vv       subtype1 subtype2 subtype3
  COLON       150       80      175
  RECTUM       61       15       64
[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       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      32        1        8        67         4         2         8
  subtype2       9        0        5        26         0         0         3
  subtype3      53        0       23        61         6         0        16
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          9         33         13       16        11         1
  subtype2          3         15         14        7         8         0
  subtype3          4         21         18       34         4         0
D9V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          32        9       53
  STAGE IA          1        0        0
  STAGE II          8        5       23
  STAGE IIA        67       26       61
  STAGE IIB         4        0        6
  STAGE IIC         2        0        0
  STAGE III         8        3       16
  STAGE IIIA        9        3        4
  STAGE IIIB       33       15       21
  STAGE IIIC       13       14       18
  STAGE IV         16        7       34
  STAGE IVA        11        8        4
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   8  33 151  18
  subtype2   2  10  69  15
  subtype3  10  52 156  23
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        2       10
  T2       33       10       52
  T3      151       69      156
  T4       18       15       23
[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 120  58  31
  subtype2  43  29  23
  subtype3 149  46  46
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      120       43      149
  N1       58       29       46
  N2       31       23       46
[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"
D9V7, binary
          cls
clus         0   1
  subtype1 149  26
  subtype2  65  14
  subtype3 198  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  149   26
  subtype2   65   14
  subtype3  198   38
   clus
vv  subtype1 subtype2 subtype3
  0      149       65      198
  1       26       14       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1 102 110
  subtype2  40  56
  subtype3 115 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102  110
  subtype2   40   56
  subtype3  115  126
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      102       40      115
  MALE        110       56      126
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  140                            10
  subtype2                   61                            19
  subtype3                  150                            24
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    60                              1
  subtype2                    13                              2
  subtype3                    54                              7
D9V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                140       61      150
  COLON MUCINOUS ADENOCARCINOMA        10       19       24
  RECTAL ADENOCARCINOMA                60       13       54
  RECTAL MUCINOUS ADENOCARCINOMA        1        2        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus         0   1
  subtype1   3 209
  subtype2   4  92
  subtype3   2 239
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  209
  subtype2    4   92
  subtype3    2  239
     clus
vv    subtype1 subtype2 subtype3
  NO         3        4        2
  YES      209       92      239
[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 121   2   5  17
  subtype2  66   0   2   7
  subtype3 197   3  29   2
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      121       66      197
  R1        2        0        3
  R2        5        2       29
  RX       17        7        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        14
  subtype2                                1     4                         7
  subtype3                                0     1                         5
          vv
clus       WHITE
  subtype1   171
  subtype2    73
  subtype3    36
D9V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   7        4        1
  BLACK OR AFRICAN AMERICAN              14        7        5
  WHITE                                 171       73       36
[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"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 175  49
  subtype2 110  27
  subtype3 133  31
subtype1 subtype2 subtype3 
     224      137      164 
subtype1 subtype2 subtype3 
      49       27       31 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       43.43        14.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.06        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 
        1.02        61.02        78.08         6.97        85.05        19.04 
TCGA-AA-3861 TCGA-AA-A010 TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-5900 TCGA-AD-6888 
       30.05        34.98         2.96         2.01         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.46        14.50        27.09        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       17.82         5.13        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.06         3.25         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       17.56        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 
        2.93         2.01       124.27        23.05        27.02        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        14.04        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        17.75        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 
        1.51        12.00        10.26       119.70        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76        14.04        26.47        81.37       119.93 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18         8.61        11.11        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        39.42        36.00        26.43        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       17.23        19.10        37.74        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3594 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3892 
       10.39         2.01         7.99        32.98         0.99        13.02 
TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 
        0.99         0.49         1.45         0.72        10.19         6.97 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6156 TCGA-DC-6157 
        9.37         7.17        10.98        11.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        24.13        51.48        32.61         2.40 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6464 
       17.00        18.28        15.85        17.69        16.31         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 
       37.51        31.30        32.19         0.66         0.69        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

$subtype2
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-3809 TCGA-A6-5660 
       43.76        24.33        42.28        13.94        32.75        29.19 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3494 
       22.09        32.71        25.08        21.76        20.12         1.02 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        58.03        62.96         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       24.03         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 
       26.01        12.99        24.00        23.01        13.94        19.99 
TCGA-AA-3662 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3812 
        6.05        47.01        11.01        36.00         5.03        35.05 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3852 TCGA-AA-3867 TCGA-AA-3875 
       25.02        17.98        38.99         0.00        24.03        18.05 
TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00L TCGA-AA-A00U 
       26.01        19.07         7.96        19.00        38.04        17.03 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02J TCGA-AA-A02K TCGA-AD-6548 
        1.02        35.01        26.01         5.03        14.01        21.37 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-6599 
       10.88         0.20         0.92        16.31         1.41         6.77 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5914 
        2.14         3.29         0.07         0.26       102.44        21.99 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6164 
        8.02        13.02        22.98         5.03        15.02        29.03 
TCGA-CM-6166 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 
       21.99        12.26        13.51        11.51         1.32        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A282 
       14.30        13.41        38.20       130.65       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 
        6.12        35.97        60.79       117.07        13.38        13.64 
TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 
       16.24         8.35        23.51        55.04        35.93        36.72 
TCGA-G4-6323 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-5654 TCGA-AG-3574 
       13.78        24.13        39.48        13.55        16.83        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 
       32.02         8.02        36.03        20.05        46.03        34.03 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 
        0.99         1.02         0.99        35.01        14.01        36.03 
TCGA-AG-A00C TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 
        6.02        64.01        49.97       117.11        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-5337 
        6.05         6.05         4.73        13.97        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 
       12.99        13.97        57.24       129.27         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6513 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6641 
       20.91        16.34        28.57         0.39        26.43 

$subtype3
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        46.65        42.90        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3808 
       16.57        37.05        37.25        37.02        34.65        33.34 
TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3510 
       36.53        32.45         5.03         3.02        37.05        63.98 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3543 
       13.02        37.05        36.03         8.05        19.07         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       20.98        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.05        15.02         5.98        37.05        19.00 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        19.04        10.06        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        53.00        17.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       36.03        16.08        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A00O 
       24.00        27.02        27.02        27.02        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01P 
       42.02        14.99        10.98        32.02        12.00        38.07 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        33.04        37.02        39.06        51.98        39.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4071 
        0.92        22.03        39.98        18.05        40.96         0.95 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       75.25        50.37        58.39         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       22.36        65.00        70.16        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-5341 TCGA-D5-6932 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 
       26.04        29.06        11.38        43.04        12.72        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 
       12.00         7.07        24.00         1.02        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 
        6.05         0.99        15.95        19.99        19.99        29.98 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
       19.99         1.02        36.95        17.03         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       20.98        13.94        37.02        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        70.03        10.98         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-EI-6507 
       41.00        19.96 

subtype1 subtype2 subtype3 
    0.07     0.00     0.00 
