[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/22506534/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/22555066/COADREAD-TP.mergedcluster.txt"

nPatients in clinical file=629, in cluster file=628, common to both=626
[1]  12 626
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
47 63 68 44 
 1  2  3  4 
47 63 68 44 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
52 90 80 
 1  2  3 
52 90 80 
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
215 246 131  22 
  1   2   3   4 
215 246 131  22 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
116 130 145 
  1   2   3 
116 130 145 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
113 196 180 
  1   2   3 
113 196 180 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
236 167  86 
  1   2   3 
236 167  86 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
157 129 132 203 
  1   2   3   4 
157 129 132 203 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 81  86  64  57  90 140 103 
  1   2   3   4   5   6   7 
 81  86  64  57  90 140 103 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
154  95  87 213 
  1   2   3   4 
154  95  87 213 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
49 74 30 89 78 55 57 33 84 
 1  2  3  4  5  6  7  8  9 
49 74 30 89 78 55 57 33 84 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
35 40 39 22 
 1  2  3  4 
35 40 39 22 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
63 16 34 23 
 1  2  3  4 
63 16 34 23 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 626 columns.

[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=112,	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=318,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR_STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 626 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"        "TUMOR_TISSUE_SITE"     "PATHOLOGIC_STAGE"     
 [4] "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"    
 [7] "GENDER"                "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"    
[10] "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES" "ETHNICITY"            
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 20 107 426  70 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 107 426  70 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 107 426  70 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 107 426  70 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
354 150 118 
[1] "table(vv)"
vv
 N0  N1  N2 
354 150 118 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
354 150 118 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
354 150 118 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 34  9
  subtype2 43 15
  subtype3 57  9
  subtype4 37  7
subtype1 subtype2 subtype3 subtype4 
      43       58       66       44 
subtype1 subtype2 subtype3 subtype4 
       9       15        9        7 
$subtype1
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3715 
       13.02        24.03         0.99        17.95         0.92        19.04 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       31.07        29.98        24.00        46.65        43.76        42.90 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3710 TCGA-AA-3811 
       33.34        32.75        36.53         1.02        26.99        10.06 
TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3866 TCGA-AA-3869 
       33.04        15.95        37.02         0.00        17.03        27.02 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       31.00         2.01        33.01        26.01         2.01        25.02 
TCGA-AA-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-3881 TCGA-AG-3883 
       34.49        12.00         6.05         0.99        19.04         1.02 
TCGA-AG-3901 
       25.02 

$subtype2
TCGA-A6-2677 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.33        34.03        19.99         2.01        50.99        26.01 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       38.04        21.99        10.39        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3517 
       15.95        31.00        51.98        16.57        34.65        38.99 
TCGA-AA-3519 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        9.07        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3696 TCGA-AA-3837 TCGA-AA-3875 
       21.01        24.00         2.01         5.03        38.99        18.05 
TCGA-AA-3973 TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       13.05        27.02        42.02        15.02        15.02        31.00 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 
        2.96        39.98         2.01         5.03        41.00        16.31 
TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3893 TCGA-AG-3894 
       36.03        24.00        19.99         7.99        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A016 
       48.03        28.04        36.03        14.04         1.02         9.07 
TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
        1.02         1.94        38.96        38.04 

$subtype3
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       36.03        19.07        13.02        19.99        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3862 TCGA-AA-3867 TCGA-AA-3979 TCGA-AA-3986 TCGA-AG-3580 
       14.93        30.05        24.03        24.00        19.07         8.02 
TCGA-AG-3611 TCGA-A6-2678 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3667 TCGA-AA-3673 
       13.94        42.28         0.00        29.00        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 
       47.01        15.02        37.05        35.05        25.02        17.98 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 
       36.95        17.03        10.06         0.00        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
        0.99        31.07        20.98        34.03        21.99        36.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00F 
       16.08        34.06        27.02        27.02         7.96        34.03 
TCGA-AA-A00W TCGA-AY-4071 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3578 TCGA-AG-3581 
       14.99         0.95        43.04        13.55        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       36.03        20.05         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3882 
       12.03         0.99        15.95         0.99        29.98        19.99 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A025 
        1.02        19.99         6.02        23.01        37.02        49.97 

$subtype4
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3939 TCGA-AA-A024 TCGA-AG-A00H 
       37.05         8.05        23.01        12.99        39.06        25.97 
TCGA-AG-A015 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       36.03         1.02        19.07        29.95        20.98        13.94 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3818 TCGA-AA-3821 
       54.02        47.05        11.01         5.98         0.99         1.02 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3994 
        0.00        36.03        30.05        53.00        24.00        27.02 
TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 
       13.94        18.05        18.05         4.01        17.03        34.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01Q TCGA-AA-A029 TCGA-AF-2689 
       32.02        12.00        31.00         1.02        51.98        39.48 
TCGA-AG-3594 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A002 
        2.01        17.95        36.95        13.02        32.02        20.98 
TCGA-AG-A008 TCGA-AG-A02X 
       13.94        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 
  24.000   20.500   21.485   20.980 
[1] "0.0 - 46.6 (24.0)" "1.0 - 52.0 (20.5)" "0.0 - 50.0 (21.5)"
[4] "0.0 - 54.0 (21.0)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 40  7
  subtype2 38 25
  subtype3 41 25
  subtype4 33 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    7
  subtype2   38   25
  subtype3   41   25
  subtype4   33   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        40       38       41       33
  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        16         3         3          1          4
  subtype2       9        3        14         0         2          2          5
  subtype3      19        3        20         0         4          0          7
  subtype4      11        6        15         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        3        3        6
  STAGE IIA        16       14       20       15
  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 31  6
  subtype2  1 12 42  8
  subtype3  5 16 47  0
  subtype4  2  9 28  5
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        1        5        2
  T2        9       12       16        9
  T3       31       42       47       28
  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 31  6 10
  subtype2 29 17 17
  subtype3 42 12 14
  subtype4 34  8  2
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31       29       42       34
  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 40  6
  subtype2 46 17
  subtype3 59  8
  subtype4 41  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    6
  subtype2   46   17
  subtype3   59    8
  subtype4   41    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       40       46       59       41
  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 29 18
  subtype2 33 30
  subtype3 28 40
  subtype4 16 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   18
  subtype2   33   30
  subtype3   28   40
  subtype4   16   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       29       33       28       16
  MALE         18       30       40       28
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1 34  2
  subtype2 46  3
  subtype3 53  5
  subtype4 34  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    2
  subtype2   46    3
  subtype3   53    5
  subtype4   34    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        34       46       53       34
  YES        2        3        5        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"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   29                            11
  subtype2                   37                             1
  subtype3                   40                             1
  subtype4                   23                             9
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     4                              2
  subtype2                    25                              0
  subtype3                    21                              2
  subtype4                     8                              3
D1V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 29       37       40       23
  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"
          vv
clus       R0 R1 R2
  subtype1 39  0  4
  subtype2 46  2 15
  subtype3 58  0  8
  subtype4 42  0  2
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       39       46       58       42
  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
D1V13, binary
          cls
clus       0
  subtype1 7
  subtype2 5
  subtype3 4
  subtype4 1
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 39 11
  subtype2 65 16
  subtype3 67 13
subtype1 subtype2 subtype3 
      50       81       80 
subtype1 subtype2 subtype3 
      11       16       13 
$subtype1
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       13.02         8.05         0.99        17.95        23.01         0.92 
TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       19.04        29.98        24.00        46.65        43.76        42.90 
TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       33.34        32.75         1.02         1.02        19.07        29.95 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 
       26.99        10.06        33.04         1.02        15.95        37.02 
TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00         0.00        36.03        53.00        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 
       24.00        33.01        26.01         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-3881 
        1.02        22.03        34.49         2.01         6.05        19.04 
TCGA-AG-3901 TCGA-AG-A02X 
       25.02        41.00 

$subtype2
TCGA-A6-2677 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        34.03        13.02        19.99        19.99        19.00 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AF-3913 
       31.07        24.03         2.01        38.04        21.99        10.39 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N TCGA-A6-2683 TCGA-A6-3807 
       19.99        17.03        17.03        31.00        16.57        34.65 
TCGA-A6-3810 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       36.53        38.99         9.07        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 
       14.01        21.01        24.00        14.01        15.02        37.05 
TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3858 
        5.03        35.05        36.95        17.03         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3973 
       17.03        20.98        21.99        36.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A010 
       34.06        27.02        34.03        27.02        42.02        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       15.02        15.02        31.00         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 TCGA-AY-4071 TCGA-AG-3574 TCGA-AG-3582 
        5.03        41.00        16.31         0.95        36.03        36.03 
TCGA-AG-3584 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3882 
       24.00         0.99        15.95        19.99        29.98        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
        1.02        36.95        35.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A011 TCGA-AG-A01J 
       28.04        36.03        14.04         1.02        37.02         1.02 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
        1.94        38.96        38.04 

$subtype3
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3692 TCGA-AA-3844 
       24.03        37.05        36.03        19.07        36.00        14.93 
TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       30.05        12.99        50.99        26.01        24.00        19.07 
TCGA-AA-A024 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       39.06         8.02        13.94        25.97        15.95        36.03 
TCGA-AG-A023 TCGA-A6-2678 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3548 TCGA-AA-3558 
       51.98        42.28         0.00        29.00        33.99        20.98 
TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       13.94        54.02         2.01        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
       11.01         5.98         0.99        25.02        17.98        38.99 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3861 TCGA-AA-3869 
       10.06         0.00        33.07        32.05        30.05        27.02 
TCGA-AA-3875 TCGA-AA-3956 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       18.05        34.03        27.02         7.96        13.94        19.00 
TCGA-AA-A00K TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       18.05        17.03        14.99        32.02        12.00        31.00 
TCGA-AA-A029 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3578 
       51.98        39.48        43.04        13.55        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        7.07        20.05         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3892 
       12.03         7.99         0.99         0.99        17.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.01        32.02        20.98        13.94         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A025 
        9.07        49.97 

subtype1 subtype2 subtype3 
    0.00     0.95     0.00 
subtype1 subtype2 subtype3 
   53.00    48.03    54.02 
subtype1 subtype2 subtype3 
   22.52    21.01    20.98 
[1] "0.0 - 53.0 (22.5)" "0.9 - 48.0 (21.0)" "0.0 - 54.0 (21.0)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 46  6
  subtype2 57 32
  subtype3 49 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    6
  subtype2   57   32
  subtype3   49   30
        clus
vv       subtype1 subtype2 subtype3
  COLON        46       57       49
  RECTUM        6       32       30
[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 II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        17         4         3          1          6
  subtype2      15        4        23         1         2          1         11
  subtype3      23        8        25         0         5          1          5
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        5         1
  subtype2         14       19         0
  subtype3          4        9         0
D2V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9       15       23
  STAGE II          3        4        8
  STAGE IIA        17       23       25
  STAGE IIB         4        1        0
  STAGE III         3        2        5
  STAGE IIIA        1        1        1
  STAGE IIIB        6       11        5
  STAGE IIIC        2       14        4
  STAGE IV          5       19        9
  STAGE IVA         1        0        0
[1] 10  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 10 33  8
  subtype2  1 18 63  8
  subtype3  7 18 52  3
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        1        7
  T2       10       18       18
  T3       33       63       52
  T4        8        8        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"
          vv
clus       N0 N1 N2
  subtype1 34  9  9
  subtype2 46 23 21
  subtype3 56 11 13
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       34       46       56
  N1        9       23       11
  N2        9       21       13
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 45  6
  subtype2 70 19
  subtype3 71  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    6
  subtype2   70   19
  subtype3   71    9
   clus
vv  subtype1 subtype2 subtype3
  0       45       70       71
  1        6       19        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1 30 22
  subtype2 44 46
  subtype3 32 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   22
  subtype2   44   46
  subtype3   32   48
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       30       44       32
  MALE         22       46       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"
D2V9, binary
          cls
clus        0  1
  subtype1 38  2
  subtype2 67  3
  subtype3 62  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    2
  subtype2   67    3
  subtype3   62    8
     clus
vv    subtype1 subtype2 subtype3
  NO        38       67       62
  YES        2        3        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   27                            18
  subtype2                   57                             0
  subtype3                   45                             4
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     2                              3
  subtype2                    31                              1
  subtype3                    25                              3
D2V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 27       57       45
  COLON MUCINOUS ADENOCARCINOMA        18        0        4
  RECTAL ADENOCARCINOMA                 2       31       25
  RECTAL MUCINOUS ADENOCARCINOMA        3        1        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"
          vv
clus       R0 R1 R2
  subtype1 45  0  3
  subtype2 70  2 17
  subtype3 70  0  9
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       45       70       70
  R1        0        2        0
  R2        3       17        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
D2V13, binary
          cls
clus       0
  subtype1 6
  subtype2 7
  subtype3 4
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 163  46
  subtype2 188  49
  subtype3  99  29
  subtype4  16   4
subtype1 subtype2 subtype3 subtype4 
     209      237      128       20 
subtype1 subtype2 subtype3 subtype4 
      46       49       29        4 
$subtype1
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        37.05         8.05        19.07 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3939 
        0.99        17.95         0.92        19.04        19.04        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       24.00         2.01        19.07        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       10.88        75.95       100.01        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-AG-3580 TCGA-3L-AA1B TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       79.69         8.02        15.62         9.53        46.65        42.90 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       37.05        37.25        32.75        33.53        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         7.04         3.02        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 
       19.07        29.00        29.95        20.98        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3812 
       54.02        47.05        11.01         5.98        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
        0.99         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
        0.00        53.00        18.05        31.00        33.01        26.01 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       10.98        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       22.03        39.98        18.05        12.16        83.24        24.53 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.92        27.09        21.44        17.82        17.85        19.33 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39         1.41        32.94         5.13        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.36        12.39        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       17.56        85.45        70.16        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5861 TCGA-CM-6161 
      124.27        23.05        37.02        26.04        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       12.00        16.04        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-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       17.75        43.27        17.85         4.80        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
      119.70        24.43       135.65         7.76       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        95.18        11.11        35.74         6.18        47.87 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       41.42        35.31       133.18        67.30        53.62        85.48 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       26.04        13.78        74.79        19.33         9.93        31.30 
TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3594 TCGA-AG-3598 
       70.03        34.49        16.83        12.00         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-A002 
       12.03         0.99        13.02        14.01        25.02        20.98 
TCGA-AG-A008 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       13.94        49.97        61.97        38.56         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 
       26.43        19.46        33.17        26.04        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       12.62        32.61        20.55        19.96        20.91        18.28 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         8.45        37.18        38.14 

