[1] "ofn"        "-oTREAD-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/22507018/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/22541962/READ-TP.mergedcluster.txt"

nPatients in clinical file=171, in cluster file=169, common to both=169
[1]  12 169
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4  5 
13  8 20 13 15 
 1  2  3  4  5 
13  8 20 13 15 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
 6 10  7  9  9  8  9  8  3 
 1  2  3  4  5  6  7  8  9 
 6 10  7  9  9  8  9  8  3 
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
26 40 27 42 30 
 1  2  3  4  5 
26 40 27 42 30 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
14 23 17 26 18 
 1  2  3  4  5 
14 23 17 26 18 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
42 28 26 31  4 
 1  2  3  4  5 
42 28 26 31  4 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
20 21 25 19 30 16 
 1  2  3  4  5  6 
20 21 25 19 30 16 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
32 14 34 28 58 
 1  2  3  4  5 
32 14 34 28 58 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
27 36 12 20 33 18 20 
 1  2  3  4  5  6  7 
27 36 12 20 33 18 20 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
24 56 63 
 1  2  3 
24 56 63 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
24 63 56 
 1  2  3 
24 63 56 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
17 15 13  6 
 1  2  3  4 
17 15 13  6 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
12 12 16  6  5 
 1  2  3  4  5 
12 12 16  6  5 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 169 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=26,	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=106,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "84"                  
freq.contrast "84"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 169 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES"
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  29 115  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  29 115  14 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  29 115  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  29 115  14 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
85 45 35 
[1] "table(vv)"
vv
N0 N1 N2 
85 45 35 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
85 45 35 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
85 45 35 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=18, binary=FALSE, numeric=TRUE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  8  0
  subtype3 14  4
  subtype4 11  1
  subtype5 11  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      13        8       18       12       14 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        0        4        1        3 
$subtype1
TCGA-AG-3580 TCGA-AG-A00H TCGA-AF-2689 TCGA-AG-3575 TCGA-AG-3594 TCGA-AG-3885 
        8.02        25.97        39.48        12.00         2.01        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-A002 
       36.95        13.02        14.01        25.02        32.02        20.98 
TCGA-AG-A02X 
       41.00 

$subtype2
TCGA-AG-3611 TCGA-AF-2691 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3896 
       13.94        43.04        32.02         7.07        46.03         1.02 
TCGA-AG-3909 TCGA-AG-A011 
       19.99        37.02 

$subtype3
TCGA-AG-A014 TCGA-AG-A015 TCGA-AF-2692 TCGA-AG-3574 TCGA-AG-3583 TCGA-AG-3586 
       15.95        36.03        13.55        36.03        20.05         1.02 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-A008 
       34.03        12.03         0.99         7.99         0.99        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        6.02        23.01         9.07        49.97         1.94        38.96 

$subtype4
TCGA-AG-3612 TCGA-AF-3400 TCGA-AG-3582 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 
       19.99        34.49        36.03        50.04         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       19.99        29.98         0.99        19.04        19.99         1.02 

$subtype5
TCGA-AF-3913 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-3584 
       10.39        17.03        17.03        31.00        51.98        24.00 
TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       35.01        48.03        28.04        36.03        14.04         1.02 
TCGA-AG-A01J TCGA-AG-A032 
        1.02        38.04 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.01     1.02     0.99     0.99     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   41.00    46.03    49.97    50.04    51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 
  20.980   26.005   13.745   19.990   26.020 
[1] "2.0 - 41.0 (21.0)" "1.0 - 46.0 (26.0)" "1.0 - 50.0 (13.7)"
[4] "1.0 - 50.0 (20.0)" "1.0 - 52.0 (26.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       4        1         5         0          2          0        1
  subtype2       4        0         3         0          1          0        0
  subtype3       6        2         3         2          3          0        4
  subtype4       3        0         4         0          2          3        1
  subtype5       1        0         5         0          2          1        6
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           4        4        6        3        1
  STAGE II          1        0        2        0        0
  STAGE IIA         5        3        3        4        5
  STAGE III         0        0        2        0        0
  STAGE IIIB        2        1        3        2        2
  STAGE IIIC        0        0        0        3        1
  STAGE IV          1        0        4        1        6
[1] 7 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  2  9  0
  subtype2  1  3  4  0
  subtype3  2  5 11  2
  subtype4  0  3 10  0
  subtype5  0  2 11  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        1        2        0        0
  T2        2        3        5        3        2
  T3        9        4       11       10       11
  T4        0        0        2        0        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 10  2  1
  subtype2  7  1  0
  subtype3 11  6  3
  subtype4  7  3  3
  subtype5  7  3  5
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10        7       11        7        7
  N1        2        1        6        3        3
  N2        1        0        3        3        5
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2  8  0
  subtype3 16  4
  subtype4 12  1
  subtype5  9  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2    8    0
  subtype3   16    4
  subtype4   12    1
  subtype5    9    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12        8       16       12        9
  1        1        0        4        1        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  4  9
  subtype2  4  4
  subtype3 11  9
  subtype4  6  7
  subtype5  6  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    9
  subtype2    4    4
  subtype3   11    9
  subtype4    6    7
  subtype5    6    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        4        4       11        6        6
  MALE          9        4        9        7        9
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1  8  4
  subtype2  6  1
  subtype3 10  2
  subtype4  8  2
  subtype5 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    4
  subtype2    6    1
  subtype3   10    2
  subtype4    8    2
  subtype5   11    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         8        6       10        8       11
  YES        4        1        2        2        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1 10  3
  subtype2  7  1
  subtype3 15  2
  subtype4 11  1
  subtype5 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    3
  subtype2    7    1
  subtype3   15    2
  subtype4   11    1
  subtype5   15    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                10        7       15       11       15
  RECTAL MUCINOUS ADENOCARCINOMA        3        1        2        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 13  0  0
  subtype2  8  0  0
  subtype3 14  1  5
  subtype4 11  0  1
  subtype5 11  0  4
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       13        8       14       11       11
  R1        0        0        1        0        0
  R2        0        0        5        1        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 4 2
  subtype2 9 0
  subtype3 7 0
  subtype4 8 1
  subtype5 5 2
  subtype6 7 1
  subtype7 7 1
  subtype8 6 2
  subtype9 2 1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       6        9        7        9        7        8        8        8 
subtype9 
       3 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        0        0        1        2        1        1        2 
subtype9 
       1 
$subtype1
TCGA-AG-3580 TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3593 TCGA-AG-3726 TCGA-AG-3894 
        8.02        39.48        36.03        34.03         7.99        14.01 

$subtype2
TCGA-AG-A00H TCGA-AG-A014 TCGA-AF-2691 TCGA-AG-3575 TCGA-AG-3885 TCGA-AG-3902 
       25.97        15.95        43.04        12.00        17.95        32.02 
TCGA-AG-A002 TCGA-AG-A016 TCGA-AG-A01J 
       20.98         9.07         1.02 

$subtype3
TCGA-AG-A015 TCGA-AF-2692 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        13.55        12.03         0.99        13.94         6.02 
TCGA-AG-A00Y 
       23.01 

$subtype4
TCGA-AG-3611 TCGA-AF-3400 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3881 TCGA-AG-3887 
       13.94        34.49        46.03         2.01        19.04        36.95 
TCGA-AG-3892 TCGA-AG-3901 TCGA-AG-A02X 
       13.02        25.02        41.00 

$subtype5
TCGA-AF-3913 TCGA-AG-4008 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       10.39        17.03        48.03        28.04        36.03        14.04 
TCGA-AG-A026 
        1.94 

$subtype6
TCGA-AG-A01N TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3728 TCGA-AG-3893 TCGA-AG-3896 
       31.00        32.02        24.00        29.98        35.01         1.02 
TCGA-AG-3909 TCGA-AG-A032 
       19.99        38.04 