subtype1 subtype2 subtype3 
  140.38   139.17    83.80 
subtype1 subtype2 subtype3 
  17.395   19.070   25.020 
[1] "0.1 - 140.4 (17.4)" "0.0 - 139.2 (19.1)" "0.0 - 83.8 (25.0)" 
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1 176  51
  subtype2 100  43
  subtype3 129  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  176   51
  subtype2  100   43
  subtype3  129   46
        clus
vv       subtype1 subtype2 subtype3
  COLON       176      100      129
  RECTUM       51       43       46
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      36        0       10        78         4         1         8
  subtype2      22        1        6        34         2         1         7
  subtype3      36        0       20        42         4         0        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          8         28         18       13        14         1
  subtype2          6         21         14       23         4         0
  subtype3          2         20         13       21         5         0
D10V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          36       22       36
  STAGE IA          0        1        0
  STAGE II         10        6       20
  STAGE IIA        78       34       42
  STAGE IIB         4        2        4
  STAGE IIC         1        1        0
  STAGE III         8        7       12
  STAGE IIIA        8        6        2
  STAGE IIIB       28       21       20
  STAGE IIIC       18       14       13
  STAGE IV         13       23       21
  STAGE IVA        14        4        5
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   8  37 158  25
  subtype2   6  22 101  14
  subtype3   6  36 117  17
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        6        6
  T2       37       22       36
  T3      158      101      117
  T4       25       14       17
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 137  53  36
  subtype2  69  42  32
  subtype3 106  38  32
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      137       69      106
  N1       53       42       38
  N2       36       32       32
[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"
D10V7, binary
          cls
clus         0   1
  subtype1 163  25
  subtype2 103  27
  subtype3 146  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  163   25
  subtype2  103   27
  subtype3  146   26
   clus
vv  subtype1 subtype2 subtype3
  0      163      103      146
  1       25       27       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1 101 128
  subtype2  72  72
  subtype3  84  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101  128
  subtype2   72   72
  subtype3   84   92
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      101       72       84
  MALE        128       72       92
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  151                            25
  subtype2                   90                             9
  subtype3                  110                            19
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    49                              2
  subtype2                    40                              3
  subtype3                    38                              5
D10V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                151       90      110
  COLON MUCINOUS ADENOCARCINOMA        25        9       19
  RECTAL ADENOCARCINOMA                49       40       38
  RECTAL MUCINOUS ADENOCARCINOMA        2        3        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus         0   1
  subtype1   6 223
  subtype2   1 143
  subtype3   2 174
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  223
  subtype2    1  143
  subtype3    2  174
     clus
vv    subtype1 subtype2 subtype3
  NO         6        1        2
  YES      223      143      174
[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 142   2   4  17
  subtype2  95   1  15   7
  subtype3 147   2  17   2
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142       95      147
  R1        2        1        2
  R2        4       15       17
  RX       17        7        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        15
  subtype2                                0     4                         7
  subtype3                                0     0                         4
          vv
clus       WHITE
  subtype1   181
  subtype2    68
  subtype3    31
D10V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   8        4        0
  BLACK OR AFRICAN AMERICAN              15        7        4
  WHITE                                 181       68       31
[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"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 17  6
  subtype2 14  6
  subtype3 22  6
  subtype4 17 10
  subtype5 13  5
  subtype6 13  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      23       20       28       27       18       17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        6        6       10        5        4 
$subtype1
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-AD-6965 TCGA-D5-5537 
       43.43        27.09        24.13        20.61         0.20        45.40 
TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 
      130.65         7.50        35.97        33.67        28.21         8.35 
TCGA-G4-6306 TCGA-AF-6672 TCGA-AG-3732 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       44.68        10.39        32.98         7.17        11.01        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A1DG TCGA-EI-6511 TCGA-EI-6513 
       36.00        10.98        51.48        15.85        16.34 

$subtype2
TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3489 TCGA-AD-5900 
       31.63        22.52        21.76        23.87         7.04         0.07 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6167 
        0.20         1.41         5.13         3.19        27.02        14.99 
TCGA-CM-6674 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 
       12.95         1.55        16.31        16.24        13.25        67.30 
TCGA-G4-6314 TCGA-G4-6627 
       35.93        47.15 

$subtype3
TCGA-A6-5667 TCGA-CA-6719 TCGA-D5-6922 TCGA-F4-6459 TCGA-F4-6460 TCGA-G4-6303 
       29.16         1.35        10.13         8.61        13.38        65.85 