$subtype2
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3560 
       45.60        14.53         1.02        36.03        34.03        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3972 
       19.99        19.00        85.05        14.93        31.07        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-6608 
       26.01        24.00        38.04        21.99        15.52         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       49.08        28.21        63.62        91.79        17.85        10.39 
TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        25.97        15.95        36.03        31.00 
TCGA-G5-6233 TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2678 
       18.28         4.80        39.45        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       44.91        35.11        16.57        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       32.91        30.44        29.19        23.61        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       22.52        24.13        25.08        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       20.28        61.84        56.25         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       38.99         9.07        12.99        14.01        33.99        21.01 
TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 
       13.94         2.01        14.01        15.02        37.05        25.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3869 
       36.95        37.02        17.03        32.05        17.03        27.02 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       24.00        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.06        34.03        42.02        14.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F 
       32.02        12.00        31.00        33.04         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
        2.01        40.96         5.79        27.42        16.44        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 
        0.95        33.01        17.26        18.84       109.28        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5914 TCGA-CK-6748 
       29.56         5.23        12.46        12.59        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5864 
       25.02         8.02        13.02        29.06        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       17.03        14.04        29.03        15.02        11.01        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       10.06        54.61        19.59        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
       25.48        15.12        17.13        11.38        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59         7.50       131.51 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6808 
       14.04        26.47       119.93        35.97        31.96        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6626 
       13.25         0.53        82.39        65.85        61.91        46.75 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QL-A97D 
       18.18        19.33        15.65        16.80        42.77        21.90 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       60.13        11.90        39.48        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        29.98        24.36        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
       11.84        36.03         7.07        36.03        20.05        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 
       34.03        34.03        15.95        19.99        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 
       29.98         0.99        19.99         1.02        17.95        35.01 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00C 
       19.99        36.03        14.04         1.02        46.03         6.02 
TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       23.01         9.07         1.02         1.94        38.96        38.04 
TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
       27.55        13.78        44.78        47.44         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.05        31.00        12.00        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         3.48         4.18 
TCGA-EI-6509 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       17.00        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       19.66        11.87        47.08 

$subtype3
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3662 
       24.33        13.94        24.16        13.02        23.01         6.05 
TCGA-AA-3692 TCGA-AA-3867 TCGA-AA-3870 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6298 
       36.00        24.03        29.98       106.75         5.88        23.51 
TCGA-G4-6314 TCGA-AG-3611 TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-4T-AA8H 
       35.93        13.94        51.98        55.76        26.43        12.66 
TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-6137 TCGA-A6-6648 
        1.61        43.76        37.02        31.63        27.09        25.18 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 
        1.02        37.05        35.01         0.00        29.00        26.01 
TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3851 
       24.00        78.08        47.01         5.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3858 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3982 
        0.00        36.03        31.07         2.01         2.01        27.02 
TCGA-AA-A00D TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O 
       19.00        17.03         1.02        37.02         5.03         0.92 
TCGA-AA-A02W TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4684 
       41.00        26.47         0.46        16.31         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       62.79        88.21        12.69        12.59        14.30       148.01 
TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       15.62        27.02        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-6541 TCGA-D5-6898 
       15.02        21.99        13.02        11.08        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D9 TCGA-DM-A1DB 
       10.13        12.43         9.04        13.41       140.38        44.32 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6805 TCGA-F4-6807 
      117.07        98.24         8.61        35.74        34.42        43.04 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
        8.35        74.56        44.68        55.04        39.42        36.00 
TCGA-G4-6320 TCGA-NH-A50U TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       26.43        10.98        29.46        32.98         8.42        38.70 
TCGA-AF-2690 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 
       17.23        24.59        32.02        24.00         1.02        34.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
        6.05         0.99         7.99        37.02        32.98        19.04 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-A011 
       36.95         1.02        32.02        28.04         3.98        37.02 
TCGA-AG-A01J TCGA-AG-A02X TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6156 
        1.02        41.00        48.20        78.12        13.97        31.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-EI-6511 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       10.98        25.05        15.85        10.78        13.64         9.96 
TCGA-F5-6702 TCGA-F5-6864 
       28.57        12.46 

$subtype4
TCGA-AG-3890 TCGA-BM-6198 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3856 TCGA-AA-A01X 
       17.03        21.24        50.04        10.06         0.99        26.01 
TCGA-AA-A029 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CM-4744 
       51.98        22.42         0.20        12.10         3.19        20.02 
TCGA-D5-6539 TCGA-F4-6704 TCGA-F4-6855 TCGA-NH-A6GC TCGA-AF-2687 TCGA-AG-3898 
       12.49         1.55        47.41        12.79        46.92        48.03 
TCGA-CI-6619 TCGA-DC-6157 
        6.05        51.98 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.39     0.00     0.20 
subtype1 subtype2 subtype3 subtype4 
  139.17   131.51   148.01    51.98 
subtype1 subtype2 subtype3 subtype4 
  20.420   23.610   24.095   18.525 
[1] "0.0 - 139.2 (20.4)" "0.4 - 131.5 (23.6)" "0.0 - 148.0 (24.1)"
[4] "0.2 - 52.0 (18.5)" 
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1 180  35
  subtype2 159  83
  subtype3  93  38
  subtype4  16   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  180   35
  subtype2  159   83
  subtype3   93   38
  subtype4   16    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       180      159       93       16
  RECTUM       35       83       38        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      47        1       18        80         7         0         8
  subtype2      32        0       10        62         5         2         8
  subtype3      21        0        7        27         0         0         6
  subtype4       4        0        2         3         0         0         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         22         11        8         3         1
  subtype2          9         43         24       29        13         0
  subtype3          4         18         17       22         8         0
  subtype4          0          1          3        4         0         1
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          47       32       21        4
  STAGE IA          1        0        0        0
  STAGE II         18       10        7        2
  STAGE IIA        80       62       27        3
  STAGE IIB         7        5        0        0
  STAGE IIC         0        2        0        0
  STAGE III         8        8        6        2
  STAGE IIIA        2        9        4        0
  STAGE IIIB       22       43       18        1
  STAGE IIIC       11       24       17        3
  STAGE IV          8       29       22        4
  STAGE IVA         3       13        8        0
  STAGE IVB         1        0        0        1
[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   9  43 137  25
  subtype2   9  34 174  27
  subtype3   2  23  92  14
  subtype4   0   5  14   3
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        9        9        2        0
  T2       43       34       23        5
  T3      137      174       92       14
  T4       25       27       14        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 157  32  26
  subtype2 117  80  46
  subtype3  61  33  37
  subtype4  11   5   6
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      157      117       61       11
  N1       32       80       33        5
  N2       26       46       37        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"
D3V7, binary
          cls
clus         0   1
  subtype1 175  13
  subtype2 178  41
  subtype3  88  29
  subtype4  12   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  175   13
  subtype2  178   41
  subtype3   88   29
  subtype4   12    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      175      178       88       12
  1       13       41       29        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1 106 109
  subtype2 112 134
  subtype3  64  67
  subtype4   7  15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106  109
  subtype2  112  134
  subtype3   64   67
  subtype4    7   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      106      112       64        7
  MALE        109      134       67       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus         0   1
  subtype1 178   6
  subtype2 189  15
  subtype3 100   7
  subtype4  15   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  178    6
  subtype2  189   15
  subtype3  100    7
  subtype4   15    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       178      189      100       15
  YES        6       15        7        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  138                            41
  subtype2                  151                             6
  subtype3                   80                            12
  subtype4                   13                             3
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    26                              8
  subtype2                    81                              2
  subtype3                    33                              3
  subtype4                     6                              0
D3V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                138      151       80       13
  COLON MUCINOUS ADENOCARCINOMA        41        6       12        3
  RECTAL ADENOCARCINOMA                26       81       33        6
  RECTAL MUCINOUS ADENOCARCINOMA        8        2        3        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 164   2   6  15
  subtype2 173   1  17   8
  subtype3  94   3  13   4
  subtype4  15   0   1   2
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      164      173       94       15
  R1        2        1        3        0
  R2        6       17       13        1
  RX       15        8        4        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
D3V13, binary
          cls
clus         0   1
  subtype1   1 125
  subtype2   2 139
  subtype3   2  75
  subtype4   0  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  125
  subtype2    2  139
  subtype3    2   75
  subtype4    0   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        2        0
  NOT HISPANIC OR LATINO      125      139       75       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  90  25
  subtype2  98  29
  subtype3 109  33
subtype1 subtype2 subtype3 
     115      127      142 
subtype1 subtype2 subtype3 
      25       29       33 
$subtype1
TCGA-A6-2682 TCGA-A6-6649 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6314 
       13.94        24.16        10.88        75.95       100.01        35.93 
TCGA-G4-6625 TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B TCGA-5M-AAT6 TCGA-A6-2675 
       91.79        21.24        55.76        15.62         9.53        43.43 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6142 
       37.05        37.25        31.63        22.09         8.38        25.08 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 TCGA-AA-3489 
       21.76        23.87        19.66        16.24        61.84         7.04 
TCGA-AA-3510 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 
       63.98        27.42        14.50        27.09        33.01         0.20 
TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 
       18.84        58.39         1.41         5.13        62.79        12.10 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
        5.23         3.19        12.36        12.76        10.06       148.01 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       23.05        26.04        13.02        22.03        22.98        30.08 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        14.04        29.03        14.99        12.99 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6534 
       11.01        12.95        11.01        20.19        20.42        43.27 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       17.85        12.49        12.39         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A280 TCGA-F4-6460 TCGA-F4-6463 
       13.35        38.20        49.91         7.76        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
       35.74        47.87         1.55        34.42        43.04        13.25 
TCGA-F4-6856 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6311 
       35.31        82.39        67.30        53.62        85.48        39.42 
TCGA-G4-6627 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 
       74.79        70.03        46.92        17.23        37.97        29.98 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-3732 TCGA-AH-6544 TCGA-AH-6547 
       20.02        24.59        37.02        32.98        38.56         2.50 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-6160 
       19.46         6.05        13.78        47.44        48.20        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6884 
       25.97        25.05        20.55        19.96        17.00        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
       17.46         8.45         9.96        28.57        36.49        19.66 
TCGA-F5-6861 
       38.14 

$subtype2
TCGA-A6-2677 TCGA-AA-3697 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       24.33        85.05        15.52       106.75         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AATE 
       28.21        23.51        63.62        17.85         4.80        39.45 
TCGA-A6-2671 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       43.76        36.53        32.91        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       29.16        27.09        24.13        25.18        20.61        24.69 
TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3509 
       20.28        56.25         5.03         1.02        37.05        62.96 
TCGA-AA-3511 TCGA-AA-3660 TCGA-AD-6890 TCGA-AM-5820 TCGA-AZ-4308 TCGA-AZ-4682 
        6.97        78.08        24.53         0.46       109.28        22.36 
TCGA-AZ-4684 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-5914 
       65.00        29.56        12.46        12.59        12.59        21.99 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
        2.01         8.02        29.06         5.03        17.03        15.02 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 
       16.04        21.99        15.02        11.08        10.06        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6898 TCGA-D5-6922 
       55.92        18.25        25.48         4.80         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 
       12.43        14.30         9.04        11.38       130.65        13.32 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-F4-6459 
       44.32       139.17        26.47        81.37       119.93         8.61 
TCGA-F4-6808 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 
       33.67         0.53         8.35        65.85        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       36.00        46.75        18.18        42.77        32.98         8.42 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-3911 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       38.70        11.90        37.74        86.63        65.98        11.84 
TCGA-AG-3592 TCGA-AG-4022 TCGA-AG-A026 TCGA-AG-A036 TCGA-CI-6622 TCGA-CL-5917 
       34.03        46.03         1.94       117.11        44.78        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        21.01        25.05        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       31.00        51.98        10.98        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       57.24       129.27        51.48        32.61         4.18        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        13.64        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       49.51        42.35         0.39        32.19        11.87        12.46 
TCGA-G5-6572 
       47.08 