$subtype7
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        7.07        20.05        50.04         6.05         0.99        15.95 
TCGA-AG-3878 TCGA-AG-A011 
        0.99        37.02 

$subtype8
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3883 
       19.99        17.03        36.03        19.99        19.99         1.02 
TCGA-AG-4007 TCGA-AG-A02G 
        1.02        38.96 

$subtype9
TCGA-AG-A023 TCGA-AG-3586 TCGA-AG-A025 
       51.98         1.02        49.97 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    7.99     1.02     0.99     2.01     1.94     1.02     0.99     1.02 
subtype9 
    1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   39.48    43.04    36.03    46.03    48.03    38.04    50.04    38.96 
subtype9 
   51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   24.02    17.95    13.55    25.02    17.03    30.49    11.51    19.99 
subtype9 
   49.97 
[1] "8.0 - 39.5 (24.0)" "1.0 - 43.0 (17.9)" "1.0 - 36.0 (13.6)"
[4] "2.0 - 46.0 (25.0)" "1.9 - 48.0 (17.0)" "1.0 - 38.0 (30.5)"
[7] "1.0 - 50.0 (11.5)" "1.0 - 39.0 (20.0)" "1.0 - 52.0 (50.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       2        1         2         0          0          0        1
  subtype2       3        1         3         0          2          0        1
  subtype3       3        0         2         1          1          0        0
  subtype4       3        0         5         0          1          0        0
  subtype5       0        1         4         0          1          1        2
  subtype6       1        0         1         0          4          0        2
  subtype7       2        0         3         0          0          2        2
  subtype8       3        0         0         0          1          1        3
  subtype9       1        0         0         1          0          0        1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           2        3        3        3        0        1        2
  STAGE II          1        1        0        0        1        0        0
  STAGE IIA         2        3        2        5        4        1        3
  STAGE III         0        0        1        0        0        0        0
  STAGE IIIB        0        2        1        1        1        4        0
  STAGE IIIC        0        0        0        0        1        0        2
  STAGE IV          1        1        0        0        2        2        2
            clus
vv           subtype8 subtype9
  STAGE I           3        1
  STAGE II          0        0
  STAGE IIA         0        0
  STAGE III         0        1
  STAGE IIIB        1        0
  STAGE IIIC        1        0
  STAGE IV          3        1
[1] 7 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  1  1  4  0
  subtype2  1  2  7  0
  subtype3  1  2  4  0
  subtype4  1  2  6  0
  subtype5  0  0  7  2
  subtype6  0  2  6  0
  subtype7  0  2  7  0
  subtype8  0  4  3  1
  subtype9  1  0  1  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        1        1        1        1        0        0        0        0
  T2        1        2        2        2        0        2        2        4
  T3        4        7        4        6        7        6        7        3
  T4        0        0        0        0        2        0        0        1
    clus
vv   subtype9
  T1        1
  T2        0
  T3        1
  T4        1
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  5  0  1
  subtype2  7  2  1
  subtype3  5  2  0
  subtype4  8  1  0
  subtype5  5  2  2
  subtype6  3  4  1
  subtype7  5  1  3
  subtype8  3  3  2
  subtype9  1  0  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        5        7        5        8        5        3        5        3
  N1        0        2        2        1        2        4        1        3
  N2        1        1        0        0        2        1        3        2
    clus
vv   subtype9
  N0        1
  N1        0
  N2        2
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 9 1
  subtype3 7 0
  subtype4 9 0
  subtype5 7 2
  subtype6 6 2
  subtype7 7 2
  subtype8 5 3
  subtype9 2 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    9    1
  subtype3    7    0
  subtype4    9    0
  subtype5    7    2
  subtype6    6    2
  subtype7    7    2
  subtype8    5    3
  subtype9    2    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0        5        9        7        9        7        6        7        5
  1        1        1        0        0        2        2        2        3
   clus
vv  subtype9
  0        2
  1        1
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus       0 1
  subtype1 4 2
  subtype2 3 7
  subtype3 5 2
  subtype4 3 6
  subtype5 3 6
  subtype6 4 4
  subtype7 3 6
  subtype8 3 5
  subtype9 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    3    7
  subtype3    5    2
  subtype4    3    6
  subtype5    3    6
  subtype6    4    4
  subtype7    3    6
  subtype8    3    5
  subtype9    3    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        4        3        5        3        3        4        3
  MALE          2        7        2        6        6        4        6
        clus
vv       subtype8 subtype9
  FEMALE        3        3
  MALE          5        0
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus       0 1
  subtype1 4 2
  subtype2 5 2
  subtype3 5 1
  subtype4 5 3
  subtype5 6 0
  subtype6 6 1
  subtype7 5 1
  subtype8 6 0
  subtype9 1 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    5    2
  subtype3    5    1
  subtype4    5    3
  subtype5    6    0
  subtype6    6    1
  subtype7    5    1
  subtype8    6    0
  subtype9    1    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         4        5        5        5        6        6        5        6
  YES        2        2        1        3        0        1        1        0
     clus
vv    subtype9
  NO         1
  YES        0
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1  6  0
  subtype2 10  0
  subtype3  4  1
  subtype4  4  4
  subtype5  9  0
  subtype6  7  1
  subtype7  8  1
  subtype8  8  0
  subtype9  2  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    0
  subtype2   10    0
  subtype3    4    1
  subtype4    4    4
  subtype5    9    0
  subtype6    7    1
  subtype7    8    1
  subtype8    8    0
  subtype9    2    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                 6       10        4        4        9
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        4        0
                                clus
vv                               subtype6 subtype7 subtype8 subtype9
  RECTAL ADENOCARCINOMA                 7        8        8        2
  RECTAL MUCINOUS ADENOCARCINOMA        1        1        0        0
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  6  0  0
  subtype2  9  0  1
  subtype3  7  0  0
  subtype4  8  0  0
  subtype5  7  1  1
  subtype6  6  0  2
  subtype7  7  0  2
  subtype8  5  0  3
  subtype9  2  0  1
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0        6        9        7        8        7        6        7        5
  R1        0        0        0        0        1        0        0        0
  R2        0        1        0        0        1        2        2        3
    clus
vv   subtype9
  R0        2
  R1        0
  R2        1
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 23  3
  subtype2 31  7
  subtype3 20  5
  subtype4 30 10
  subtype5 27  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      26       38       25       40       29 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        7        5       10        2 
$subtype1
TCGA-AG-3890 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       17.03        21.24        55.76        46.92        43.04        13.55 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3901 TCGA-AG-4005 
       34.49        16.83        37.02         1.02        25.02        14.04 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-6155 TCGA-DY-A1DE 
        6.05        33.17        13.78        48.20        13.97       129.27 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       32.61        20.55        10.78        11.97         9.96        49.51 
TCGA-F5-6812 TCGA-F5-6814 
       36.49        37.18 

$subtype2
TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A01N TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-A56K 
       19.99        17.03        31.00        39.48        17.23        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 
       65.98        11.84        36.03        36.03        34.03        34.03 
TCGA-AG-3608 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3909 
       15.95         0.99        19.99        35.01        48.03        19.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A032 
       36.03         1.02        46.03         1.02         1.94        38.04 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        7.17        21.01        25.05        31.00        12.00        51.98 
TCGA-DC-6683 TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       25.05        51.48         4.18        15.85        17.69        16.31 
TCGA-F5-6811 TCGA-G5-6572 
       32.19        47.08 

$subtype3
TCGA-AF-3913 TCGA-AG-A00H TCGA-AG-A015 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       10.39        25.97        36.03        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A00C 
       24.36        20.98        29.98        17.95         1.02         6.02 
TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A02G TCGA-CI-6623 TCGA-DC-6156 TCGA-DY-A1DF 
       23.01         9.07        38.96        47.44        31.00        24.13 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6813 
       17.00        16.34        16.41        42.35         0.39        19.66 
TCGA-F5-6863 
       11.87 