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-3731 TCGA-AG-4022 TCGA-AH-6549 
       24.13        37.74        14.50         1.02         0.99        17.49 
TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE 
        6.05         6.05        12.95        10.06        57.24       129.27 
TCGA-EI-6509 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.00        16.31         9.96        37.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6572 
        0.39        32.19         0.66        47.08 

$subtype4
TCGA-A6-6141 TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-6605 TCGA-CM-6677 TCGA-CM-6678 
        8.38        27.42        10.88         5.23        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.06        12.03        24.43        38.20        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A280 TCGA-G4-6299 TCGA-G4-6625 TCGA-AF-6655 TCGA-AH-6544 
      140.38         7.76        74.56        91.79        20.02         0.49 
TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 
        1.45        10.19         4.73        13.05        41.36        32.61 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$subtype5
TCGA-A6-6142 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-AZ-5403 
       25.08        19.66        20.28         6.97        22.42        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-6748 TCGA-CM-5860 TCGA-CM-6676 TCGA-D5-6534 
       12.10        29.56         2.01        16.01        11.08        43.27 
TCGA-D5-6924 TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6569 TCGA-DC-5869 TCGA-DC-6156 
       14.30       139.17         6.12        13.45        12.99        15.02 

$subtype6
TCGA-A6-6649 TCGA-A6-6653 TCGA-AD-6548 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6601 
       24.16        24.39        21.37        56.55        49.41       100.01 
TCGA-CA-6718 TCGA-CK-5916 TCGA-D5-6533 TCGA-D5-6536 TCGA-DM-A1HA TCGA-F4-6570 
        0.10        21.14         1.32        17.85       131.51         6.18 
TCGA-G4-6309 TCGA-G4-6628 TCGA-AH-6643 TCGA-EI-6506 TCGA-EI-6507 
       51.75        52.80         0.69        20.55        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.20     0.07     0.39     0.49     2.01     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  130.65    67.30   129.27   140.38   139.17   131.51 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  24.130   15.615   15.405   13.050   15.515   21.370 
[1] "0.2 - 130.7 (24.1)" "0.1 - 67.3 (15.6)"  "0.4 - 129.3 (15.4)"
[4] "0.5 - 140.4 (13.1)" "2.0 - 139.2 (15.5)" "0.1 - 131.5 (21.4)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 13 11
  subtype2 20  0
  subtype3  6 22
  subtype4 16 12
  subtype5 16  2
  subtype6 14  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   11
  subtype2   20    0
  subtype3    6   22
  subtype4   16   12
  subtype5   16    2
  subtype6   14    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COLON        13       20        6       16       16       14
  RECTUM       11        0       22       12        2        3
[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       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       6        1         7         0         0         1          0
  subtype2       2        1         4         0         0         0          0
  subtype3       0        1         8         0         0         0          1
  subtype4       1        0        10         0         1         1          3
  subtype5       2        2         4         1         0         0          0
  subtype6       4        2         6         0         0         0          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          1        2         1
  subtype2          4          4        4         1
  subtype3          5          4        4         4
  subtype4          4          2        0         1
  subtype5          1          1        3         2
  subtype6          3          2        0         0
D11V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           6        2        0        1        2        4
  STAGE II          1        1        1        0        2        2
  STAGE IIA         7        4        8       10        4        6
  STAGE IIB         0        0        0        0        1        0
  STAGE IIC         0        0        0        1        0        0
  STAGE III         1        0        0        1        0        0
  STAGE IIIA        0        0        1        3        0        0
  STAGE IIIB        4        4        5        4        1        3
  STAGE IIIC        1        4        4        2        1        2
  STAGE IV          2        4        4        0        3        0
  STAGE IVA         1        1        4        1        2        0
[1] 11  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  5 15  2
  subtype2  0  2 16  2
  subtype3  0  0 26  2
  subtype4  1  3 21  3
  subtype5  0  3 10  5
  subtype6  1  3 12  1
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        2        0        0        1        0        1
  T2        5        2        0        3        3        3
  T3       15       16       26       21       10       12
  T4        2        2        2        3        5        1
[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 13  6  5
  subtype2  7  5  8
  subtype3  9 10  8
  subtype4 13 10  5
  subtype5 10  6  2
  subtype6 13  2  2
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       13        7        9       13       10       13
  N1        6        5       10       10        6        2
  N2        5        8        8        5        2        2
[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"
D11V7, binary
          cls
clus        0  1
  subtype1 17  2
  subtype2 11  5
  subtype3 17  7
  subtype4 18  2
  subtype5  8  5
  subtype6 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    2
  subtype2   11    5
  subtype3   17    7
  subtype4   18    2
  subtype5    8    5
  subtype6   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       17       11       17       18        8       16
  1        2        5        7        2        5        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1  8 16
  subtype2  9 11
  subtype3 15 14
  subtype4 12 16
  subtype5  7 11
  subtype6  7 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   16