$subtype3
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3662 TCGA-AA-3713 
       45.60        14.53         1.02        58.03         6.05        19.04 
TCGA-AD-6548 TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       21.37        25.08         5.88        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-G5-6233 TCGA-G5-6641 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2679 
       79.69        18.28        26.43        12.66         1.61        44.91 
TCGA-A6-2680 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 
       35.11        37.02        32.75        32.45        30.44        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-A566 TCGA-A6-A5ZU 
       22.06        22.52        24.39        20.12        24.92         9.63 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3655 TCGA-AA-3663 TCGA-AD-5900 TCGA-AD-6889 
        3.02        35.01        61.02         6.97        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6197 
        5.79        22.42        26.47        16.44         0.92        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4615 
       17.82        17.26        17.85        19.33         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 
       88.21        49.41         6.77        11.74        12.69        12.39 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.20        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       51.32        21.14        82.95       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6169 
       25.02        27.02        32.02        15.02        15.02        13.02 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       14.04        13.05        11.08        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       19.59        17.75        15.12        17.13        16.14        15.58 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 
       12.00        10.26       119.70        24.43        92.75        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A288 TCGA-DM-A28F 
      140.38         7.50       131.51       135.65        14.04        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6570 
       60.79       117.07        98.24        95.18        11.11         6.18 
TCGA-F4-6806 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6320 
       41.42        47.41       133.18        74.56        44.68        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.04        13.78        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-QL-A97D 
       15.65        12.79        16.80        29.46        31.30        21.90 
TCGA-SS-A7HO TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3742 TCGA-AG-4021 
       60.13        24.36        34.03        20.98         0.99         3.98 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
        1.02        61.97        17.49        43.20        27.55        26.43 
TCGA-CI-6620 TCGA-DC-5337 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6508 
       33.17        26.04        12.62        24.13         3.48        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-F5-6814 
       18.28        17.69         8.61        37.18 

subtype1 subtype2 subtype3 
    0.20     0.39     0.92 
subtype1 subtype2 subtype3 
  148.01   139.17   140.38 
subtype1 subtype2 subtype3 
  22.090   24.690   21.405 
[1] "0.2 - 148.0 (22.1)" "0.4 - 139.2 (24.7)" "0.9 - 140.4 (21.4)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  84  30
  subtype2  88  42
  subtype3 121  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84   30
  subtype2   88   42
  subtype3  121   24
        clus
vv       subtype1 subtype2 subtype3
  COLON        84       88      121
  RECTUM       30       42       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      13        0        5        35         1         0         2
  subtype2      14        0        7        37         2         2         2
  subtype3      27        1        9        41         5         0         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         17         13       13         8         0
  subtype2          7         25          8        9        11         0
  subtype3          2         20         15        7         4         2
D4V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          13       14       27
  STAGE IA          0        0        1
  STAGE II          5        7        9
  STAGE IIA        35       37       41
  STAGE IIB         1        2        5
  STAGE IIC         0        2        0
  STAGE III         2        2        5
  STAGE IIIA        3        7        2
  STAGE IIIB       17       25       20
  STAGE IIIC       13        8       15
  STAGE IV         13        9        7
  STAGE IVA         8       11        4
  STAGE IVB         0        0        2
[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 11 85 17
  subtype2  3 18 92 15
  subtype3  5 26 94 19
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        3        5
  T2       11       18       26
  T3       85       92       94
  T4       17       15       19
[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 57 35 24
  subtype2 68 40 20
  subtype3 88 28 27
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       57       68       88
  N1       35       40       28
  N2       24       20       27
[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  77  20
  subtype2  89  20
  subtype3 100  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   20
  subtype2   89   20
  subtype3  100   13
   clus
vv  subtype1 subtype2 subtype3
  0       77       89      100
  1       20       20       13
[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 50 66
  subtype2 56 74
  subtype3 73 72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   66
  subtype2   56   74
  subtype3   73   72
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       56       73
  MALE         66       74       72
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus         0   1
  subtype1 102   3
  subtype2 100   9
  subtype3 116   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102    3
  subtype2  100    9
  subtype3  116    4
     clus
vv    subtype1 subtype2 subtype3
  NO       102      100      116
  YES        3        9        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   66                            17
  subtype2                   86                             1
  subtype3                   99                            21
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    28                              2
  subtype2                    42                              0
  subtype3                    20                              4
D4V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 66       86       99
  COLON MUCINOUS ADENOCARCINOMA        17        1       21
  RECTAL ADENOCARCINOMA                28       42       20
  RECTAL MUCINOUS ADENOCARCINOMA        2        0        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 80  1  2  5
  subtype2 86  1  2  8
  subtype3 93  3  3 16
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       80       86       93
  R1        1        1        3
  R2        2        2        3
  RX        5        8       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"
D4V12, continuous
D4V13, binary
          cls
clus         0   1
  subtype1   2 104
  subtype2   2 113
  subtype3   1 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  104
  subtype2    2  113
  subtype3    1  121
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        1
  NOT HISPANIC OR LATINO      104      113      121
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  81  27
  subtype2 145  46
  subtype3 145  32
subtype1 subtype2 subtype3 
     108      191      177 
subtype1 subtype2 subtype3 
      27       46       32 
$subtype1
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3522 
       24.33        45.60        24.16        58.03        24.03        37.05 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A00Z 
       13.02        19.99        19.99        19.04        19.04        21.99 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-4008 TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2678 
       63.62        91.79        17.03        15.62        43.76        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       35.11        16.57        37.25        33.34        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6782 
       30.44        23.61        29.16        24.13         8.38        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 
        7.04         3.02        35.01         1.02         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3655 TCGA-AA-3678 TCGA-AA-3812 TCGA-AA-3818 
       29.00        24.00        61.02        47.01        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3955 
       25.02         0.00        36.03         0.99        53.00        20.98 
TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A01D TCGA-AA-A01P 
       21.99        27.02        18.05        18.05        10.98        38.07 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02K TCGA-AA-A02W TCGA-AY-6196 TCGA-AY-6386 
       33.04         2.96        14.01        41.00         0.20        17.82 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4682 TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4747 
       19.33        18.84        22.36        12.39         2.01        25.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 TCGA-DM-A280 TCGA-F4-6459 TCGA-F4-6570 
       29.06        22.98        11.08         7.76         8.61         6.18 
TCGA-F4-6809 TCGA-G4-6297 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       13.25        82.39        13.78        19.33         9.93        12.79 
TCGA-QG-A5Z1 TCGA-AF-2690 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
        8.42        17.23        36.03        32.02         7.07        36.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 
        2.01        12.03        19.99        20.98        37.02         0.99 
TCGA-AG-3885 TCGA-AG-3891 TCGA-AG-3901 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       17.95        18.02        25.02        36.03         1.02        46.03 
TCGA-AG-A011 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-DC-6156 TCGA-DC-6681 
       37.02       117.11        38.56        17.49        31.00        25.97 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6572 
       20.91        17.00        16.31        28.57        32.19        47.08 

$subtype2
TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3688 TCGA-AA-3697 
        1.02         8.05        19.07        34.03        19.00        85.05 
TCGA-AA-3844 TCGA-AA-3972 TCGA-AA-A024 TCGA-AZ-6608 TCGA-G4-6294 TCGA-AG-3580 
       14.93        50.99        39.06         1.94        28.21         8.02 
TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H 
       19.99        36.03        51.98        26.43         4.80        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5664 
        9.53        46.65        42.90        37.02        32.75        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-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3548 
       23.87        63.98         6.97        38.99         9.07        33.99 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3696 TCGA-AA-3811 
       29.95        20.98        13.94        54.02         5.03        10.06 
TCGA-AA-3831 TCGA-AA-3848 TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3973 
       17.98        10.06        30.05        27.02         2.01        13.05 
TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
       34.06         7.96        30.02        34.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I 
       14.99        34.98        15.02        15.02        32.02        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F 
       35.01         1.02         1.02        26.01        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 
        2.01         5.03         0.92        39.98        40.96        83.24 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A69D 
        5.79        26.47        33.01        21.44        17.26        17.85 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94        65.00        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-4746 
       12.59        12.20        14.30        21.99        82.95        37.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6172 
       22.03        15.02        15.02        15.02        21.99        11.01 
TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       13.05        10.06        12.03        56.09        55.92        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6931 
       15.12         4.80        17.13        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-A282 TCGA-DM-A28A 
      140.38         7.50        44.32       131.51       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 
       81.37       119.93        35.97        60.79        95.18        31.96 
TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 
       41.42       133.18         8.35        85.48        61.91        26.43 
TCGA-G4-6322 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D 
       26.04        42.77        29.46        32.98        31.30        21.90 
TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56N 
       11.90        39.48        16.83        24.36        24.59        11.84 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3896 
       50.04         6.05         0.99         0.99         0.99         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A020 
       20.98        13.94         6.02        23.01         9.07         1.02 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-5869 
        1.94        38.96        61.97        26.43        21.01        31.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       13.97        51.98       126.44        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6512 
       51.48        32.61         3.48         4.18        18.28        17.69 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6813 
        8.61        10.78        13.64         0.39        19.66 

$subtype3
TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3862 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
       17.95         0.92        30.05        24.00        19.07        38.04 
TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       21.37       100.01        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-A00H TCGA-AG-A014 
       26.17        79.69        17.85        10.39        25.97        15.95 
TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-A6-2684 TCGA-A6-3807 
       31.00        21.24        18.28        55.76        37.05        34.65 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       31.63        29.19        33.53        25.08        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A566 TCGA-AA-3681 TCGA-AA-3710 
       24.39        20.12        19.66        24.92         5.98        26.99 
TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 
       33.04        15.95        38.99        36.95         0.00         0.00 
TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3971 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00N 
       17.03        33.01        16.08        13.94        38.04         4.01 
TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 
        0.99        31.00         1.02        22.03        18.05        12.16 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
        0.46         0.92        27.09       109.28        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        5.13        12.10         5.23        12.59        12.76        10.06 
TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 
       21.14       124.27        23.05        20.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       13.02        30.08        32.02         5.03        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        14.04        12.95        11.08        11.01 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6533 
       54.61        19.59        20.19        20.42        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85        12.49        16.14        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        14.30         9.04         9.44        11.64        13.35 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-DM-A288 TCGA-F4-6461 TCGA-F4-6463 
       38.20       130.65       135.65        14.04        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        34.42        43.04        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        0.53        47.41        35.31        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6626 
       53.62        44.68        55.04        39.42        36.00        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL 
       74.79        18.18        19.33        15.65        16.80        38.70 
TCGA-SS-A7HO TCGA-AF-3400 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3881 TCGA-AG-3882 
       60.13        34.49        37.68        20.02        19.04        19.99 
TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A01J 
       35.01        48.03        32.02        14.04         3.98         1.02 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CL-5918 
       41.00         2.50        43.20        27.55        13.78         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       25.05        26.04        10.98        44.02        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       12.62        41.36        20.55        19.96        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 
       16.41        17.46         9.96        49.51        42.35        36.49 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       38.14        11.87        12.46 

subtype1 subtype2 subtype3 
    0.00     0.39     0.00 
subtype1 subtype2 subtype3 
  117.11   140.38   135.65 
subtype1 subtype2 subtype3 
   21.99    22.03    20.42 
[1] "0.0 - 117.1 (22.0)" "0.4 - 140.4 (22.0)" "0.0 - 135.7 (20.4)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1  81  32
  subtype2 144  52
  subtype3 133  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81   32
  subtype2  144   52
  subtype3  133   47
        clus
vv       subtype1 subtype2 subtype3
  COLON        81      144      133
  RECTUM       32       52       47
[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      16        1       10        28         1         0         5
  subtype2      30        0       13        51         5         1        11
  subtype3      29        0        5        68         4         0         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1         15         12       12         8         1
  subtype2          6         29         16       24         5         1
  subtype3          6         25         15       10         6         0
D5V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          16       30       29
  STAGE IA          1        0        0
  STAGE II         10       13        5
  STAGE IIA        28       51       68
  STAGE IIB         1        5        4
  STAGE IIC         0        1        0
  STAGE III         5       11        6
  STAGE IIIA        1        6        6
  STAGE IIIB       15       29       25
  STAGE IIIC       12       16       15
  STAGE IV         12       24       10
  STAGE IVA         8        5        6
  STAGE IVB         1        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   0  19  80  12
  subtype2   6  33 132  24
  subtype3   5  29 126  20
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        6        5
  T2       19       33       29
  T3       80      132      126
  T4       12       24       20
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  59  26  26
  subtype2 103  56  36
  subtype3 112  40  27
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       59      103      112
  N1       26       56       40
  N2       26       36       27
[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"
D5V7, binary
          cls
clus         0   1
  subtype1  82  22
  subtype2 143  29
  subtype3 143  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   22
  subtype2  143   29
  subtype3  143   16
   clus
vv  subtype1 subtype2 subtype3
  0       82      143      143
  1       22       29       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1  56  57
  subtype2  93 103
  subtype3  85  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56   57
  subtype2   93  103
  subtype3   85   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       93       85
  MALE         57      103       95
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1  93   5
  subtype2 142  11
  subtype3 151   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93    5
  subtype2  142   11
  subtype3  151    7
     clus
vv    subtype1 subtype2 subtype3
  NO        93      142      151
  YES        5       11        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"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   72                             9
  subtype2                  134                             9
  subtype3                  107                            24
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    28                              3
  subtype2                    46                              5
  subtype3                    44                              2
D5V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 72      134      107
  COLON MUCINOUS ADENOCARCINOMA         9        9       24
  RECTAL ADENOCARCINOMA                28       46       44
  RECTAL MUCINOUS ADENOCARCINOMA        3        5        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  91   0   9   2
  subtype2 123   2  18  11
  subtype3 151   1   2   6
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       91      123      151
  R1        0        2        1
  R2        9       18        2
  RX        2       11        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
D5V13, binary
          cls
clus         0   1
  subtype1   0  50
  subtype2   2 111
  subtype3   0 138
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   50
  subtype2    2  111
  subtype3    0  138
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        0
  NOT HISPANIC OR LATINO       50      111      138
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 186  47
  subtype2 118  43
  subtype3  67  15
subtype1 subtype2 subtype3 
     233      161       82 
subtype1 subtype2 subtype3 
      47       43       15 
$subtype1
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        45.60        24.16         1.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3862 TCGA-AA-3950 
        8.05        13.02        17.95        19.99        30.05        24.00 
TCGA-AA-3986 TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       19.07        21.37       100.01        23.51        63.62        35.93 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 
        8.02        25.97        15.95        31.00        21.24        18.28 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       55.76        15.62        43.76        37.05        37.25        34.65 
TCGA-A6-3808 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       33.34        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52        24.13        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-AA-3502 
       24.69        24.39        19.66        20.28        24.92        35.01 
TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3812 
        1.02         0.00        29.00        24.00        29.95        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       33.04         0.99        25.02        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-A00A TCGA-AA-A00J 
        0.00         0.00        30.05        17.03        38.04        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A02H 
       18.05         4.01         0.99        31.00         1.02         2.01 
TCGA-AA-A02K TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AM-5820 
       14.01        22.03        41.00        18.05        12.16         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A8YK 
        0.92        27.09         0.20        21.44        17.82        18.84 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 
      109.28         1.41         5.13        12.10         5.23         3.19 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 
       12.46        12.59        12.76        10.06        14.30        21.14 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
        2.01        23.05        25.02        26.04         8.02        13.02 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 
       13.02        15.02        12.95        11.08        11.01        54.61 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
       19.59        20.19        20.42        17.75        25.48        43.27 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85        12.49        16.14        15.58         7.53        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04         9.44        11.64        13.35        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 
      130.65        12.59       131.51       135.65         7.76        14.04 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6627 
       44.68        55.04        39.42        36.00        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5Z1 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3578 
        8.42        17.23        34.49        37.68        20.02        32.02 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3882 TCGA-AG-3891 TCGA-AG-3893 TCGA-AG-3898 
        7.07        46.03        19.99        18.02        35.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-A01J TCGA-AG-A02X TCGA-AG-A036 
       25.02        32.02        14.04         1.02        41.00       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CL-5918 
       38.56         2.50        43.20        27.55        13.78         7.17 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       25.05        31.00        31.00        10.98        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6507 
       25.05        12.62        41.36        24.13        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       13.64         9.96        49.51        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        38.14        11.87        12.46        47.08 