$subtype4
TCGA-AG-3611 TCGA-AG-A014 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-6655 
       13.94        15.95        51.98        18.28        26.43        20.02 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       24.59        32.02        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
        2.01         6.05         0.99         7.99         0.99        32.98 
TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-A008 
       19.04        36.95        32.02        28.04         3.98        13.94 
TCGA-AG-A01J TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CL-5917 
        1.02        41.00        38.56        43.20        27.55        78.12 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 
       10.98        25.05       126.44        41.36        57.24         3.48 
TCGA-EI-6883 TCGA-EI-6885 TCGA-F5-6702 TCGA-F5-6864 
       11.51        13.64        28.57        12.46 

$subtype5
TCGA-AG-3580 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 
        8.02        12.00         7.07        20.05        50.04        12.03 
TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A011 
       19.99         0.99        13.02        14.01        20.98        37.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
       49.97        61.97         2.50        26.43        19.46        44.78 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 
       26.04        44.02        25.97        12.62        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6861 
       18.28         8.61        17.46         8.45        38.14 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.02     0.99     0.39     0.99     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    86.63    47.44   126.44    61.97 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.130   25.050   23.010   24.295   19.960 
[1] "1.0 - 129.3 (23.1)" "1.0 - 86.6 (25.1)"  "0.4 - 47.4 (23.0)" 
[4] "1.0 - 126.4 (24.3)" "1.0 - 62.0 (20.0)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       5        0         7         0         0         0          3
  subtype2       4        3        13         0         0         1          0
  subtype3       4        0         3         0         0         1          1
  subtype4       7        2        11         1         1         2          2
  subtype5      10        3         6         1         0         0          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          2        4         1
  subtype2         10          2        4         2
  subtype3          7          4        3         2
  subtype4          2          4        6         1
  subtype5          2          2        1         1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           5        4        4        7       10
  STAGE II          0        3        0        2        3
  STAGE IIA         7       13        3       11        6
  STAGE IIB         0        0        0        1        1
  STAGE IIC         0        0        0        1        0
  STAGE III         0        1        1        2        0
  STAGE IIIA        3        0        1        2        1
  STAGE IIIB        4       10        7        2        2
  STAGE IIIC        2        2        4        4        2
  STAGE IV          4        4        3        6        1
  STAGE IVA         1        2        2        1        1
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  6 18  1
  subtype2  1  4 30  4
  subtype3  2  3 17  4
  subtype4  1  8 30  3
  subtype5  4  7 17  2
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        2        1        4
  T2        6        4        3        8        7
  T3       18       30       17       30       17
  T4        1        4        4        3        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 12 10  4
  subtype2 21 13  5
  subtype3  7 11  8
  subtype4 22  8 11
  subtype5 22  3  5
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       12       21        7       22       22
  N1       10       13       11        8        3
  N2        4        5        8       11        5
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 18  5
  subtype2 32  6
  subtype3 18  4
  subtype4 31  7
  subtype5 26  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    5
  subtype2   32    6
  subtype3   18    4
  subtype4   31    7
  subtype5   26    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       18       32       18       31       26
  1        5        6        4        7        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 12 14
  subtype2 23 17
  subtype3 10 17
  subtype4 21 21
  subtype5 10 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   14
  subtype2   23   17
  subtype3   10   17
  subtype4   21   21
  subtype5   10   20
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       12       23       10       21       10
  MALE         14       17       17       21       20
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1 18  2
  subtype2 28  5
  subtype3 17  5
  subtype4 26  5
  subtype5 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    2
  subtype2   28    5
  subtype3   17    5
  subtype4   26    5
  subtype5   23    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        18       28       17       26       23
  YES        2        5        5        5        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1 23  2
  subtype2 39  1
  subtype3 25  0
  subtype4 35  5
  subtype5 24  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    2
  subtype2   39    1
  subtype3   25    0
  subtype4   35    5
  subtype5   24    5
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                23       39       25       35       24
  RECTAL MUCINOUS ADENOCARCINOMA        2        1        0        5        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 18  1  1  0
  subtype2 30  1  4  2
  subtype3 19  0  2  0
  subtype4 30  0  4  1
  subtype5 26  0  1  1
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       18       30       19       30       26
  R1        1        1        0        0        0
  R2        1        4        2        4        1
  RX        0        2        0        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 12  2
  subtype2 20  3
  subtype3 13  4
  subtype4 20  5
  subtype5 13  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       23       17       25       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        3        4        5        3 
$subtype1
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AG-3731 TCGA-AH-6547 TCGA-CI-6619 
       55.76        26.43        46.92        37.02         2.50         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6917 
       33.17        48.20        25.05        12.62        19.96        17.46 
TCGA-EI-7004 TCGA-F5-6464 
        8.45         9.96 

$subtype2
TCGA-BM-6198 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56N 
       21.24        17.23        37.97        29.98        20.02        11.84 
TCGA-AG-3732 TCGA-AH-6544 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-DC-4745 
       32.98        38.56        19.46        44.78        47.44        21.01 
TCGA-DC-4749 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6881 
       25.05        25.97        32.61        20.55        15.85        16.41 
TCGA-EI-6884 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       10.78        42.35        36.49        19.66        38.14 

$subtype3
TCGA-AF-3911 TCGA-AF-A56K TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       37.74        86.63        31.00        12.00        51.98        10.98 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6513 TCGA-EI-6514 
       25.05        57.24       129.27        51.48        16.34        16.31 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6864 
       49.51        28.57         0.39        32.19        12.46 

$subtype4
TCGA-G5-6233 TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3742 
       18.28        24.36        34.03        34.03        20.98         0.99 
TCGA-AG-4021 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A036 TCGA-AH-6643 
        3.98         1.02         1.94        61.97       117.11        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CL-5918 TCGA-DC-5337 TCGA-DY-A1DF TCGA-EF-5830 
       27.55        26.43         7.17        26.04        24.13         3.48 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
        4.18        20.91        18.28        17.69         8.61        11.51 
TCGA-F5-6814 
       37.18 