  subtype2    9   11
  subtype3   15   14
  subtype4   12   16
  subtype5    7   11
  subtype6    7   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        8        9       15       12        7        7
  MALE         16       11       14       16       11       10
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   13                             0
  subtype2                   16                             4
  subtype3                    6                             0
  subtype4                   14                             2
  subtype5                   12                             4
  subtype6                   14                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    11                              0
  subtype2                     0                              0
  subtype3                    22                              0
  subtype4                    11                              1
  subtype5                     2                              0
  subtype6                     3                              0
D11V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 13       16        6       14       12
  COLON MUCINOUS ADENOCARCINOMA         0        4        0        2        4
  RECTAL ADENOCARCINOMA                11        0       22       11        2
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        0        1        0
                                clus
vv                               subtype6
  COLON ADENOCARCINOMA                 14
  COLON MUCINOUS ADENOCARCINOMA         0
  RECTAL ADENOCARCINOMA                 3
  RECTAL MUCINOUS ADENOCARCINOMA        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
          cls
clus        0  1
  subtype1  1 23
  subtype2  0 20
  subtype3  2 27
  subtype4  1 27
  subtype5  0 18
  subtype6  0 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    0   20
  subtype3    2   27
  subtype4    1   27
  subtype5    0   18
  subtype6    0   17
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         1        0        2        1        0        0
  YES       23       20       27       27       18       17
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 12  0  0  2
  subtype2 14  0  0  0
  subtype3 18  0  2  2
  subtype4 11  1  0  0
  subtype5  9  0  0  1
  subtype6  9  0  0  2
D11V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       12       14       18       11        9        9
  R1        0        0        0        1        0        0
  R2        0        0        2        0        0        0
  RX        2        0        2        0        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"
D11V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                1     0                         2
  subtype3                                0     1                         0
  subtype4                                0     0                         1
  subtype5                                0     0                         2
  subtype6                                0     2                         1
          vv
clus       WHITE
  subtype1    20
  subtype2    16
  subtype3    25
  subtype4    27
  subtype5    15
  subtype6    14
D11V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        0        1        0        0
  BLACK OR AFRICAN AMERICAN               2        2        0        1        2
  WHITE                                  20       16       25       27       15
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   2
  BLACK OR AFRICAN AMERICAN               1
  WHITE                                  14
[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"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 37 18
  subtype2 12  3
  subtype3 24  9
  subtype4 23  7
subtype1 subtype2 subtype3 subtype4 
      55       15       33       30 
subtype1 subtype2 subtype3 subtype4 
      18        3        9        7 
$subtype1
TCGA-A6-2675 TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       43.43        31.63        22.52         8.38        24.16        21.76 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-5900 TCGA-AD-6548 
       23.87        19.66        20.28         7.04         0.07        21.37 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 
       22.42        27.42        10.88         0.20         1.41         5.13 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-6167 
        0.10        21.14         2.01        27.02        16.01        14.99 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6534 
       12.95        11.08        11.01        10.06        12.03        43.27 
TCGA-D5-6536 TCGA-DM-A280 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       17.85         7.76        13.45         6.18         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6314 TCGA-G4-6625 
       16.24        13.25        74.56        67.30        35.93        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-AG-3732 TCGA-AH-6547 TCGA-DC-6157 TCGA-DC-6158 
       47.15        52.80        32.98         1.45        36.00        10.98 
TCGA-F5-6464 
        9.96 

$subtype2
TCGA-A6-5667 TCGA-CA-6719 TCGA-D5-6922 TCGA-F4-6459 TCGA-G4-6303 TCGA-AF-3911 
       29.16         1.35        10.13         8.61        65.85        37.74 
TCGA-AF-4110 TCGA-AG-4022 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE 
       14.50         0.99        12.95        10.06        57.24       129.27 
TCGA-EI-6514 TCGA-F5-6571 TCGA-F5-6812 
       16.31        31.30         0.66 

$subtype3
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6965 
       27.09        24.13        20.61        24.39        56.55         0.20 
TCGA-AZ-6598 TCGA-D5-5537 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.41        45.40        24.43       130.65         7.50       131.51 
TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 
       35.97        33.67        28.21         8.35        44.68        51.75 
TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-5918 
       10.39         0.49         0.69        10.19         4.73         7.17 
TCGA-DC-4749 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       11.01        51.48        32.61        19.96        15.85        16.34 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$subtype4