$subtype2
TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AZ-6608 
        0.92        14.93        38.04        21.99        39.06         1.94 
TCGA-G4-6321 TCGA-AG-A015 TCGA-AG-A023 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       22.09        36.03        51.98         4.80        12.66         9.53 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6650 
       42.90        42.28        22.09        22.06        32.71        20.61 
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
       23.87        20.12        63.98        38.99         9.07        29.00 
TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3681 TCGA-AA-3831 TCGA-AA-3848 TCGA-AA-3854 
       33.99        20.98         5.98        17.98        10.06        36.03 
TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F 
       27.02         2.01         7.96        13.94        30.02        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       10.98        32.02        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        26.01        51.98         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6899 
        5.03         0.92        39.98        40.96        83.24         5.79 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       26.47        33.01        17.26        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94        22.36        65.00        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-5914 
       29.56        11.74        12.69        12.39        12.59        21.99 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5864 TCGA-CM-6166 
       82.95       124.27        20.02        37.02        15.02        21.99 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       14.04        13.05        10.06        12.03        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 TCGA-D5-6923 
       18.25        15.12         4.80        17.13        12.39        12.43 
TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00       119.70        38.20        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      140.38         7.50        44.32       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6806 
      119.93        35.97        60.79        95.18        11.11        41.42 
TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       61.91        46.75        18.18        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-5654 
       31.30        21.90        38.70        60.13        11.90        16.83 
TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3598 
       24.59        20.05        24.00         1.02        34.03        50.04 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6549 TCGA-AH-6897 
        1.02         1.94        38.96        61.97        17.49        26.43 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       21.01        26.04        13.97        51.98        44.02       126.44 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6813 
       17.69         8.61        10.78        17.46        19.66 

$subtype3
TCGA-AA-3506 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3697 
       58.03        19.07        34.03        19.99        19.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3972 TCGA-G4-6294 TCGA-AG-3612 TCGA-AG-4008 
       19.04        19.04        50.99        28.21        19.99        17.03 
TCGA-G5-6641 TCGA-A6-2672 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3809 
       26.43        46.65        35.11        16.57        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3492 
       36.53        23.61        29.16         8.38         7.04         3.02 
TCGA-AA-3511 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3696 
        6.97        13.94        61.02        54.02        47.01         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3947 
       26.99        10.06         0.00         0.99        53.00        33.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
       20.98        21.99        16.08        13.05        34.06        27.02 
TCGA-AZ-5407 TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       88.21        12.36        12.20        29.06        22.03        22.98 
TCGA-CM-6161 TCGA-CM-6172 TCGA-CM-6676 TCGA-F4-6460 TCGA-G4-6295 TCGA-G4-6297 
       15.02        11.01        11.08        31.96         8.35        82.39 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-AF-2689 TCGA-AF-6136 TCGA-AF-A56N 
       85.48        26.43        26.04        39.48        24.36        11.84 
TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
       36.03        36.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99        19.99        20.98         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 
        0.99        19.04        17.95         1.02        36.03         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-EI-6510 TCGA-F5-6810 
        3.98        46.03        18.28         0.39 

subtype1 subtype2 subtype3 
    0.00     0.92     0.00 
subtype1 subtype2 subtype3 
  135.65   140.38    88.21 
subtype1 subtype2 subtype3 
  20.550   22.360   20.485 
[1] "0.0 - 135.7 (20.6)" "0.9 - 140.4 (22.4)" "0.0 - 88.2 (20.5)" 
D6V2, continuous
D6V3, binary
          cls
clus         0   1
  subtype1 175  61
  subtype2 127  40
  subtype3  56  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  175   61
  subtype2  127   40
  subtype3   56   30
        clus
vv       subtype1 subtype2 subtype3
  COLON       175      127       56
  RECTUM       61       40       30
[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        1        6        84         3         0         4
  subtype2      28        0        9        47         5         1        12
  subtype3      11        0       13        16         2         0         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          5         35         23       16        13         1
  subtype2          6         20         16       15         5         1
  subtype3          2         14          4       15         1         0
D6V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          36       28       11
  STAGE IA          1        0        0
  STAGE II          6        9       13
  STAGE IIA        84       47       16
  STAGE IIB         3        5        2
  STAGE IIC         0        1        0
  STAGE III         4       12        6
  STAGE IIIA        5        6        2
  STAGE IIIB       35       20       14
  STAGE IIIC       23       16        4
  STAGE IV         16       15       15
  STAGE IVA        13        5        1
  STAGE IVB         1        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   5  35 168  26
  subtype2   3  33 108  23
  subtype3   3  13  62   7
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        3        3
  T2       35       33       13
  T3      168      108       62
  T4       26       23        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 137  54  43
  subtype2  92  41  33
  subtype3  45  27  13
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      137       92       45
  N1       54       41       27
  N2       43       33       13
[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 180  31
  subtype2 125  20
  subtype3  63  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  180   31
  subtype2  125   20
  subtype3   63   16
   clus
vv  subtype1 subtype2 subtype3
  0      180      125       63
  1       31       20       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1 111 125
  subtype2  78  89
  subtype3  45  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111  125
  subtype2   78   89
  subtype3   45   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      111       78       45
  MALE        125       89       41
[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"
D6V9, binary
          cls
clus         0   1
  subtype1 195  10
  subtype2 126   5
  subtype3  65   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  195   10
  subtype2  126    5
  subtype3   65    8
     clus
vv    subtype1 subtype2 subtype3
  NO       195      126       65
  YES       10        5        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  147                            27
  subtype2                  114                            11
  subtype3                   52                             4
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    57                              4
  subtype2                    35                              4
  subtype3                    26                              2
D6V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                147      114       52
  COLON MUCINOUS ADENOCARCINOMA        27       11        4
  RECTAL ADENOCARCINOMA                57       35       26
  RECTAL MUCINOUS ADENOCARCINOMA        4        4        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 192   1   4   7
  subtype2 108   2  13  10
  subtype3  65   0  12   2
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      192      108       65
  R1        1        2        0
  R2        4       13       12
  RX        7       10        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"
D6V12, continuous
D6V13, binary
          cls
clus         0   1
  subtype1   0 173
  subtype2   1  96
  subtype3   1  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  173
  subtype2    1   96
  subtype3    1   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        1
  NOT HISPANIC OR LATINO      173       96       30
[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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 113  40
  subtype2 109  19
  subtype3  95  35
  subtype4 157  34
subtype1 subtype2 subtype3 subtype4 
     153      128      130      191 
subtype1 subtype2 subtype3 subtype4 
      40       19       35       34 
$subtype1
TCGA-A6-2677 TCGA-AA-3697 TCGA-AA-A00L TCGA-AD-6888 TCGA-AZ-6608 TCGA-CK-5912 
       24.33        85.05        38.04        15.52         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-AG-A00H TCGA-AG-A01N 
        5.88        28.21        63.62        17.85        25.97        31.00 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-5656 TCGA-A6-5659 
       15.62         4.80         1.61        39.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 
       29.19        23.61        32.71        29.16        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-A567 TCGA-AA-3494 TCGA-AA-3509 TCGA-AA-3511 
       20.61        24.69        61.84         1.02        62.96         6.97 
TCGA-AA-3517 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3955 
       38.99        19.07        29.00        26.01        78.08        20.98 
TCGA-AA-3973 TCGA-AA-A00O TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       13.05        27.02        26.01        39.98         5.03        14.01 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       41.00        24.53        27.42        26.47        16.44        14.50 
TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 
       18.84        22.36        62.79        29.56        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5862 
       12.59        12.20        21.99        25.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        29.03        21.99 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-5541 
       15.02        11.08        11.01        45.40        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
       18.25        25.48         4.80        17.13        14.30        13.41 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        13.32        12.59       140.38        44.32 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6854 TCGA-G4-6303 
      117.07         8.61        31.96        33.67         0.53        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       55.04        61.91        36.00        46.75        18.18        10.98 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-3911 
       42.77         8.42        38.70        60.13        11.90        37.74 
TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3592 TCGA-AG-3593 
       16.83        86.63        11.84        36.03        34.03        34.03 
TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6549 
        0.99        46.03         1.94        38.96        38.04        17.49 
TCGA-AH-6897 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       26.43        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6509 
       57.24        51.48        32.61         3.48        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6810 
       15.85        16.34        16.31        11.51        11.97         0.39 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

$subtype2
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 
       14.53        24.16        58.03        37.05         8.05        23.01 
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-A024 TCGA-AZ-4313 TCGA-G4-6321 TCGA-G4-6586 
        6.05        19.04        39.06        75.95        22.09        35.80 
TCGA-G4-6588 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4T-AA8H TCGA-A6-5661 
       26.17        18.28        55.76        26.43        12.66        33.53 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-A565 
       22.06        27.09         8.38        24.39        20.12        16.24 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3675 
        3.02        37.05        35.01        61.02         6.97        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       11.01         5.98        37.05        33.07        36.03        32.05 
TCGA-AA-3861 TCGA-AA-A01Z TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 TCGA-AY-5543 
       30.05        37.02        39.98        18.05        83.24        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       21.44        17.82        17.26        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.65        65.00        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 
       11.74        12.69        12.36        12.39        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       15.62        51.32        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6171 TCGA-CM-6172 
       37.02        27.02        15.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6539 
       13.05        12.03        19.59        20.42        15.12        12.49 
TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
       12.39        12.00       119.70        92.75        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6806 
      135.65         7.76        14.04        98.24        95.18        41.42 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6320 
       35.31       133.18        53.62        44.68        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX 
       26.04        13.78        15.65        12.79        29.46        32.98 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       31.30        21.90        37.97        29.98        24.36        24.59 
TCGA-AG-3591 TCGA-AG-3599 TCGA-AG-3725 TCGA-AG-3732 TCGA-AG-3902 TCGA-AG-A008 
       34.03        12.03        20.98        32.98        32.02        13.94 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       61.97        38.56         2.50        19.46         6.05        33.17 
TCGA-CI-6624 TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       48.20        44.02        20.55        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6884 
        8.61        10.78 

$subtype3
TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3870 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       13.94         1.02        29.98        21.37        25.08        10.88 
TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6628 TCGA-BM-6198 
      100.01        23.51        35.93        91.79        79.69        21.24 
TCGA-5M-AAT6 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
        9.53        43.76        43.43        37.05        37.25        37.02 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 
       33.34        36.53        31.63        22.09        22.52        25.08 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B 
       21.76        23.87        19.66        20.28        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6901 
        9.63         7.04        38.07        12.16         5.79        22.42 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4615 
        0.46         0.92        27.09         0.20         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        5.13         5.23         3.19        12.76        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-5349 
      148.01        70.16        21.14         2.01        22.98        30.08 
TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       32.02        12.00        16.04        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 
       12.95        11.08        10.06        54.61        20.19        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        17.85        16.14        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       12.43         9.04         9.44        11.64        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1HA TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       10.26        24.43       131.51        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87         1.55        34.42        43.04        13.25 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6311 
       47.41         8.35        82.39        74.56        67.30        39.42 
TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-WS-AB45 
       74.79        19.33        19.33         9.93        16.80        70.03 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3731 TCGA-AG-3901 
       46.92        17.23        20.02        65.98        37.02        25.02 
TCGA-AG-4021 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 
        3.98        43.20        27.55        31.00        10.98        12.62 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6885 TCGA-EI-6917 
      129.27        24.13         4.18        19.96        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        49.51        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6864 
       36.49        19.66        37.18        12.46 

$subtype4
TCGA-A6-2681 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 
       45.60        13.02        24.03        36.03        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
        0.99        13.02        17.95        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3862 
       19.00        36.00        19.04        14.93        31.07        30.05 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AZ-4681 TCGA-AF-3913 TCGA-AG-3580 
       24.00        19.07        21.99       106.75        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
       13.94        19.99        17.03        17.03        15.95        36.03 
TCGA-AG-A023 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       51.98        43.76        46.65        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-AA-3488 
       35.11        16.57        34.65        32.75        32.45         5.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 
       63.98         1.02         1.02         9.07         0.00        29.00 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       13.94        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       15.02         5.03        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.00         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 
       34.03         2.01        21.99        36.03        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03J 
       51.98         2.96         2.01         0.92        22.03        40.96 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
       16.31         0.95       109.28        26.04         8.02        13.02 
TCGA-CM-5341 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
       29.06        43.04        13.55        34.49        12.00        32.02 
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-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        7.99         0.99        29.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        1.02        20.98         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02X TCGA-AG-A036 
        1.02         1.02        49.97        41.00       117.11 