$subtype5
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-4022 TCGA-AH-6549 TCGA-CI-6621 TCGA-CL-5917 
       24.59        65.98        46.03        17.49        13.78        78.12 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-EI-6509 
       13.97        31.00        44.02       126.44        41.36        17.00 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 TCGA-G5-6572 
       13.64        11.97        11.87        47.08 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.50    10.78     0.39     0.99    11.87 
subtype1 subtype2 subtype3 subtype4 subtype5 
   55.76    47.44   129.27   117.11   126.44 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.505   25.050   31.000   20.910   27.795 
[1] "2.5 - 55.8 (22.5)"   "10.8 - 47.4 (25.1)"  "0.4 - 129.3 (31.0)" 
[4] "1.0 - 117.1 (20.9)"  "11.9 - 126.4 (27.8)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        1         2         0         0         0          2
  subtype2       4        0         5         1         0         0          4
  subtype3       2        0         5         0         0         0          0
  subtype4       3        3         6         1         1         3          0
  subtype5       1        2         2         0         0         0          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          2        2         1
  subtype2          4          2        0         2
  subtype3          5          1        0         3
  subtype4          3          2        1         0
  subtype5          2          3        3         1
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        4        2        3        1
  STAGE II          1        0        0        3        2
  STAGE IIA         2        5        5        6        2
  STAGE IIB         0        1        0        1        0
  STAGE IIC         0        0        0        1        0
  STAGE III         0        0        0        3        0
  STAGE IIIA        2        4        0        0        1
  STAGE IIIB        1        4        5        3        2
  STAGE IIIC        2        2        1        2        3
  STAGE IV          2        0        0        1        3
  STAGE IVA         1        2        3        0        1
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  1 10  2
  subtype2  1  5 14  3
  subtype3  0  2 13  1
  subtype4  2  2 20  2
  subtype5  0  2 12  3
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        0        2        0
  T2        1        5        2        2        2
  T3       10       14       13       20       12
  T4        2        3        1        2        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  5  6  3
  subtype2 10  9  4
  subtype3  7  6  3
  subtype4 15  4  6
  subtype5  5  5  6
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        5       10        7       15        5
  N1        6        9        6        4        5
  N2        3        4        3        6        6
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1  8  3
  subtype2 18  2
  subtype3 12  3
  subtype4 21  1
  subtype5 10  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    3
  subtype2   18    2
  subtype3   12    3
  subtype4   21    1
  subtype5   10    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        8       18       12       21       10
  1        3        2        3        1        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  5  9
  subtype2  9 14
  subtype3  8  9
  subtype4 12 14
  subtype5 10  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    9
  subtype2    9   14
  subtype3    8    9
  subtype4   12   14
  subtype5   10    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        5        9        8       12       10
  MALE          9       14        9       14        8
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2 18  3
  subtype3 12  1
  subtype4 17  3
  subtype5 12  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2   18    3
  subtype3   12    1
  subtype4   17    3
  subtype5   12    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        10       18       12       17       12
  YES        2        3        1        3        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1 11  3
  subtype2 20  1
  subtype3 17  0
  subtype4 24  2
  subtype5 18  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    3
  subtype2   20    1
  subtype3   17    0
  subtype4   24    2
  subtype5   18    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                11       20       17       24       18
  RECTAL MUCINOUS ADENOCARCINOMA        3        1        0        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  7  1  1  1
  subtype2 18  0  0  0
  subtype3 12  0  0  0
  subtype4 20  1  1  1
  subtype5  9  0  0  3
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7       18       12       20        9
  R1        1        0        0        1        0
  R2        1        0        0        1        0
  RX        1        0        0        1        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 32  9
  subtype2 20  8
  subtype3 19  5
  subtype4 24  5
  subtype5  4  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      41       28       24       29        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9        8        5        5        0 
$subtype1
TCGA-AG-3580 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-5654 
        8.02        36.03        51.98        26.43        39.48        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       24.36        24.59        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3727 
       34.03        34.03        50.04         0.99        20.98         0.99 
TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A02G TCGA-AH-6897 
        1.02        13.94        23.01         9.07        38.96        26.43 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A1DD TCGA-DY-A1DE 
       21.01        31.00        13.97        51.98        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         3.48         4.18        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6810 
       17.69         8.61        10.78        13.64         0.39 

$subtype2
TCGA-AG-A014 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3578 
       15.95        18.28        55.76        17.23        20.02        32.02 
TCGA-AG-3581 TCGA-AG-3901 TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
        7.07        25.02        41.00       117.11        38.56         2.50 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6509 
       31.00        25.97        25.05        24.13        20.55        17.00 
TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       16.31         9.96        42.35        28.57        32.19        36.49 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

$subtype3
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-4008 TCGA-AF-3400 TCGA-AF-A56N TCGA-AG-3574 
       10.39        19.99        17.03        34.49        11.84        36.03 
TCGA-AG-3582 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3731 
       36.03         2.01        12.03         6.05        19.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3891 TCGA-AG-4001 
        0.99         0.99        19.04        17.95        18.02        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-DC-5337 TCGA-DT-5265 
       14.04         1.02         3.98        46.03        26.04        12.62 

$subtype4
TCGA-AG-A00H TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3914 TCGA-AG-3882 TCGA-AG-3898 
       25.97        31.00        21.24        37.68        19.99        48.03 
TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N 
       32.02        20.98         6.02         1.02         1.94        61.97 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6158 
       43.20        27.55        13.78         7.17        25.05        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-EI-6507 TCGA-EI-6511 
       44.02        25.05       126.44        41.36        19.96        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6813 
       16.34        16.41        17.46        49.51        19.66 

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

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     2.50     0.99     1.02     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27   117.11    46.03   126.44    37.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.010   25.035   17.490   21.240   26.250 
[1] "0.4 - 129.3 (21.0)" "2.5 - 117.1 (25.0)" "1.0 - 46.0 (17.5)" 
[4] "1.0 - 126.4 (21.2)" "1.0 - 37.0 (26.2)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       8        0         8         1         3          4          6
  subtype2       3        0         7         0         1          1          5
  subtype3       5        3         6         0         0          0          3
  subtype4       5        4         9         0         1          2          6
  subtype5       0        0         2         0         0          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          0        9         1
  subtype2          4        0         3
  subtype3          3        6         0
  subtype4          2        1         0
  subtype5          0        0         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           8        3        5        5        0
  STAGE II          0        0        3        4        0
  STAGE IIA         8        7        6        9        2
  STAGE IIB         1        0        0        0        0
  STAGE III         3        1        0        1        0
  STAGE IIIA        4        1        0        2        0
  STAGE IIIB        6        5        3        6        1
  STAGE IIIC        0        4        3        2        0
  STAGE IV          9        0        6        1        0
  STAGE IVA         1        3        0        0        0
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 10 25  3
  subtype2  0  4 20  3
  subtype3  2  3 19  2
  subtype4  0  6 23  2
  subtype5  0  0  4  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3        0        2        0        0
  T2       10        4        3        6        0
  T3       25       20       19       23        4
  T4        3        3        2        2        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 18 15  8
  subtype2 11  7  9
  subtype3 14  6  6
  subtype4 19  8  3
  subtype5  2  1  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       18       11       14       19        2
  N1       15        7        6        8        1
  N2        8        9        6        3        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 28  9
  subtype2 21  4
  subtype3 20  6
  subtype4 26  1
  subtype5  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    9
  subtype2   21    4
  subtype3   20    6
  subtype4   26    1
  subtype5    3    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       28       21       20       26        3
  1        9        4        6        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 24 18
  subtype2 14 14
  subtype3 12 14
  subtype4 10 21
  subtype5  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   18
  subtype2   14   14
  subtype3   12   14
  subtype4   10   21
  subtype5    1    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       14       12       10        1
  MALE         18       14       14       21        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 27  5
  subtype2 24  1
  subtype3 15  6
  subtype4 19  4
  subtype5  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    5
  subtype2   24    1
  subtype3   15    6
  subtype4   19    4
  subtype5    3    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        27       24       15       19        3
  YES        5        1        6        4        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus        0  1
  subtype1 37  4
  subtype2 26  2
  subtype3 21  3
  subtype4 30  1
  subtype5  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    4
  subtype2   26    2
  subtype3   21    3
  subtype4   30    1
  subtype5    4    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                37       26       21       30        4
  RECTAL MUCINOUS ADENOCARCINOMA        4        2        3        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 30  0  6  0
  subtype2 22  1  0  0
  subtype3 19  0  5  1
  subtype4 24  1  1  1
  subtype5  3  0  0  1
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       30       22       19       24        3
  R1        0        1        0        1        0
  R2        6        0        5        1        0
  RX        0        0        1        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 14  4
  subtype2 15  6
  subtype3 20  4
  subtype4 15  4
  subtype5 22  6
  subtype6 13  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       21       24       19       28       16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        6        4        4        6        3 
$subtype1
TCGA-AG-3612 TCGA-AG-4008 TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3593 
       19.99        17.03        39.48        36.03        24.00        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
        2.01        12.03         6.05         0.99        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 
        0.99        37.02         0.99         0.99        36.03         1.02 

$subtype2
TCGA-AG-A014 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3581 
       15.95        18.28        55.76        17.23        20.02         7.07 
TCGA-AG-3901 TCGA-AG-A01J TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6547 TCGA-DC-5869 
       25.02         1.02        41.00       117.11         2.50        31.00 
TCGA-DC-6681 TCGA-DC-6683 TCGA-EI-6506 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       25.97        25.05        20.55         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6861 TCGA-F5-6863 
       28.57        38.14        11.87 