TCGA-A6-6142 TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF 
       25.08         6.97        11.08         1.32        14.30        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6460 
       13.32        12.59       140.38       139.17         6.12        13.38 
TCGA-AF-2687 TCGA-AF-6655 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       24.13        20.02         1.02        17.49         6.05         6.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EI-6506 
       15.02        12.99        15.02        13.05        41.36        20.55 
TCGA-EI-6509 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6572 
       17.00        37.51        28.57         0.39        32.19        47.08 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.66     0.20     0.39 
subtype1 subtype2 subtype3 subtype4 
  100.01   129.27   131.51   140.38 
subtype1 subtype2 subtype3 subtype4 
   16.24    14.50    24.39    15.02 
[1] "0.1 - 100.0 (16.2)" "0.7 - 129.3 (14.5)" "0.2 - 131.5 (24.4)"
[4] "0.4 - 140.4 (15.0)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 50  5
  subtype2  5  9
  subtype3 18 16
  subtype4 12 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    5
  subtype2    5    9
  subtype3   18   16
  subtype4   12   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        50        5       18       12
  RECTUM        5        9       16       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       9        3        15         1         0         0          0
  subtype2       0        1         5         0         0         0          1
  subtype3       4        2         9         0         1         1          2
  subtype4       2        1        10         0         0         1          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          7          7        6         2
  subtype2          4          1        1         2
  subtype3          7          3        2         1
  subtype4          3          3        4         4
D12V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        0        4        2
  STAGE II          3        1        2        1
  STAGE IIA        15        5        9       10
  STAGE IIB         1        0        0        0
  STAGE IIC         0        0        1        0
  STAGE III         0        0        1        1
  STAGE IIIA        0        1        2        1
  STAGE IIIB        7        4        7        3
  STAGE IIIC        7        1        3        3
  STAGE IV          6        1        2        4
  STAGE IVA         2        2        1        4
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  9 36  9
  subtype2  0  0 14  1
  subtype3  2  5 25  2
  subtype4  1  2 25  3
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        2        1
  T2        9        0        5        2
  T3       36       14       25       25
  T4        9        1        2        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 31 12 12
  subtype2  6  5  4
  subtype3 14 12  8
  subtype4 14 10  6
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31        6       14       14
  N1       12        5       12       10
  N2       12        4        8        6
[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"
D12V7, binary
          cls
clus        0  1
  subtype1 34  8
  subtype2 10  2
  subtype3 23  3
  subtype4 20  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    8
  subtype2   10    2
  subtype3   23    3
  subtype4   20    8
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       34       10       23       20
  1        8        2        3        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus        0  1
  subtype1 23 32
  subtype2  9  6
  subtype3 11 23
  subtype4 15 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   32
  subtype2    9    6
  subtype3   11   23
  subtype4   15   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23        9       11       15
  MALE         32        6       23       17
[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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   42                             8
  subtype2                    5                             0
  subtype3                   18                             0
  subtype4                   10                             2
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     5                              0
  subtype2                     9                              0
  subtype3                    15                              1
  subtype4                    20                              0
D12V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 42        5       18       10
  COLON MUCINOUS ADENOCARCINOMA         8        0        0        2
  RECTAL ADENOCARCINOMA                 5        9       15       20
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        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"
D12V10, binary
          cls
clus        0  1
  subtype1  0 55
  subtype2  1 14
  subtype3  2 32
  subtype4  1 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   55
  subtype2    1   14
  subtype3    2   32
  subtype4    1   31
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        2        1
  YES       55       14       32       31
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 33  0  0  3
  subtype2 11  0  0  1
  subtype3 13  1  0  2
  subtype4 16  0  2  1
D12V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       33       11       13       16
  R1        0        0        1        0
  R2        0        0        0        2
  RX        3        1        2        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         5
  subtype2                                0     1                         0
  subtype3                                0     1                         2
  subtype4                                0     0                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    13
  subtype3    30
  subtype4    28
D12V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        1        1        0
  BLACK OR AFRICAN AMERICAN               5        0        2        1
  WHITE                                  46       13       30       28
[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"