subtype1 subtype2 subtype3 subtype4 
    0.39     2.50     0.20     0.00 
subtype1 subtype2 subtype3 subtype4 
  140.38   135.65   148.01   117.11 
subtype1 subtype2 subtype3 subtype4 
  25.180   23.605   20.710   19.990 
[1] "0.4 - 140.4 (25.2)" "2.5 - 135.7 (23.6)" "0.2 - 148.0 (20.7)"
[4] "0.0 - 117.1 (20.0)"
D7V2, continuous
D7V3, binary
          cls
clus         0   1
  subtype1 108  49
  subtype2 102  25
  subtype3 103  29
  subtype4 141  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108   49
  subtype2  102   25
  subtype3  103   29
  subtype4  141   60
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       108      102      103      141
  RECTUM       49       25       29       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        8        39         3         2         2
  subtype2      28        1        9        35         1         0         6
  subtype3      13        0        5        46         2         0         3
  subtype4      40        0       16        57         6         0        14
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         27         12       16        13         0
  subtype2          4         18          7        7         5         2
  subtype3          3         18         18       15         5         0
  subtype4          5         21         18       24         1         0
D7V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          23       28       13       40
  STAGE IA          0        1        0        0
  STAGE II          8        9        5       16
  STAGE IIA        39       35       46       57
  STAGE IIB         3        1        2        6
  STAGE IIC         2        0        0        0
  STAGE III         2        6        3       14
  STAGE IIIA        3        4        3        5
  STAGE IIIB       27       18       18       21
  STAGE IIIC       12        7       18       18
  STAGE IV         16        7       15       24
  STAGE IVA        13        5        5        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  26 104  19
  subtype2   3  29  84  12
  subtype3   1  13  95  23
  subtype4  10  37 140  16
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        6        3        1       10
  T2       26       29       13       37
  T3      104       84       95      140
  T4       19       12       23       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  85  45  24
  subtype2  79  32  18
  subtype3  67  30  34
  subtype4 121  43  39
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       85       79       67      121
  N1       45       32       30       43
  N2       24       18       34       39
[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 103  29
  subtype2  89  13
  subtype3  93  20
  subtype4 175  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  103   29
  subtype2   89   13
  subtype3   93   20
  subtype4  175   25
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      103       89       93      175
  1       29       13       20       25
[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  69  88
  subtype2  62  67
  subtype3  56  76
  subtype4 103 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   88
  subtype2   62   67
  subtype3   56   76
  subtype4  103  100
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       69       62       56      103
  MALE         88       67       76      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"
D7V9, binary
          cls
clus         0   1
  subtype1 117  10
  subtype2 110   5
  subtype3 116   3
  subtype4 146  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  117   10
  subtype2  110    5
  subtype3  116    3
  subtype4  146   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       117      110      116      146
  YES       10        5        3       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  104                             2
  subtype2                   80                            20
  subtype3                   84                            19
  subtype4                  120                            21
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    49                              0
  subtype2                    20                              4
  subtype3                    26                              3
  subtype4                    52                              6
D7V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                104       80       84      120
  COLON MUCINOUS ADENOCARCINOMA         2       20       19       21
  RECTAL ADENOCARCINOMA                49       20       26       52
  RECTAL MUCINOUS ADENOCARCINOMA        0        4        3        6
[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        R0  R1  R2  RX
  subtype1  98   2   8  10
  subtype2  84   2   3   9
  subtype3  95   1   4  11
  subtype4 175   1  21   0
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       98       84       95      175
  R1        2        2        1        1
  R2        8        3        4       21
  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
D7V13, binary
          cls
clus         0   1
  subtype1   4 118
  subtype2   0  93
  subtype3   1 118
  subtype4   0  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  118
  subtype2    0   93
  subtype3    1  118
  subtype4    0   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        0        1        0
  NOT HISPANIC OR LATINO      118       93      118       23
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  58  22
  subtype2  68  16
  subtype3  45  17
  subtype4  49   8
  subtype5  67  23
  subtype6 108  20
  subtype7  79  22
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      80       84       62       57       90      128      101 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      22       16       17        8       23       20       22 
$subtype1
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-NH-A8F7 
        1.94        49.08         5.88        28.21        23.51        17.85 
TCGA-3L-AA1B TCGA-5M-AATE TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 
       15.62        39.45        32.91        29.19        22.09        32.71 
TCGA-A6-6652 TCGA-A6-A5ZU TCGA-AA-3675 TCGA-AA-A02K TCGA-AD-6965 TCGA-AD-A5EK 
       24.69         9.63        47.05        14.01        26.47        16.44 
TCGA-AU-3779 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CM-5862 
       14.50        12.46        12.59        12.20       148.01         5.03 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       15.02        15.02        21.99        11.08        11.01        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 
       54.61        56.09        18.25        25.48        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 
       17.13        13.41        11.38        38.20       130.65        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      140.38        44.32       131.51       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 TCGA-F4-6808 TCGA-F4-6855 
      119.93        60.79       117.07        35.74        33.67        47.41 
TCGA-G4-6307 TCGA-G4-6317 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-5654 TCGA-AF-A56N 
       55.04        36.00        38.70        60.13        16.83        11.84 
TCGA-AG-3742 TCGA-AG-4021 TCGA-AG-A002 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6897 
        0.99         3.98        20.98        17.49        43.20        26.43 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.17        31.00        12.00        51.98       126.44        41.36 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       51.48        32.61         3.48        17.00        15.85        16.34 
TCGA-F5-6811 TCGA-F5-6861 
       32.19        38.14 

$subtype2
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3662 TCGA-AD-6888 
       13.94        14.53         1.02        58.03         6.05        15.52 
TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-6141 TCGA-A6-6650 
       26.43         4.80        12.66         1.61         8.38        20.61 
TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3502 TCGA-AA-3509 TCGA-AA-3526 TCGA-AA-3655 
       20.12        24.92        35.01        62.96        19.07        61.02 
TCGA-AA-3660 TCGA-AA-A01Z TCGA-AA-A02Y TCGA-AD-6890 TCGA-AD-6963 TCGA-AY-5543 
       78.08        37.02        39.98        24.53        27.42        33.01 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-5407 
       17.82        17.26        17.85        19.33        58.39        88.21 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-5860 
        6.77        11.74        21.99        82.95       124.27        32.02 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6172 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6529 
       15.02        12.00        11.01        12.03        19.59        20.19 
TCGA-D5-6535 TCGA-D5-6541 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       15.12        15.58       119.70        92.75        49.91        13.32 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6806 
        7.76        14.04        35.97        95.18        11.11        41.42 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6320 TCGA-G4-6322 
      133.18         8.35        53.62        44.68        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GB 
       13.78        46.75        18.18        10.98        19.33        15.65 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.79        42.77        29.46        32.98        31.30        21.90 
TCGA-T9-A92H TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-CI-6620 TCGA-CI-6623 
       11.90        24.59        34.03        34.03        33.17        47.44 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-7004 
       25.05        26.04        13.97        18.28        17.69         8.45 

$subtype3
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 
       25.08        10.88        75.95       100.01        35.80        26.17 
TCGA-G4-6628 TCGA-BM-6198 TCGA-5M-AAT6 TCGA-A6-2686 TCGA-A6-5661 TCGA-A6-5665 
       79.69        21.24         9.53        37.02        33.53        22.06 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-A01P TCGA-AD-5900 
       24.39        19.66         3.02         6.97        38.07        12.16 
TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4614 
       83.24         0.92        27.09         0.20        21.44         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6718 
       32.94         5.13        49.41        12.69        12.36        10.06 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4744 
       70.16        15.62        51.32        21.14        23.05        20.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6540 
       15.02        14.04        12.95        13.05        20.42        16.14 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1DA 
        9.44        11.64        13.35        10.26        24.43         7.50 
TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 
      135.65        98.24        35.74         6.18        47.87        35.31 
TCGA-G4-6299 TCGA-G4-6309 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-WS-AB45 TCGA-EI-6507 
       74.56        85.48        19.33         9.93        70.03        19.96 
TCGA-EI-6882 TCGA-EI-6917 
        8.61        17.46 

$subtype4
TCGA-A6-6649 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6548 TCGA-G4-6321 TCGA-G4-6625 
       24.16        85.05        19.04        21.37        22.09        91.79 
TCGA-G5-6233 TCGA-G5-6235 TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 
       18.28        55.76        43.43        27.09        24.13        25.18 
TCGA-A6-A565 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3685 TCGA-AY-A8YK TCGA-AZ-4682 
       16.24        37.05         6.97        37.05        18.84        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CA-5796 TCGA-CK-4947 
       65.00        62.79        12.10         5.23        12.39        17.56 
TCGA-CK-4950 TCGA-CM-4751 TCGA-CM-6163 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6931 
       85.45        27.02        14.04        12.49        12.39        12.00 
TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6627 TCGA-AF-2693 TCGA-AF-3911 
       82.39        39.42        61.91        74.79        37.97        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3732 
       29.98        24.36        20.02        20.98        37.02        32.98 
TCGA-AG-3902 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 
       32.02        38.56         2.50        19.46         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6158 TCGA-DC-6160 TCGA-EI-6506 
       44.78        48.20        21.01        10.98        44.02        20.55 
TCGA-EI-6508 TCGA-EI-6881 TCGA-EI-6884 
       20.91        16.41        10.78 

$subtype5
TCGA-G4-6310 TCGA-G4-6314 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 
       63.62        35.93        37.05        37.25        31.63        30.44 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 
       23.61        29.16        22.52        25.08        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-A01X TCGA-AD-6899 
       20.28        61.84        56.25         7.04        26.01         5.79 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-4323 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
       22.42         0.46         1.41        29.56         3.19        12.59 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 
       12.76        14.30         2.01        25.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       30.08        17.03        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6531 
       13.02        15.02        11.08        10.06        55.92        17.75 
TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       43.27         7.53        10.13        12.43        14.30         9.04 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        8.61        31.96         1.55        34.42        43.04        13.25 
TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6303 TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-AF-2687 
        0.53        67.30        65.85        16.80         8.42        46.92 
TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-4022 TCGA-AH-6644 TCGA-CL-5917 
       17.23        86.63        65.98        46.03        27.55        78.12 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD 
       31.00        25.97        25.05        25.05        12.62        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 
      129.27        24.13         4.18        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        49.51        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        37.18        11.87        12.46        47.08 

$subtype6
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        36.03        34.03        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-4681 TCGA-AF-3913 TCGA-AG-3580 
       19.07        38.04        21.99       106.75        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       19.99        17.03        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       51.98        43.76        44.91        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       36.53         5.03         1.02         1.02        38.99         9.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3549 
        0.00        29.00        29.00        26.01        12.99        21.01 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3812 
       24.00        13.94        14.01        47.01        15.02        35.05 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 
       25.02        17.98        38.99        36.95        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3875 
        0.00        32.05         0.99        31.07        17.03        18.05 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03        21.99        36.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00K 
       34.06        27.02         7.96        13.94        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       27.02        42.02        14.99        15.02        15.02        32.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
        1.02        33.04        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-CM-4748 TCGA-CM-4750 
       40.96        16.31         0.95       109.28        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       13.02        29.06        36.03         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        1.02        46.03        34.03         0.99        15.95        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-3885 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       17.95        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A00Y 
       28.04        36.03        14.04         1.02         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

$subtype7
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       13.02        24.03        37.05         8.05        19.07         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3692 
       13.02        17.95        23.01        19.99         0.92        36.00 
TCGA-AA-3715 TCGA-AA-3862 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3979 
       19.04        30.05        29.98        12.99        24.00        24.00 
TCGA-AA-A024 TCGA-AG-3611 TCGA-AG-A015 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       39.06        13.94        36.03        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4107 TCGA-AA-3510 TCGA-AA-3518 
       42.28        33.34        32.75        32.45        63.98         1.02 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       14.01        33.99        29.95        54.02         2.01        50.04 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 
       11.01         5.98         5.03        26.99        10.06        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 
        0.99         1.02        15.95        37.02         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 
        0.00        36.03        30.05        53.00        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
        2.01        24.00        33.01        26.01         2.01        25.02 
TCGA-AA-3980 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        27.02        38.04        19.00        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
        4.01         0.99        17.03        34.98        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 
       31.00        31.00         1.02        35.01         1.02        51.98 
TCGA-AA-A02E TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-CM-4746 TCGA-AF-2691 
        2.96         0.92        22.03        18.05        37.02        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3594 
       13.55        34.49        12.00        32.02        20.05         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 
       50.04        12.03         6.05        19.04        36.95        13.02 
TCGA-AG-3901 TCGA-AG-A008 TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
       25.02        13.94         1.02        61.97        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.99     1.02     0.20     2.50     0.39     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  148.01   133.18   135.65    91.79   129.27   117.11    63.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  25.955   21.255   20.220   24.130   22.470   20.995   24.000 
[1] "1.0 - 148.0 (26.0)" "1.0 - 133.2 (21.3)" "0.2 - 135.7 (20.2)"
[4] "2.5 - 91.8 (24.1)"  "0.4 - 129.3 (22.5)" "0.0 - 117.1 (21.0)"
[7] "0.0 - 64.0 (24.0)" 
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 59 22
  subtype2 73 13
  subtype3 60  4
  subtype4 32 23
  subtype5 59 31
  subtype6 88 51
  subtype7 83 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   22
  subtype2   73   13
  subtype3   60    4
  subtype4   32   23
  subtype5   59   31
  subtype6   88   51
  subtype7   83   19
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COLON        59       73       60       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        26         2         1         1
  subtype2      15        1        6        23         1         0         3
  subtype3      13        0        4        28         1         0         1
  subtype4       8        0        4         8         1         0         3
  subtype5       7        0        3        25         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          2         11         10        5         5         0
  subtype2          3         14          5        5         3         1
  subtype3          1          5          6        2         1         1
  subtype4          3         12          3        6         5         0
  subtype5          1         17         11        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        4        3        7       13
  STAGE IIA        26       23       28        8       25       37       30
  STAGE IIB         2        1        1        1        1        1        5
  STAGE IIC         1        0        0        0        1        0        0
  STAGE III         1        3        1        3        1        8        8
  STAGE IIIA        2        3        1        3        1        4        1
  STAGE IIIB       11       14        5       12       17       16        9
  STAGE IIIC       10        5        6        3       11       14        6
  STAGE IV          5        5        2        6        9       25       10
  STAGE IVA         5        3        1        5        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 55 10
  subtype2  5 15 53 12
  subtype3  2 11 44  7
  subtype4  1  9 40  7
  subtype5  0  9 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       15       11        9        9       30       17
  T3       55       53       44       40       66       94       71
  T4       10       12        7        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 45 18 17
  subtype2 52 23 11
  subtype3 46  9  9
  subtype4 26 22  9
  subtype5 38 27 22
  subtype6 77 34 29
  subtype7 68 17 18
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       45       52       46       26       38       77       68
  N1       18       23        9       22       27       34       17
  N2       17       11        9        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  58  10
  subtype2  57   8
  subtype3  47   4
  subtype4  34  11
  subtype5  60  18
  subtype6 113  25
  subtype7  91  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   10
  subtype2   57    8
  subtype3   47    4
  subtype4   34   11
  subtype5   60   18
  subtype6  113   25
  subtype7   91   11
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       58       57       47       34       60      113       91
  1       10        8        4       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 38 43
  subtype2 41 45
  subtype3 29 35
  subtype4 18 39
  subtype5 43 47
  subtype6 68 72
  subtype7 53 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   43
  subtype2   41   45
  subtype3   29   35
  subtype4   18   39
  subtype5   43   47
  subtype6   68   72
  subtype7   53   50
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       38       41       29       18       43       68       53
  MALE         43       45       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"
D8V9, binary
          cls
clus        0  1
  subtype1 59  3
  subtype2 72  2
  subtype3 53  1
  subtype4 50  4
  subtype5 79  5
  subtype6 97 10
  subtype7 79  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    3
  subtype2   72    2
  subtype3   53    1
  subtype4   50    4
  subtype5   79    5
  subtype6   97   10
  subtype7   79    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        59       72       53       50       79       97       79
  YES        3        2        1        4        5       10        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   56                             2
  subtype2                   58                            14
  subtype3                   47                            12
  subtype4                   29                             3
  subtype5                   53                             6
  subtype6                   85                             3
  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
D8V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 56       58       47       29       53
  COLON MUCINOUS ADENOCARCINOMA         2       14       12        3        6
  RECTAL ADENOCARCINOMA                22       11        3       22       30
  RECTAL MUCINOUS ADENOCARCINOMA        0        2        1        1        1
                                clus
vv                               subtype6 subtype7
  COLON ADENOCARCINOMA                 85       60
  COLON MUCINOUS ADENOCARCINOMA         3       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"
          vv
clus        R0  R1  R2  RX
  subtype1  46   1   2   8
  subtype2  58   0   1   4
  subtype3  43   1   1   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       46       58       43       34       66      115       90
  R1        1        0        1        2        0        2        0
  R2        2        1        1        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
D8V13, binary
          cls
clus        0  1
  subtype1  1 72
  subtype2  2 67
  subtype3  1 59
  subtype4  0 45
  subtype5  1 81
  subtype6  0 17
  subtype7  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   72
  subtype2    2   67
  subtype3    1   59
  subtype4    0   45
  subtype5    1   81
  subtype6    0   17
  subtype7    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        1        0        1        0
  NOT HISPANIC OR LATINO       72       67       59       45       81       17
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       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"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 128  23
  subtype2  68  27
  subtype3  59  26
  subtype4 159  40
subtype1 subtype2 subtype3 subtype4 
     151       95       85      199 
subtype1 subtype2 subtype3 subtype4 
      23       27       26       40 
$subtype1
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6548 
       14.53         1.02         6.05        85.05        19.04        21.37 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        23.51        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-BM-6198 TCGA-A6-2675 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       79.69        21.24        43.43        30.44        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.09        22.06        32.71        25.08        25.18        20.61 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       61.02        78.08         6.97        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 
       33.01         0.20        21.44        17.82         5.13        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       49.41         6.77        12.10        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.39        12.59        12.59        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       23.05        27.02        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       29.03        16.04        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       13.05        11.08        12.03        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       20.19        20.42        17.75        18.25        25.48        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6923 TCGA-D5-6929 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       12.43        13.41        24.43         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        7.76        14.04        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 
       95.18        35.74         6.18        33.67        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 
      133.18         8.35        82.39        74.56        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        39.42        61.91        26.43        26.04        13.78 
TCGA-AF-5654 TCGA-AG-3591 TCGA-AG-3732 TCGA-AG-3742 TCGA-AH-6549 TCGA-CI-6619 
       16.83        34.03        32.98         0.99        17.49         6.05 
TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       33.17        78.12         7.17        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 TCGA-EF-5831 
       31.00        51.98        10.98        44.02         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-F5-6465 
       20.55        20.91        18.28        17.69        16.34        49.51 
TCGA-F5-6811 
       32.19 