$subtype3
TCGA-AG-A00H TCGA-AG-A01N TCGA-AF-3400 TCGA-AF-3914 TCGA-AG-3578 TCGA-AG-3587 
       25.97        31.00        34.49        37.68        32.02        46.03 
TCGA-AG-3893 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6156 TCGA-DC-6158 TCGA-DY-A0XA 
       35.01         7.17        25.05        31.00        10.98       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
       41.36        24.13        19.96        20.91        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6572 
       16.34        16.41        17.46        32.19        12.46        47.08 

$subtype4
TCGA-AF-3913 TCGA-BM-6198 TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3881 TCGA-AG-3882 
       10.39        21.24        11.84        36.03        19.04        19.99 
TCGA-AG-3891 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       18.02        48.03        32.02        14.04         3.98        46.03 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6682 
       43.20        27.55        13.78        26.04        44.02        25.05 
TCGA-DT-5265 
       12.62 

$subtype5
TCGA-AG-3580 TCGA-AG-A015 TCGA-AG-A023 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3583 
        8.02        36.03        51.98        16.83        24.59        20.05 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3598 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        34.03        50.04        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         9.07         1.02         1.94        38.96 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-6155 TCGA-DY-A1H8 
       61.97        38.56        17.49        26.43        13.97        32.61 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69         8.61        10.78        13.64 

$subtype6
TCGA-G5-6641 TCGA-AF-6136 TCGA-AG-3885 TCGA-AG-3896 TCGA-DC-4745 TCGA-DC-6157 
       26.43        24.36        17.95         1.02        21.01        51.98 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 
       57.24       129.27        51.48         3.48         4.18        18.28 
TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       16.31         0.39        36.49        19.66 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.99     1.02     7.17     3.98     1.02     0.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   39.48   117.11   126.44    48.03    61.97   129.27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  18.510   25.020   25.510   21.240   18.870   20.335 
[1] "1.0 - 39.5 (18.5)"  "1.0 - 117.1 (25.0)" "7.2 - 126.4 (25.5)"
[4] "4.0 - 48.0 (21.2)"  "1.0 - 62.0 (18.9)"  "0.4 - 129.3 (20.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       3        1         4         0         2          0          2
  subtype2       3        0         5         0         1          1          5
  subtype3       3        1         8         0         0          2          6
  subtype4       4        2         5         0         0          0          2
  subtype5       6        3         6         0         2          3          2
  subtype6       2        0         4         1         0          1          4
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          3        5         0
  subtype2          2        0         2
  subtype3          2        1         1
  subtype4          1        4         0
  subtype5          0        6         0
  subtype6          1        0         1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           3        3        3        4        6        2
  STAGE II          1        0        1        2        3        0
  STAGE IIA         4        5        8        5        6        4
  STAGE IIB         0        0        0        0        0        1
  STAGE III         2        1        0        0        2        0
  STAGE IIIA        0        1        2        0        3        1
  STAGE IIIB        2        5        6        2        2        4
  STAGE IIIC        3        2        2        1        0        1
  STAGE IV          5        0        1        4        6        0
  STAGE IVA         0        2        1        0        0        1
[1] 10  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  2 15  2
  subtype2  0  4 15  2
  subtype3  0  4 19  1
  subtype4  1  3 15  0
  subtype5  2  7 18  3
  subtype6  1  3  9  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        0        0        1        2        1
  T2        2        4        4        3        7        3
  T3       15       15       19       15       18        9
  T4        2        2        1        0        3        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  8  5  7
  subtype2  9  7  5
  subtype3 13  6  5
  subtype4 11  4  3
  subtype5 15  9  5
  subtype6  8  6  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        8        9       13       11       15        8
  N1        5        7        6        4        9        6
  N2        7        5        5        3        5        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 15  5
  subtype2 17  2
  subtype3 21  2
  subtype4 12  4
  subtype5 22  6
  subtype6 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    5
  subtype2   17    2
  subtype3   21    2
  subtype4   12    4
  subtype5   22    6
  subtype6   11    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       15       17       21       12       22       11
  1        5        2        2        4        6        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 11  9
  subtype2 12  9
  subtype3 10 15
  subtype4  6 13
  subtype5 14 16
  subtype6  8  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    9
  subtype2   12    9
  subtype3   10   15
  subtype4    6   13
  subtype5   14   16
  subtype6    8    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       11       12       10        6       14        8
  MALE          9        9       15       13       16        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 11  2
  subtype2 17  1
  subtype3 16  5
  subtype4 15  3
  subtype5 20  3
  subtype6  9  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    2
  subtype2   17    1
  subtype3   16    5
  subtype4   15    3
  subtype5   20    3
  subtype6    9    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        11       17       16       15       20        9
  YES        2        1        5        3        3        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1 18  1
  subtype2 20  1
  subtype3 23  2
  subtype4 17  1
  subtype5 25  4
  subtype6 15  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   20    1
  subtype3   23    2
  subtype4   17    1
  subtype5   25    4
  subtype6   15    1
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                18       20       23       17       25
  RECTAL MUCINOUS ADENOCARCINOMA        1        1        2        1        4
                                clus
vv                               subtype6
  RECTAL ADENOCARCINOMA                15
  RECTAL MUCINOUS ADENOCARCINOMA        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 15  0  5  0
  subtype2 19  1  0  0
  subtype3 18  0  1  1
  subtype4 13  0  2  1
  subtype5 21  1  4  1
  subtype6 12  0  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       15       19       18       13       21       12
  R1        0        1        0        0        1        0
  R2        5        0        1        2        4        0
  RX        0        0        1        1        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 24  8
  subtype2 13  1
  subtype3 31  3
  subtype4 20  7
  subtype5 45  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      32       14       34       27       52 
subtype1 subtype2 subtype3 subtype4 subtype5 
       8        1        3        7        7 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       46.92        17.23        37.74        20.02        86.63        65.98 
TCGA-AG-3731 TCGA-AG-3901 TCGA-AG-4021 TCGA-AG-4022 TCGA-AH-6644 TCGA-DC-4745 
       37.02        25.02         3.98        46.03        27.55        21.01 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF 
       31.00        10.98        25.97        12.62       129.27        24.13 
TCGA-EF-5831 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
        4.18        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6863 TCGA-F5-6864 
       11.87        12.46 

$subtype2
TCGA-G5-6235 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3581 TCGA-AG-3732 
       55.76        37.97        29.98        24.36         7.07        32.98 
TCGA-AG-3902 TCGA-AH-6547 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-EI-6506 
       32.02         2.50        13.78        44.78        48.20        20.55 
TCGA-EI-6508 TCGA-EI-6884 
       20.91        10.78 

$subtype3
TCGA-AG-A015 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-5654 TCGA-AF-6672 
       36.03        21.24        18.28        26.43        16.83        24.59 
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3599 TCGA-AG-3725 TCGA-AG-3887 TCGA-AG-3894 
       32.02        34.03        12.03        20.98        36.95        14.01 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6549 
       20.98        13.94        61.97        41.00        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6155 
       43.20        19.46         6.05        33.17        26.04        13.97 
TCGA-DC-6160 TCGA-DC-6682 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       44.02        25.05        19.96        17.00        18.28        17.69 
TCGA-EI-6881 TCGA-EI-6882 TCGA-F5-6814 TCGA-F5-6861 
       16.41         8.61        37.18        38.14 

$subtype4
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3742 TCGA-AG-A02G 
       11.84        36.03        34.03        19.99         0.99        38.96 
TCGA-AH-6897 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
       26.43        47.44        78.12         7.17        25.05        31.00 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.00        51.98        25.05       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       51.48        32.61         3.48        15.85        16.34        16.31 
TCGA-EI-6883 TCGA-EI-7002 TCGA-G5-6572 
       11.51        11.97        47.08 

$subtype5
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-AF-2691 TCGA-AF-2692 
       25.97        15.95        31.00        51.98        43.04        13.55 
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       34.49        12.00        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3881 
       15.95         7.99         0.99        29.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        17.95        13.02        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.04       117.11 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     2.50     6.05     0.99     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    55.76    61.97   126.44   117.11 
subtype1 subtype2 subtype3 subtype4 subtype5 
  24.575   27.170   21.110   26.430   17.490 
[1] "0.4 - 129.3 (24.6)" "2.5 - 55.8 (27.2)"  "6.0 - 62.0 (21.1)" 
[4] "1.0 - 126.4 (26.4)" "1.0 - 117.1 (17.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        2         7         0         0         0          2
  subtype2       4        0         2         1         0         0          1
  subtype3       8        1         9         0         0         1          3
  subtype4       5        1         6         1         1         0          1
  subtype5      12        4        16         0         0         4          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          7        3         3
  subtype2          4          0        0         1
  subtype3          3          2        2         1
  subtype4          5          2        2         2
  subtype5          9          3       10         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        4        8        5       12
  STAGE II          2        0        1        1        4
  STAGE IIA         7        2        9        6       16
  STAGE IIB         0        1        0        1        0
  STAGE IIC         0        0        0        1        0
  STAGE III         0        0        1        0        4
  STAGE IIIA        2        1        3        1        0
  STAGE IIIB        4        4        3        5        9
  STAGE IIIC        7        0        2        2        3
  STAGE IV          3        0        2        2       10
  STAGE IVA         3        1        1        2        0
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  2 24  5
  subtype2  0  4  8  2
  subtype3  3  8 22  1
  subtype4  2  5 18  2
  subtype5  4  9 41  4
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        3        2        4
  T2        2        4        8        5        9
  T3       24        8       22       18       41
  T4        5        2        1        2        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 10  8 12
  subtype2  8  5  1
  subtype3 19  9  5
  subtype4 14  9  4
  subtype5 33 14 11
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10        8       19       14       33
  N1        8        5        9        9       14
  N2       12        1        5        4       11
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 23  6
  subtype2  8  0
  subtype3 26  3
  subtype4 21  4
  subtype5 48 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    6
  subtype2    8    0
  subtype3   26    3
  subtype4   21    4
  subtype5   48   10
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       23        8       26       21       48
  1        6        0        3        4       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 17 15
  subtype2  6  8
  subtype3 11 23
  subtype4 14 14
  subtype5 27 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   15
  subtype2    6    8
  subtype3   11   23
  subtype4   14   14
  subtype5   27   31
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17        6       11       14       27
  MALE         15        8       23       14       31
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 25  4
  subtype2 10  2
  subtype3 27  4
  subtype4 19  2
  subtype5 31  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    4
  subtype2   10    2
  subtype3   27    4
  subtype4   19    2
  subtype5   31    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        25       10       27       19       31
  YES        4        2        4        2        9
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 29  3
  subtype2 12  0
  subtype3 27  6
  subtype4 28  0
  subtype5 51  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    3
  subtype2   12    0
  subtype3   27    6
  subtype4   28    0
  subtype5   51    4
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                29       12       27       28       51
  RECTAL MUCINOUS ADENOCARCINOMA        3        0        6        0        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 23  0  2  2
  subtype2  7  1  0  0
  subtype3 29  0  0  1
  subtype4 17  0  1  2
  subtype5 47  1  9  0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       23        7       29       17       47
  R1        0        1        0        0        1
  R2        2        0        0        1        9
  RX        2        0        1        2        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 19  8
  subtype2 33  2
  subtype3  8  4
  subtype4 17  3
  subtype5 23  6
  subtype6 17  1
  subtype7 16  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      27       35       12       20       29       18       18 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       8        2        4        3        6        1        2 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-4021 TCGA-DC-6156 
       46.92        17.23        86.63        65.98         3.98        31.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       51.98        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 
      129.27        24.13         4.18        15.85        16.31        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       13.64        11.97        42.35         0.39        36.49        19.66 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

$subtype2
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-4110 
       18.28        55.76        26.43        43.04        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3732 
       24.36        24.59        34.03        20.98        37.02        32.98 
TCGA-AG-3902 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 
       32.02        46.03        38.56         2.50        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6160 
       33.17        13.78        44.78        48.20        21.01        44.02 
TCGA-DC-6681 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       25.97        20.55        20.91        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6861 
        8.61        10.78         8.45        49.51        38.14 

$subtype3
TCGA-BM-6198 TCGA-AF-3911 TCGA-AF-6655 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6158 
       21.24        37.74        20.02        43.20        27.55        10.98 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6814 
       12.62        19.96        17.46         9.96        28.57        37.18 

$subtype4
TCGA-AF-5654 TCGA-AF-A56N TCGA-AG-3592 TCGA-AG-3742 TCGA-AH-6549 TCGA-AH-6897 
       16.83        11.84        34.03         0.99        17.49        26.43 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       47.44        78.12         7.17        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 
       12.00        13.97        51.48        32.61         3.48        17.00 
TCGA-EI-6513 TCGA-F5-6811 
       16.34        32.19 

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

$subtype6
TCGA-AG-3611 TCGA-AG-A015 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 
       13.94        36.03        34.49        12.00        32.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3901 
       50.04        12.03        19.04        36.95        13.02        25.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
       20.98        13.94         6.02         1.02        61.97        41.00 