$subtype2
TCGA-A6-2681 TCGA-A6-6649 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6310 
       45.60        24.16        25.08        10.88       100.01        63.62 
TCGA-G4-6314 TCGA-AG-A015 TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 
       35.93        36.03        43.76        37.05        37.25        32.91 
TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 
       31.63        23.61        29.16        22.52         8.38        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3514 
       24.69        23.87        19.66        20.28         7.04         1.02 
TCGA-AA-3818 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A00O TCGA-AA-A01X TCGA-AA-A02E 
        0.99        13.05        27.02        27.02        26.01         2.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        5.79        22.42         1.41        62.79        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-6748 
        3.19        12.20        12.76        10.06        14.30         2.01 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6167 
       25.02        26.04        17.03        14.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6898 
       12.99        12.95        10.06        19.59        43.27         7.53 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       10.13        14.30         9.04        11.64        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A1D6 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
       10.26        49.91         8.61        31.96        11.11        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6627 TCGA-AF-2687 TCGA-AF-2690 
        0.53        67.30        65.85        74.79        46.92        17.23 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3901 TCGA-AH-6547 
       37.74        29.98        29.98        37.02        25.02         2.50 
TCGA-AH-6644 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 
       27.55        25.97        12.62       129.27        16.31         9.96 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
       28.57         0.39        36.49        19.66        47.08 

$subtype3
TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6294 TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-4008 
       15.52         1.94        28.21        10.39        19.99        17.03 
TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-A6-3807 TCGA-A6-4107 
       31.00        18.28        55.76        26.43        34.65        32.45 
TCGA-A6-6137 TCGA-A6-6140 TCGA-AA-3488 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3968 
       27.09        24.13         5.03        62.96         6.97        21.99 
TCGA-AA-3975 TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       34.06        14.99        32.02         1.02        33.04        37.02 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4682 TCGA-CM-4750 
       39.98         2.01         0.95       109.28        22.36         8.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.08        11.01        45.40       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 
       92.75        13.32        12.59       140.38        44.32       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6626 
       26.47        81.37       119.93        44.68        36.00        46.75 
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3592 TCGA-AG-3725 
       37.97        24.36        20.02        24.59        34.03        20.98 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       36.95        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A026 TCGA-AG-A02X 
       28.04        36.03         3.98        46.03         1.94        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       38.56        43.20        13.78        44.78        47.44        48.20 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       21.01        25.05        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6509 TCGA-EI-6511 
       57.24        24.13        51.48        32.61        17.00        15.85 
TCGA-F5-6571 
       42.35 

$subtype4
TCGA-A6-2677 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        13.94        58.03        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3867 
       36.00        19.04        14.93        31.07        30.05        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AZ-4313 TCGA-AZ-4681 
       24.00        19.07        38.04        39.06        75.95       106.75 
TCGA-G4-6588 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-A6-2672 TCGA-A6-2674 
       26.17         8.02        13.94        17.03        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 
       42.90        42.28        44.91        35.11        16.57        37.02 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       33.34        32.75        36.53        24.39        20.12         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 
        1.02        37.05        35.01        63.98        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
        5.03        26.99        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3970 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        36.03        16.08 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00J 
       25.02        27.02        27.02         7.96        19.00        18.05 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01P 
       42.02        17.03        34.98        10.98        12.00        38.07 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       35.01         1.02        51.98         5.03        14.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AZ-4315 
       22.03        39.98        18.05        40.96        16.31        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-4951 TCGA-CM-4744 
        5.65        32.94        65.00        12.46        70.16        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6931 
       37.02        13.02        29.06        12.39         9.44        12.00 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 
       39.48        43.04        13.55        34.49        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3898 
       19.04        19.99         1.02        17.95        13.02        48.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
       14.04         1.02        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A036 
        9.07         1.02        49.97        38.96        61.97       117.11 
TCGA-EI-6507 
       19.96 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.39     0.95     0.00 
subtype1 subtype2 subtype3 subtype4 
  148.01   129.27   140.38   117.11 
subtype1 subtype2 subtype3 subtype4 
   21.99    22.42    31.00    21.01 
[1] "0.2 - 148.0 (22.0)" "0.4 - 129.3 (22.4)" "0.9 - 140.4 (31.0)"
[4] "0.0 - 117.1 (21.0)"
D9V2, continuous
D9V3, binary
          cls
clus         0   1
  subtype1 127  27
  subtype2  75  19
  subtype3  41  44
  subtype4 162  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127   27
  subtype2   75   19
  subtype3   41   44
  subtype4  162   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       127       75       41      162
  RECTUM       27       19       44       50
[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      27        1        7        45         2         1         6
  subtype2      11        0        4        25         1         0         1
  subtype3      11        0        5        22         1         0         3
  subtype4      45        0       21        60         6         0        15
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          1         28         11       10         7         1
  subtype2          2         15         12        9         8         0
  subtype3          5         16          8        9         3         0
  subtype4          3         14         16       29         3         0
D9V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          27       11       11       45
  STAGE IA          1        0        0        0
  STAGE II          7        4        5       21
  STAGE IIA        45       25       22       60
  STAGE IIB         2        1        1        6
  STAGE IIC         1        0        0        0
  STAGE III         6        1        3       15
  STAGE IIIA        1        2        5        3
  STAGE IIIB       28       15       16       14
  STAGE IIIC       11       12        8       16
  STAGE IV         10        9        9       29
  STAGE IVA         7        8        3        3
  STAGE IVB         1        0        0        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   6  25 108  14
  subtype2   2  11  64  16
  subtype3   5  13  63   6
  subtype4   7  45 141  20
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        6        2        5        7
  T2       25       11       13       45
  T3      108       64       63      141
  T4       14       16        6       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"
          vv
clus        N0  N1  N2
  subtype1  90  41  22
  subtype2  44  28  20
  subtype3  41  31  15
  subtype4 136  34  43
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       90       44       41      136
  N1       41       28       31       34
  N2       22       20       15       43
[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"
D9V7, binary
          cls
clus         0   1
  subtype1 108  18
  subtype2  63  16
  subtype3  65  12
  subtype4 177  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108   18
  subtype2   63   16
  subtype3   65   12
  subtype4  177   32
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      108       63       65      177
  1       18       16       12       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"
D9V8, binary
          cls
clus         0   1
  subtype1  76  78
  subtype2  39  56
  subtype3  40  47
  subtype4 102 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76   78
  subtype2   39   56
  subtype3   40   47
  subtype4  102  111
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       76       39       40      102
  MALE         78       56       47      111
[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"
D9V9, binary
          cls
clus         0   1
  subtype1 128   3
  subtype2  84   5
  subtype3  51   7
  subtype4 164  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  128    3
  subtype2   84    5
  subtype3   51    7
  subtype4  164   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       128       84       51      164
  YES        3        5        7       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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  110                            16
  subtype2                   61                            14
  subtype3                   39                             0
  subtype4                  137                            24
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    27                              0
  subtype2                    17                              2
  subtype3                    42                              2
  subtype4                    41                              6
D9V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                110       61       39      137
  COLON MUCINOUS ADENOCARCINOMA        16       14        0       24
  RECTAL ADENOCARCINOMA                27       17       42       41
  RECTAL MUCINOUS ADENOCARCINOMA        0        2        2        6
[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        R0  R1  R2  RX
  subtype1 102   2   2  16
  subtype2  61   0   3   7
  subtype3  49   2   6   1
  subtype4 174   2  25   2
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      102       61       49      174
  R1        2        0        2        2
  R2        2        3        6       25
  RX       16        7        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, continuous
D9V13, binary
          cls
clus         0   1
  subtype1   2 137
  subtype2   0  79
  subtype3   0  54
  subtype4   0  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  137
  subtype2    0   79
  subtype3    0   54
  subtype4    0   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        0        0        0
  NOT HISPANIC OR LATINO      137       79       54       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"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 42  7
  subtype2 56 17
  subtype3 23  6
  subtype4 62 23
  subtype5 54 22
  subtype6 44  8
  subtype7 38 19
  subtype8 23  5
  subtype9 72  9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      49       73       29       85       76       52       57       28 
subtype9 
      81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       7       17        6       23       22        8       19        5 
subtype9 
       9 
$subtype1
TCGA-A6-4105 TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6321 TCGA-A6-2675 TCGA-A6-5665 
       14.53        85.05        19.04        22.09        43.43        22.06 
TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3655 TCGA-AD-6890 TCGA-AD-6901 
        8.38        20.28         7.04        61.02        24.53        22.42 
TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-CA-5796 TCGA-CK-4947 
       14.50         0.20        21.44        17.82        12.39        17.56 
TCGA-CK-4950 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 
       85.45        82.95       124.27        27.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 TCGA-D5-6529 
       32.02        15.02        14.04        16.04        15.02        20.19 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       18.25        15.12         4.80        12.49        15.58        12.39 
TCGA-D5-6923 TCGA-DM-A28A TCGA-DM-A28M TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6311 
       12.43        26.47        95.18        47.41        82.39        39.42 
TCGA-G4-6320 TCGA-AG-3732 TCGA-DC-6158 TCGA-DC-6160 TCGA-EI-6509 TCGA-F5-6811 
       26.43        32.98        10.98        44.02        17.00        32.19 
TCGA-G5-6572 
       47.08 

$subtype2
TCGA-A6-6649 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6310 TCGA-A6-5656 TCGA-A6-5657 
       24.16        25.08       100.01        63.62        32.91        31.63 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6654 TCGA-A6-6781 TCGA-AD-5900 
       23.61        29.16        22.52        23.87        19.66        12.16 
TCGA-AD-6899 TCGA-AM-5820 TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        5.79         0.46        27.09        62.79        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.19        12.69        12.36        12.76        10.06        14.30 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6167 
       21.14         2.01        15.02        17.03        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6534 
       12.99        12.95        10.06        19.59        17.75        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-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6703 
       13.35        10.26         8.61        11.11        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6302 
        1.55        34.42        13.25         0.53        35.31        67.30 
TCGA-G4-6303 TCGA-G4-6627 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 
       65.85        74.79        17.23        37.74        29.98        46.03 
TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF 
       27.55        21.01        25.97        25.05        12.62        24.13 
TCGA-EF-5831 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 
        4.18        16.31         9.96        49.51        42.35        36.49 
TCGA-F5-6813 
       19.66 