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

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.39     2.50     9.96     0.99     0.99     1.02     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  129.27    55.76    43.20    78.12   117.11    61.97    51.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   25.05    25.97    20.63    21.27    19.99    20.01    16.49 
[1] "0.4 - 129.3 (25.1)" "2.5 - 55.8 (26.0)"  "10.0 - 43.2 (20.6)"
[4] "1.0 - 78.1 (21.3)"  "1.0 - 117.1 (20.0)" "1.0 - 62.0 (20.0)" 
[7] "1.0 - 52.0 (16.5)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0         9         0         1         0          0
  subtype2       5        1         6         1         0         1          3
  subtype3       1        1         2         0         0         0          2
  subtype4       6        0         4         1         0         0          2
  subtype5       7        4         8         0         0         2          0
  subtype6       6        2         7         0         0         1          0
  subtype7       4        0         4         0         0         1          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          5          5        3         1
  subtype2          7          0        3         3
  subtype3          1          3        0         1
  subtype4          2          2        0         2
  subtype5          4          2        6         0
  subtype6          2          0        0         0
  subtype7          4          2        5         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        5        1        6        7        6        4
  STAGE II          0        1        1        0        4        2        0
  STAGE IIA         9        6        2        4        8        7        4
  STAGE IIB         0        1        0        1        0        0        0
  STAGE IIC         1        0        0        0        0        0        0
  STAGE III         0        1        0        0        2        1        1
  STAGE IIIA        0        3        2        2        0        0        0
  STAGE IIIB        5        7        1        2        4        2        4
  STAGE IIIC        5        0        3        2        2        0        2
  STAGE IV          3        3        0        0        6        0        5
  STAGE IVA         1        3        1        2        0        0        0
[1] 11  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  1 21  3
  subtype2  2  5 25  4
  subtype3  0  2  9  1
  subtype4  3  5 10  2
  subtype5  1  7 22  3
  subtype6  2  4 12  0
  subtype7  1  4 14  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        0        2        0        3        1        2        1
  T2        1        5        2        5        7        4        4
  T3       21       25        9       10       22       12       14
  T4        3        4        1        2        3        0        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 11  5  9
  subtype2 15 15  6
  subtype3  4  4  3
  subtype4 11  5  3
  subtype5 19  8  6
  subtype6 15  3  0
  subtype7  9  5  6
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       11       15        4       11       19       15        9
  N1        5       15        4        5        8        3        5
  N2        9        6        3        3        6        0        6
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 21  4
  subtype2 22  5
  subtype3  8  1
  subtype4 15  2
  subtype5 27  6
  subtype6 18  0
  subtype7 15  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2   22    5
  subtype3    8    1
  subtype4   15    2
  subtype5   27    6
  subtype6   18    0
  subtype7   15    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       21       22        8       15       27       18       15
  1        4        5        1        2        6        0        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 13 14
  subtype2 19 17
  subtype3  1 11
  subtype4 10 10
  subtype5 14 19
  subtype6  8 10
  subtype7 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   14
  subtype2   19   17
  subtype3    1   11
  subtype4   10   10
  subtype5   14   19
  subtype6    8   10
  subtype7   10   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       13       19        1       10       14        8       10
  MALE         14       17       11       10       19       10       10
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 19  2
  subtype2 28  5
  subtype3 10  2
  subtype4 15  1
  subtype5 18  6
  subtype6 12  3
  subtype7 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    2
  subtype2   28    5
  subtype3   10    2
  subtype4   15    1
  subtype5   18    6
  subtype6   12    3
  subtype7   10    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        19       28       10       15       18       12       10
  YES        2        5        2        1        6        3        2
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus        0  1
  subtype1 27  0
  subtype2 30  4
  subtype3 11  1
  subtype4 20  0
  subtype5 31  1
  subtype6  9  7
  subtype7 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    0
  subtype2   30    4
  subtype3   11    1
  subtype4   20    0
  subtype5   31    1
  subtype6    9    7
  subtype7   19    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                27       30       11       20       31
  RECTAL MUCINOUS ADENOCARCINOMA        0        4        1        0        1
                                clus
vv                               subtype6 subtype7
  RECTAL ADENOCARCINOMA                 9       19
  RECTAL MUCINOUS ADENOCARCINOMA        7        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 19  0  1  1
  subtype2 23  1  1  0
  subtype3  9  0  0  1
  subtype4 13  0  0  3
  subtype5 26  1  6  0
  subtype6 17  0  0  0
  subtype7 16  0  4  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       19       23        9       13       26       17       16
  R1        0        1        0        0        1        0        0
  R2        1        1        0        0        6        0        4
  RX        1        0        1        3        0        0        0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 17  7
  subtype2 45 10
  subtype3 49  8
subtype1 subtype2 subtype3 
      24       55       57 
subtype1 subtype2 subtype3 
       7       10        8 
$subtype1
TCGA-AF-3913 TCGA-AG-A015 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 
       10.39        36.03        46.92        17.23        37.74        29.98 
TCGA-AG-3731 TCGA-AG-3901 TCGA-AG-4001 TCGA-AG-A025 TCGA-AH-6547 TCGA-AH-6644 
       37.02        25.02        36.03        49.97         2.50        27.55 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 
       25.97        12.62       129.27        16.31         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
       42.35        28.57         0.39        36.49        19.66        47.08 

$subtype2
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2693 TCGA-AF-5654 
       21.24        18.28        55.76        26.43        37.97        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3725 
       24.36        20.02        24.59        34.03        34.03        20.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-4021 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6549 
       32.98         0.99         3.98        46.03        38.56        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       43.20         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       31.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-F5-6811 
       32.19 

$subtype3
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N 
        8.02        13.94        19.99        17.03        17.03        31.00 
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-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 
       19.99        28.04        14.04         1.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
        6.02        37.02         9.07         1.02         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       61.97        41.00       117.11 

subtype1 subtype2 subtype3 
    0.39     0.99     0.99 
subtype1 subtype2 subtype3 
  129.27   126.44   117.11 
subtype1 subtype2 subtype3 
  29.275   25.050   19.040 
[1] "0.4 - 129.3 (29.3)" "1.0 - 126.4 (25.1)" "1.0 - 117.1 (19.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       2        1         6         0         0          0          1
  subtype2      11        1        10         2         1          4         12
  subtype3      15        6        16         0         4          0          8
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          5        2         3
  subtype2          4        3         3
  subtype3          4       10         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2       11       15
  STAGE II          1        1        6
  STAGE IIA         6       10       16
  STAGE IIB         0        2        0
  STAGE III         0        1        4
  STAGE IIIA        0        4        0
  STAGE IIIB        1       12        8
  STAGE IIIC        5        4        4
  STAGE IV          2        3       10
  STAGE IVA         3        3        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  2  0 17  3
  subtype2  4 12 36  4
  subtype3  3 14 43  3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        4        3
  T2        0       12       14
  T3       17       36       43
  T4        3        4        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 10  4  7
  subtype2 25 21  9
  subtype3 38 13 12
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       10       25       38
  N1        4       21       13
  N2        7        9       12
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 14  4
  subtype2 39  6
  subtype3 53 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    4
  subtype2   39    6
  subtype3   53   10
   clus
vv  subtype1 subtype2 subtype3
  0       14       39       53
  1        4        6       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 12 12
  subtype2 26 30
  subtype3 28 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   12
  subtype2   26   30
  subtype3   28   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       26       28
  MALE         12       30       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1 18  3
  subtype2 39  6
  subtype3 37  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    3
  subtype2   39    6
  subtype3   37    9
     clus
vv    subtype1 subtype2 subtype3
  NO        18       39       37
  YES        3        6        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"
D9V9, binary
          cls
clus        0  1
  subtype1 21  2
  subtype2 54  1
  subtype3 52  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    2
  subtype2   54    1
  subtype3   52    7
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                21       54       52
  RECTAL MUCINOUS ADENOCARCINOMA        2        1        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       R0 R1 R2 RX
  subtype1 17  0  1  1
  subtype2 33  1  1  3
  subtype3 52  1  9  0
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       17       33       52
  R1        0        1        1
  R2        1        1        9
  RX        1        3        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 16  5
  subtype2 50 12
  subtype3 45  8
subtype1 subtype2 subtype3 
      21       62       53 
subtype1 subtype2 subtype3 
       5       12        8 
$subtype1
TCGA-G5-6641 TCGA-AF-2687 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3731 
       26.43        46.92        32.02        20.05        46.03        37.02 
TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 
       35.01        36.03         3.98       117.11        17.49        43.20 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6508 
        6.05        48.20        57.24       129.27         3.48        20.91 
TCGA-EI-6513 TCGA-F5-6702 TCGA-F5-6810 
       16.34        28.57         0.39 

$subtype2
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 
       21.24        18.28        55.76        17.23        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 
       29.98        16.83        24.36        20.02        24.59        34.03 
TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3901 TCGA-AG-4022 
       34.03        20.98        32.98         0.99        25.02        46.03 
TCGA-AG-A00C TCGA-AG-A025 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-CI-6620 
        6.02        49.97        38.56         2.50        27.55        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        24.13        51.48        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        17.00        18.28        15.85        17.69 
TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       16.31         9.96        49.51        42.35        32.19        36.49 
TCGA-F5-6813 TCGA-G5-6572 
       19.66        47.08 