$subtype3
TCGA-CK-5912 TCGA-A6-5659 TCGA-A6-6137 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3660 
       49.08        30.44        27.09        35.01         1.02        78.08 
TCGA-AA-3861 TCGA-AA-A010 TCGA-AA-A02H TCGA-AZ-5407 TCGA-AZ-6606 TCGA-CM-5864 
       30.05        34.98         2.01        88.21        11.74        15.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28K 
       13.02        11.01       119.70        24.43        44.32        98.24 
TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6322 TCGA-AG-3594 TCGA-AG-3726 
       33.67       133.18        53.62        26.04         2.01         7.99 
TCGA-AG-3742 TCGA-AG-3892 TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 
        0.99        13.02         7.17        31.00        51.98 

$subtype4
TCGA-A6-2677 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3556 TCGA-AA-3562 
       24.33        13.94         1.02        58.03        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3867 TCGA-AD-6548 TCGA-AD-6964 TCGA-DM-A285 
        6.05        36.00        24.03        21.37        10.88         5.88 
TCGA-G5-6641 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5666 
       26.43        43.76        42.28        32.75        29.19        32.71 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3494 TCGA-AA-3514 TCGA-AA-3517 
       25.08        21.76        20.12         1.02         1.02        38.99 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 
        0.00        29.00        29.00        26.01        12.99        24.00 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3837 TCGA-AA-3852 TCGA-AA-A00D 
       11.01         5.03        35.05        38.99         0.00        19.00 
TCGA-AA-A02K TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-6599 
       14.01        26.47         0.92        16.31         1.41         6.77 
TCGA-CA-5797 TCGA-CK-4948 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6164 
       12.59       148.01        13.02        22.98         5.03        29.03 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28F 
       54.61        56.09        55.92       130.65       131.51        35.97 
TCGA-DM-A28H TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6307 TCGA-G4-6323 TCGA-AF-2687 
      117.07        43.04         8.35        55.04        13.78        46.92 
TCGA-AF-2689 TCGA-AF-5654 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3731 
       39.48        16.83        32.02        20.05        46.03        37.02 
TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A025 TCGA-AG-A036 
       35.01        36.03         3.98         6.02        49.97       117.11 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
       17.49        43.20         6.05        33.17        48.20        78.12 
TCGA-DC-6155 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6508 TCGA-EI-6513 TCGA-F5-6702 
       13.97        57.24       129.27        20.91        16.34        28.57 
TCGA-F5-6810 
        0.39 

$subtype5
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3552 
       13.02        37.05        36.03         8.05         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-4313 TCGA-G4-6588 
       17.95        19.99        19.04        24.00        75.95        26.17 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 
       46.65        42.90        16.57        33.53        24.39         3.02 
TCGA-AA-3495 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       37.05        19.07        14.01        33.99        21.01        29.95 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3710 
        6.97        54.02         2.01        47.05         5.98        26.99 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3854 TCGA-AA-3864 
       10.06        33.04         1.02         0.00        36.03        53.00 
TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J 
       27.02         2.01        33.01         2.01        25.02        18.05 
TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
       10.98        35.01        51.98        22.03        18.05        83.24 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        5.65        32.94        49.41        70.16        15.62        51.32 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6530 TCGA-D5-6540 
       23.05        20.02        37.02        14.04        20.42        16.14 
TCGA-D5-6931 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-F4-6570 TCGA-G4-6299 
       12.00         7.50       135.65         7.76         6.18        74.56 
TCGA-G4-6309 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A008 
       85.48        34.49        12.00        32.02        20.98        13.94 
TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-EI-6507 
        1.02        38.96        61.97        19.96 

$subtype6
TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       24.03        19.07        34.03        26.01        19.07        38.04 
TCGA-G4-6298 TCGA-G4-6314 TCGA-AG-3580 TCGA-A6-5664 TCGA-AA-3509 TCGA-AA-3519 
       23.51        35.93         8.02        22.09        62.96         9.07 
TCGA-AA-3561 TCGA-AA-3678 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3875 TCGA-AA-3989 
       13.94        47.01        25.02        17.98        18.05         7.96 
TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02J TCGA-CA-5256 
       17.03         1.02         1.02        26.01         5.03        12.46 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-6161 TCGA-CM-6166 
       12.59        12.20        21.99         8.02        15.02        21.99 
TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A282 
       25.48        17.13        14.30        13.41        38.20       139.17 
TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6315 TCGA-AF-2692 TCGA-AG-3574 
       60.79        31.96        35.74        61.91        13.55        36.03 
TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3894 TCGA-CI-6621 
       36.03        34.03         0.99         0.99        14.01        13.78 
TCGA-DC-5337 TCGA-DC-5869 TCGA-EF-5830 TCGA-EI-6506 
       26.04        31.00         3.48        20.55 

$subtype7
TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       15.52         1.94        28.21        35.80        91.79        79.69 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       21.24        18.28        55.76        24.13        25.18        20.61 
TCGA-A6-6652 TCGA-AA-3511 TCGA-AA-A02E TCGA-AD-6963 TCGA-AY-5543 TCGA-AZ-4616 
       24.69         6.97         2.96        27.42        33.01         5.13 
TCGA-AZ-6600 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.10        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       45.40        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-F4-6806 TCGA-G4-6306 TCGA-G4-6317 
       14.04        81.37       119.93        41.42        44.68        36.00 
TCGA-G4-6626 TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 
       46.75        37.97        24.36        20.02        24.59        34.03 
TCGA-AG-3592 TCGA-AG-3725 TCGA-AH-6544 TCGA-AH-6547 TCGA-CI-6622 TCGA-CI-6623 
       34.03        20.98        38.56         2.50        44.78        47.44 
TCGA-DC-4749 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 
       25.05        25.05       126.44        41.36        51.48        32.61 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       18.28        15.85        17.69 

$subtype8
TCGA-A6-2681 TCGA-AA-3672 TCGA-AA-3870 TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 
       45.60         0.92        29.98        43.76        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3818 TCGA-AA-3833 TCGA-AA-3842 
       37.02        33.34        36.53         0.99        15.95        37.02 
TCGA-AA-3850 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3973 
        0.00        17.03        31.00        26.01        34.03        13.05 
TCGA-AA-3994 TCGA-AA-A00O TCGA-AA-A01P TCGA-CM-4747 TCGA-CM-4748 TCGA-D5-6932 
       27.02        27.02        38.07        25.02        26.04        11.38 
TCGA-AF-2691 TCGA-AG-3881 TCGA-AG-3901 TCGA-AG-4005 
       43.04        19.04        25.02        14.04 

$subtype9
TCGA-AA-3688 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3952 
       19.00        14.93        31.07        30.05        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A024 TCGA-AZ-4681 TCGA-AF-3913 TCGA-AG-3611 
       50.99        24.00        39.06       106.75        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A015 TCGA-AG-A01N TCGA-A6-2679 
       19.99        17.03        17.03        36.03        31.00        44.91 
TCGA-A6-2680 TCGA-A6-3807 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3510 TCGA-AA-3558 
       35.11        34.65        32.45         5.03        63.98        20.98 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3846 TCGA-AA-3848 
       14.01        50.04        15.02        37.05        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3941 TCGA-AA-3955 
       33.07        32.05         0.99        31.07        24.00        20.98 
TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        36.03        16.08        34.06        27.02        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01Z 
       42.02        14.99        32.02        12.00        33.04        37.02 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AY-4071 TCGA-AZ-4308 
       39.98         0.92        39.98        40.96         0.95       109.28 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CM-5341 TCGA-AG-3581 TCGA-AG-3584 
       58.39        22.36        65.00        29.06         7.07        24.00 
TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        1.02        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       19.99        29.98        19.99         1.02        17.95        36.95 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-A011 
        1.02        48.03        19.99        28.04         1.02        37.02 
TCGA-AG-A016 TCGA-AG-A026 TCGA-AG-A02X 
        9.07         1.94        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.20     0.46     0.99     0.00     0.00     0.99     1.94     0.00 
subtype9 
    0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  124.27   100.01   133.18   148.01   135.65   139.17   140.38    45.60 
subtype9 
  109.28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   21.44    17.85    30.05    25.08    21.52    19.81    25.05    27.02 
subtype9 
   24.00 
[1] "0.2 - 124.3 (21.4)" "0.5 - 100.0 (17.9)" "1.0 - 133.2 (30.1)"
[4] "0.0 - 148.0 (25.1)" "0.0 - 135.7 (21.5)" "1.0 - 139.2 (19.8)"
[7] "1.9 - 140.4 (25.1)" "0.0 - 45.6 (27.0)"  "0.9 - 109.3 (24.0)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1 43  6
  subtype2 57 16
  subtype3 23  7
  subtype4 59 30
  subtype5 69  9
  subtype6 41 13
  subtype7 34 22
  subtype8 29  4
  subtype9 50 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    6
  subtype2   57   16
  subtype3   23    7
  subtype4   59   30
  subtype5   69    9
  subtype6   41   13
  subtype7   34   22
  subtype8   29    4
  subtype9   50   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COLON        43       57       23       59       69       41       34
  RECTUM        6       16        7       30        9       13       22
        clus
vv       subtype8 subtype9
  COLON        29       50
  RECTUM        4       33
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       7        0        3        18         1         0         3
  subtype2       9        0        4        25         0         0         0
  subtype3      10        0        1         9         2         0         2
  subtype4      12        1        3        18         1         1         2
  subtype5      16        0       12        20         3         0         7
  subtype6      10        0        3        15         1         0         5
  subtype7       6        0        1        18         1         0         1
  subtype8       5        0        1        12         0         0         2
  subtype9      19        0        9        17         1         0         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          0          8          3        2         0         0
  subtype2          2         12         10        4         6         0
  subtype3          0          3          0        2         1         0
  subtype4          2         13         13       16         4         0
  subtype5          0          6          8        4         1         0
  subtype6          2          8          2        7         0         0
  subtype7          3          7          2        5         5         1
  subtype8          1          4          1        6         1         0
  subtype9          1         12          8       11         3         0
D10V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           7        9       10       12       16       10        6
  STAGE IA          0        0        0        1        0        0        0
  STAGE II          3        4        1        3       12        3        1
  STAGE IIA        18       25        9       18       20       15       18
  STAGE IIB         1        0        2        1        3        1        1
  STAGE IIC         0        0        0        1        0        0        0
  STAGE III         3        0        2        2        7        5        1
  STAGE IIIA        0        2        0        2        0        2        3
  STAGE IIIB        8       12        3       13        6        8        7
  STAGE IIIC        3       10        0       13        8        2        2
  STAGE IV          2        4        2       16        4        7        5
  STAGE IVA         0        6        1        4        1        0        5
  STAGE IVB         0        0        0        0        0        0        1
            clus
vv           subtype8 subtype9
  STAGE I           5       19
  STAGE IA          0        0
  STAGE II          1        9
  STAGE IIA        12       17
  STAGE IIB         0        1
  STAGE IIC         0        0
  STAGE III         2        3
  STAGE IIIA        1        1
  STAGE IIIB        4       12
  STAGE IIIC        1        8
  STAGE IV          6       11
  STAGE IVA         1        3
  STAGE IVB         0        0
[1] 13  9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  7 37  2
  subtype2  1  9 52 12
  subtype3  4  6 16  4
  subtype4  2 12 63 10
  subtype5  1 17 50 10
  subtype6  4 10 37  4
  subtype7  1 10 41  5
  subtype8  2  4 22  5
  subtype9  3 19 58  4
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        2        1        4        2        1        4        1        2
  T2        7        9        6       12       17       10       10        4
  T3       37       52       16       63       50       37       41       22
  T4        2       12        4       10       10        4        5        5
    clus
vv   subtype9
  T1        3
  T2       19
  T3       58
  T4        4
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 33 11  4
  subtype2 38 20 15
  subtype3 22  4  4
  subtype4 37 24 26
  subtype5 53 11 14
  subtype6 31 18  6
  subtype7 31 17  9
  subtype8 18  9  6
  subtype9 48 20 16
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       33       38       22       37       53       31       31       18
  N1       11       20        4       24       11       18       17        9
  N2        4       15        4       26       14        6        9        6
    clus
vv   subtype9
  N0       48
  N1       20
  N2       16
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 33  2
  subtype2 55  9
  subtype3 24  3
  subtype4 60 20
  subtype5 69  5
  subtype6 43  7
  subtype7 35 11
  subtype8 26  7
  subtype9 68 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    2
  subtype2   55    9
  subtype3   24    3
  subtype4   60   20
  subtype5   69    5
  subtype6   43    7
  subtype7   35   11
  subtype8   26    7
  subtype9   68   14
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       33       55       24       60       69       43       35       26
  1        2        9        3       20        5        7       11        7
   clus
vv  subtype9
  0       68
  1       14
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1 20 29
  subtype2 33 41
  subtype3 14 16
  subtype4 44 45
  subtype5 40 38
  subtype6 28 27
  subtype7 24 33
  subtype8 19 14
  subtype9 35 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   29
  subtype2   33   41
  subtype3   14   16
  subtype4   44   45
  subtype5   40   38
  subtype6   28   27
  subtype7   24   33
  subtype8   19   14
  subtype9   35   49
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       20       33       14       44       40       28       24
  MALE         29       41       16       45       38       27       33
        clus
vv       subtype8 subtype9
  FEMALE       19       35
  MALE         14       49
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1 45  1
  subtype2 63  6
  subtype3 22  0
  subtype4 64  5
  subtype5 63  3
  subtype6 41  2
  subtype7 38  5
  subtype8 25  0
  subtype9 66  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    1
  subtype2   63    6
  subtype3   22    0
  subtype4   64    5
  subtype5   63    3
  subtype6   41    2
  subtype7   38    5
  subtype8   25    0
  subtype9   66    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        45       63       22       64       63       41       38       25
  YES        1        6        0        5        3        2        5        0
     clus
vv    subtype9
  NO        66
  YES        4
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   38                             5
  subtype2                   43                            14
  subtype3                   21                             2
  subtype4                   51                             7
  subtype5                   52                            16
  subtype6                   39                             1
  subtype7                   31                             2
  subtype8                   24                             5
  subtype9                   48                             2
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     6                              0
  subtype2                    15                              1
  subtype3                     6                              1
  subtype4                    27                              3
  subtype5                     6                              3
  subtype6                    13                              0
  subtype7                    22                              0
  subtype8                     2                              1
  subtype9                    30                              1
D10V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 38       43       21       51       52
  COLON MUCINOUS ADENOCARCINOMA         5       14        2        7       16
  RECTAL ADENOCARCINOMA                 6       15        6       27        6
  RECTAL MUCINOUS ADENOCARCINOMA        0        1        1        3        3
                                clus
vv                               subtype6 subtype7 subtype8 subtype9
  COLON ADENOCARCINOMA                 39       31       24       48
  COLON MUCINOUS ADENOCARCINOMA         1        2        5        2
  RECTAL ADENOCARCINOMA                13       22        2       30
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        1
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 34  1  1  4
  subtype2 51  0  1  8
  subtype3 20  0  1  2
  subtype4 55  2 11  2
  subtype5 61  1  3  4
  subtype6 40  0  4  5
  subtype7 27  1  1  1
  subtype8 29  0  3  0
  subtype9 69  1 11  0
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       34       51       20       55       61       40       27       29
  R1        1        0        0        2        1        0        1        0
  R2        1        1        1       11        3        4        1        3
  RX        4        8        2        2        4        5        1        0
    clus
vv   subtype9
  R0       69
  R1        1
  R2       11
  RX        0
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
D10V13, binary
          cls
clus        0  1
  subtype1  1 41
  subtype2  0 70
  subtype3  0 19
  subtype4  0 50
  subtype5  0 29
  subtype6  1 26
  subtype7  0 49
  subtype8  0 11
  subtype9  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2    0   70
  subtype3    0   19
  subtype4    0   50
  subtype5    0   29
  subtype6    1   26
  subtype7    0   49
  subtype8    0   11
  subtype9    0   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        0        0        0        1
  NOT HISPANIC OR LATINO       41       70       19       50       29       26
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            0        0        0
  NOT HISPANIC OR LATINO       49       11       12
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 23 12
  subtype2 27 13
  subtype3 29 10
  subtype4 14  8
subtype1 subtype2 subtype3 subtype4 
      35       40       39       22 
subtype1 subtype2 subtype3 subtype4 
      12       13       10        8 
$subtype1
TCGA-AD-6964 TCGA-DM-A285 TCGA-G4-6625 TCGA-A6-2675 TCGA-A6-6141 TCGA-A6-6781 
       10.88         5.88        91.79        43.43         8.38        19.66 
TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-AD-6963 TCGA-AY-6196 TCGA-AZ-4616 
       20.28         6.97        22.42        27.42         0.20         5.13 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CM-5860 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       29.56         5.23        32.02        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D7 
       11.01        10.06        12.03        24.43        38.20        13.32 
TCGA-DM-A1D8 TCGA-DM-A280 TCGA-DM-A282 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6299 
       12.59         7.76       139.17         1.55        33.67        74.56 
TCGA-AF-6655 TCGA-AH-6547 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 
       20.02         2.50        26.04        31.00        51.98 

$subtype2
TCGA-A6-6649 TCGA-G4-6314 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6651 
       24.16        35.93        31.63        29.16        25.08        21.76 
TCGA-A6-6654 TCGA-AA-3489 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6607 
       23.87         7.04         1.41        62.79        12.10         3.19 
TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-6167 TCGA-D5-6534 TCGA-D5-6922 TCGA-D5-6924 
       14.30         2.01        14.99        43.27        10.13        14.30 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        8.61        31.96        35.74        34.42        43.04        13.25 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6627 TCGA-AF-2687 TCGA-AG-3731 TCGA-DC-6156 
       67.30        65.85        74.79        46.92        37.02        31.00 
TCGA-DC-6681 TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       25.97       129.27        16.31         9.96        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6572 
        0.39        32.19        36.49        47.08 

$subtype3
TCGA-G4-6294 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-A6-6137 TCGA-A6-6140 
       28.21        18.28        55.76        26.43        27.09        24.13 
TCGA-A6-6650 TCGA-AD-6965 TCGA-D5-5537 TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A28F 
       20.61        26.47        45.40       130.65       140.38        35.97 
TCGA-G4-6306 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3725 TCGA-AG-4021 
       44.68        37.74        29.98        24.59        20.98         3.98 
TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       46.03        38.56        17.49        43.20         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6682 TCGA-DC-6683 
       13.78        48.20         7.17        25.05        25.05        25.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6509 
       41.36        57.24        51.48        32.61        20.55        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-F5-6571 
       15.85        16.34        42.35 

$subtype4
TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6628 TCGA-BM-6198 TCGA-A6-6138 TCGA-A6-6653 
       21.37       100.01        79.69        21.24        22.52        24.39 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4751 
       12.16        83.24        49.41        10.06        21.14        27.02 
TCGA-D5-6533 TCGA-D5-6536 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6295 
       25.48        17.85         7.50       131.51         6.18         8.35 
TCGA-G4-6309 TCGA-AG-3732 TCGA-DC-6158 TCGA-EI-6507 
       85.48        32.98        10.98        19.96 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.39     3.98     6.18 
subtype1 subtype2 subtype3 subtype4 
  139.17   129.27   140.38   131.51 
subtype1 subtype2 subtype3 subtype4 
  13.320   28.865   27.090   21.945 
[1] "0.2 - 139.2 (13.3)" "0.4 - 129.3 (28.9)" "4.0 - 140.4 (27.1)"
[4] "6.2 - 131.5 (21.9)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 30  5
  subtype2 27 13
  subtype3 10 28
  subtype4 18  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    5
  subtype2   27   13
  subtype3   10   28
  subtype4   18    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        30       27       10       18
  RECTUM        5       13       28        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       4        1        11         1         0          1          3
  subtype2       1        2        11         0         0          1          7
  subtype3       2        1        10         0         1          2          8
  subtype4       8        3         5         0         0          0          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          5        2         1
  subtype2          4        7         5
  subtype3          4        4         3
  subtype4          2        0         0
D11V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           4        1        2        8
  STAGE II          1        2        1        3
  STAGE IIA        11       11       10        5
  STAGE IIB         1        0        0        0
  STAGE III         0        0        1        0
  STAGE IIIA        1        1        2        0
  STAGE IIIB        3        7        8        3
  STAGE IIIC        5        4        4        2
  STAGE IV          2        7        4        0
  STAGE IVA         1        5        3        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  2  4 23  6
  subtype2  0  1 32  5
  subtype3  1  4 31  3
  subtype4  1  7 13  1
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        0        1        1
  T2        4        1        4        7
  T3       23       32       31       13
  T4        6        5        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"
          vv
clus       N0 N1 N2
  subtype1 20  7  8
  subtype2 14 14 10
  subtype3 13 15 10
  subtype4 17  3  2
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       20       14       13       17
  N1        7       14       15        3
  N2        8       10       10        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"
D11V7, binary
          cls
clus        0  1
  subtype1 21  3
  subtype2 23 12
  subtype3 24  6
  subtype4 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    3
  subtype2   23   12
  subtype3   24    6
  subtype4   19    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       21       23       24       19
  1        3       12        6        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1 14 21
  subtype2 21 19
  subtype3 14 25
  subtype4  9 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   21
  subtype2   21   19
  subtype3   14   25
  subtype4    9   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       14       21       14        9
  MALE         21       19       25       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
          cls
clus        0  1
  subtype1 26  0
  subtype2 37  1
  subtype3 25  4
  subtype4 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    0
  subtype2   37    1
  subtype3   25    4
  subtype4   20    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        26       37       25       20
  YES        0        1        4        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   23                             5
  subtype2                   24                             3
  subtype3                   10                             0
  subtype4                   17                             1
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     5                              0
  subtype2                    13                              0
  subtype3                    27                              1
  subtype4                     4                              0
D11V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 23       24       10       17
  COLON MUCINOUS ADENOCARCINOMA         5        3        0        1
  RECTAL ADENOCARCINOMA                 5       13       27        4
  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"
          vv
clus       R0 R1 R2 RX
  subtype1 19  0  0  0
  subtype2 26  0  1  2
  subtype3 16  2  1  3
  subtype4 13  0  0  2
D11V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       19       26       16       13
  R1        0        0        2        0
  R2        0        1        1        0
  RX        0        2        3        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, continuous
D11V13, binary
          cls
clus        0
  subtype1 31
  subtype2 38
  subtype3 33
  subtype4 20
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 40 23
  subtype2 12  4
  subtype3 24 10
  subtype4 17  6
subtype1 subtype2 subtype3 subtype4 
      63       16       34       23 
subtype1 subtype2 subtype3 subtype4 
      23        4       10        6 
$subtype1
TCGA-A6-6649 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6314 
       24.16        21.37        10.88       100.01         5.88        35.93 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2675 TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6141 
       91.79        79.69        43.43        31.63        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       25.08        21.76        23.87        19.66        20.28         7.04 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AD-6963 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 
       12.16        22.42        27.42         0.20         1.41         5.13 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6718 
       62.79        12.10        29.56         5.23         3.19        10.06 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-6167 TCGA-CM-6674 
       21.14         2.01        27.02        32.02        14.99        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6534 TCGA-D5-6536 
       11.08        11.01        10.06        12.03        43.27        17.85 
TCGA-DM-A280 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
        7.76        35.74         6.18         1.55        34.42        43.04 
TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6627 TCGA-AG-3732 TCGA-AH-6547 
       13.25        74.56        67.30        74.79        32.98         2.50 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-EI-6509 TCGA-F5-6464 TCGA-F5-6465 
       31.00        51.98        10.98        17.00         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6572 
       28.57        32.19        47.08 

$subtype2
TCGA-A6-5667 TCGA-CA-6719 TCGA-D5-6922 TCGA-F4-6459 TCGA-G4-6303 TCGA-AF-3911 
       29.16        14.30        10.13         8.61        65.85        37.74 
TCGA-AF-4110 TCGA-AG-4021 TCGA-AG-4022 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD 
       29.98         3.98        46.03        25.97        25.05        57.24 
TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6571 TCGA-F5-6812 
      129.27        16.31        42.35        36.49 

$subtype3
TCGA-G4-6294 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-A6-6137 
       28.21        21.24        18.28        55.76        26.43        27.09 
TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6965 TCGA-AZ-6598 
       24.13        20.61        24.39        83.24        26.47        49.41 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6808 
       24.43       130.65         7.50       131.51        35.97        33.67 
TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 TCGA-AF-6672 TCGA-AG-3725 TCGA-AH-6544 
        8.35        44.68        85.48        24.59        20.98        38.56 
TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DY-A1DG TCGA-DY-A1H8 
       43.20        48.20         7.17        25.05        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       20.55        19.96        15.85        16.34 

$subtype4
TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF 
        6.97        11.08        45.40        25.48        14.30        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 TCGA-F4-6460 TCGA-AF-2687 
       13.32        12.59       140.38       139.17        31.96        46.92 
TCGA-AF-6655 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       20.02        37.02        17.49         6.05        33.17        13.78 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6682 TCGA-DY-A1DC TCGA-F5-6810 
       26.04        31.00        25.05        41.36         0.39 

subtype1 subtype2 subtype3 subtype4 
    0.20     3.98     7.17     0.39 
subtype1 subtype2 subtype3 subtype4 
  100.01   129.27   131.51   140.38 
subtype1 subtype2 subtype3 subtype4 
   21.37    29.57    26.45    25.48 
[1] "0.2 - 100.0 (21.4)" "4.0 - 129.3 (29.6)" "7.2 - 131.5 (26.4)"
[4] "0.4 - 140.4 (25.5)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 52 11
  subtype2  5 10
  subtype3 17 17
  subtype4 11 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   11
  subtype2    5   10
  subtype3   17   17
  subtype4   11   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        52        5       17       11
  RECTUM       11       10       17       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        17         1         0          0          7
  subtype2       0        1         5         0         0          1          4
  subtype3       4        2         8         0         1          2          7
  subtype4       2        1         7         0         0          1          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          8        7         5
  subtype2          1        2         2
  subtype3          4        2         1
  subtype4          2        2         1
D12V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        0        4        2
  STAGE II          3        1        2        1
  STAGE IIA        17        5        8        7
  STAGE IIB         1        0        0        0
  STAGE III         0        0        1        0
  STAGE IIIA        0        1        2        1
  STAGE IIIB        7        4        7        3
  STAGE IIIC        8        1        4        2
  STAGE IV          7        2        2        2
  STAGE IVA         5        2        1        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 42 10
  subtype2  0  0 15  1
  subtype3  2  5 25  2
  subtype4  1  2 17  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        2        1
  T2        9        0        5        2
  T3       42       15       25       17
  T4       10        1        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 33 14 15
  subtype2  6  5  5
  subtype3 15 12  7
  subtype4 10  8  3
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       33        6       15       10
  N1       14        5       12        8
  N2       15        5        7        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1 37 12
  subtype2 10  3
  subtype3 25  3
  subtype4 15  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   12
  subtype2   10    3
  subtype3   25    3
  subtype4   15    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       37       10       25       15
  1       12        3        3        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"
D12V8, binary
          cls
clus        0  1
  subtype1 27 36
  subtype2 10  6
  subtype3 12 22
  subtype4  9 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   36
  subtype2   10    6
  subtype3   12   22
  subtype4    9   14
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       27       10       12        9
  MALE         36        6       22       14
[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"
D12V9, binary
          cls
clus        0  1
  subtype1 59  0
  subtype2 12  2
  subtype3 24  2
  subtype4 13  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    0
  subtype2   12    2
  subtype3   24    2
  subtype4   13    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        59       12       24       13
  YES        0        2        2        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   43                             9
  subtype2                    5                             0
  subtype3                   17                             0
  subtype4                    9                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    11                              0
  subtype2                    10                              0
  subtype3                    16                              1
  subtype4                    12                              0
D12V10, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 43        5       17        9
  COLON MUCINOUS ADENOCARCINOMA         9        0        0        0
  RECTAL ADENOCARCINOMA                11       10       16       12
  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"
          vv
clus       R0 R1 R2 RX
  subtype1 37  0  0  3
  subtype2 11  0  1  1
  subtype3 15  2  0  1
  subtype4 11  0  1  2
D12V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       37       11       15       11
  R1        0        0        2        0
  R2        0        1        0        1
  RX        3        1        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
D12V13, binary
          cls
clus        0
  subtype1 58
  subtype2 14
  subtype3 30
  subtype4 20
[1] "NOT AVAILABLE: table only has an event [0]"