$subtype3
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       36.03        31.00        39.48        43.04        13.55        34.49 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       36.03        12.00         7.07        36.03        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
       15.95        19.99         7.99         0.99        29.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 
       14.04         1.02        20.98        13.94        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02         1.94        38.96        61.97        41.00 

subtype1 subtype2 subtype3 
    0.39     0.99     0.99 
subtype1 subtype2 subtype3 
  129.27   126.44    61.97 
subtype1 subtype2 subtype3 
   32.02    25.05    17.03 
[1] "0.4 - 129.3 (32.0)" "1.0 - 126.4 (25.1)" "1.0 - 62.0 (17.0)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       2        1         4         1         1          1          5
  subtype2      11        2        14         1         1          3         11
  subtype3      15        5        14         0         3          0          5
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        4         1
  subtype2          7        1         5
  subtype3          4       10         0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2       11       15
  STAGE II          1        2        5
  STAGE IIA         4       14       14
  STAGE IIB         1        1        0
  STAGE III         1        1        3
  STAGE IIIA        1        3        0
  STAGE IIIB        5       11        5
  STAGE IIIC        2        7        4
  STAGE IV          4        1       10
  STAGE IVA         1        5        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  2 18  2
  subtype2  4 11 41  6
  subtype3  4 13 37  2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        4        4
  T2        2       11       13
  T3       18       41       37
  T4        2        6        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  8  9  5
  subtype2 30 18 13
  subtype3 35 11 10
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0        8       30       35
  N1        9       18       11
  N2        5       13       10
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 16  5
  subtype2 44  5
  subtype3 46 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    5
  subtype2   44    5
  subtype3   46   10
   clus
vv  subtype1 subtype2 subtype3
  0       16       44       46
  1        5        5       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1  9 15
  subtype2 32 31
  subtype3 25 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   15
  subtype2   32   31
  subtype3   25   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       32       25
  MALE         15       31       31
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1 13  3
  subtype2 45  9
  subtype3 36  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    3
  subtype2   45    9
  subtype3   36    6
     clus
vv    subtype1 subtype2 subtype3
  NO        13       45       36
  YES        3        9        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1 21  3
  subtype2 59  2
  subtype3 47  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    3
  subtype2   59    2
  subtype3   47    5
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                21       59       47
  RECTAL MUCINOUS ADENOCARCINOMA        3        2        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 15  0  4  1
  subtype2 40  1  0  3
  subtype3 47  1  7  0
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       15       40       47
  R1        0        1        1
  R2        4        0        7
  RX        1        3        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 13  4
  subtype2 11  4
  subtype3 10  3
  subtype4  5  1
subtype1 subtype2 subtype3 subtype4 
      17       15       13        6 
subtype1 subtype2 subtype3 subtype4 
       4        4        3        1 
$subtype1
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-3731 TCGA-AG-4021 TCGA-AG-4022 
       46.92        37.74        29.98        37.02         3.98        46.03 
TCGA-DC-6681 TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       25.97       129.27        16.31         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6572 
       28.57         0.39        32.19        36.49        47.08 

$subtype2
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-6655 TCGA-AH-6544 
       21.24        18.28        55.76        26.43        20.02        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-6682 
        2.50        17.49         6.05        13.78        48.20        25.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1H8 
       25.05        41.36        32.61 

$subtype3
TCGA-AF-6672 TCGA-AG-3725 TCGA-AG-3732 TCGA-AH-6643 TCGA-CL-5918 TCGA-DC-4749 
       24.59        20.98        32.98        43.20         7.17        25.05 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6511 
       57.24        51.48        20.55        19.96        17.00        15.85 
TCGA-EI-6513 
       16.34 

$subtype4
TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       33.17        26.04        31.00        31.00        51.98        10.98 

subtype1 subtype2 subtype3 subtype4 
    0.39     2.50     7.17    10.98 
subtype1 subtype2 subtype3 subtype4 
  129.27    55.76    57.24    51.98 
subtype1 subtype2 subtype3 subtype4 
   36.49    25.05    20.98    31.00 
[1] "0.4 - 129.3 (36.5)" "2.5 - 55.8 (25.1)"  "7.2 - 57.2 (21.0)" 
[4] "11.0 - 52.0 (31.0)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIA STAGE IIIB
  subtype1       0        1         6         0          0          0
  subtype2       1        0         2         0          3          4
  subtype3       2        0         3         1          0          3
  subtype4       3        0         0         0          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          3        2         3
  subtype2          0        1         0
  subtype3          2        1         1
  subtype4          0        0         2
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        1        2        3
  STAGE II          1        0        0        0
  STAGE IIA         6        2        3        0
  STAGE III         0        0        1        0
  STAGE IIIA        0        3        0        0
  STAGE IIIB        0        4        3        1
  STAGE IIIC        3        0        2        0
  STAGE IV          2        1        1        0
  STAGE IVA         3        0        1        2
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  0 13  2
  subtype2  1  3 11  0
  subtype3  0  2 10  1
  subtype4  1  2  2  1
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        1        0        1
  T2        0        3        2        2
  T3       13       11       10        2
  T4        2        0        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  7  2  6
  subtype2  4  9  1
  subtype3  5  4  4
  subtype4  3  2  1
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        7        4        5        3
  N1        2        9        4        2
  N2        6        1        4        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1  9  4
  subtype2  7  2
  subtype3 10  1
  subtype4  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    4
  subtype2    7    2
  subtype3   10    1
  subtype4    4    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        9        7       10        4
  1        4        2        1        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1  9  8
  subtype2  4 11
  subtype3  5  8
  subtype4  2  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    8
  subtype2    4   11
  subtype3    5    8
  subtype4    2    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9        4        5        2
  MALE          8       11        8        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"
D11V8, binary
          cls
clus        0  1
  subtype1 12  3
  subtype2 10  0
  subtype3  9  2
  subtype4  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    3
  subtype2   10    0
  subtype3    9    2
  subtype4    6    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        12       10        9        6
  YES        3        0        2        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"
D11V9, binary
          cls
clus        0  1
  subtype1 16  0
  subtype2 14  1
  subtype3 13  0
  subtype4  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    0
  subtype2   14    1
  subtype3   13    0
  subtype4    6    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                16       14       13        6
  RECTAL MUCINOUS ADENOCARCINOMA        0        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 11  0  2  0
  subtype2  6  1  0  1
  subtype3  9  0  0  1
  subtype4  5  0  0  0
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       11        6        9        5
  R1        0        1        0        0
  R2        2        0        0        0
  RX        0        1        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"
D11V11, continuous

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 10  2
  subtype2  9  3
  subtype3 11  5
  subtype4  5  1
  subtype5  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      12       12       16        6        5 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        3        5        1        1 
$subtype1
TCGA-AF-2687 TCGA-AG-3731 TCGA-AG-4021 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       46.92        37.02         3.98        17.49         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-6682 TCGA-EI-6506 TCGA-F5-6702 TCGA-F5-6810 
       13.78        48.20        25.05        20.55        28.57         0.39 

$subtype2
TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6547 TCGA-DC-6681 TCGA-DC-6683 
       37.74        29.98        46.03         2.50        25.97        25.05 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 
       57.24       129.27        16.31         9.96        42.35        36.49 

$subtype3
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-6655 TCGA-AF-6672 
       21.24        18.28        55.76        26.43        20.02        24.59 
TCGA-AG-3725 TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-4749 TCGA-DY-A1DC TCGA-DY-A1DG 
       20.98        38.56        43.20        25.05        41.36        51.48 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       32.61        19.96        15.85        16.34 

$subtype4
TCGA-AG-3732 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
       32.98         7.17        26.04        31.00        51.98        10.98 

$subtype5
TCGA-DC-6156 TCGA-EI-6509 TCGA-F5-6465 TCGA-F5-6811 TCGA-G5-6572 
       31.00        17.00        49.51        32.19        47.08 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     2.50    15.85     7.17    17.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   48.20   129.27    55.76    51.98    49.51 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.800   33.235   24.820   28.520   32.190 
[1] "0.4 - 48.2 (22.8)"  "2.5 - 129.3 (33.2)" "15.8 - 55.8 (24.8)"
[4] "7.2 - 52.0 (28.5)"  "17.0 - 49.5 (32.2)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIA STAGE IIIB
  subtype1       1        0         2         0          0          1
  subtype2       0        1         4         0          0          2
  subtype3       1        0         2         1          3          4
  subtype4       4        0         1         0          0          1
  subtype5       0        0         2         0          0          0
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        3         2
  subtype2          2        0         2
  subtype3          1        1         1
  subtype4          0        0         0
  subtype5          1        0         1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        1        4        0
  STAGE II          0        1        0        0        0
  STAGE IIA         2        4        2        1        2
  STAGE III         0        0        1        0        0
  STAGE IIIA        0        0        3        0        0
  STAGE IIIB        1        2        4        1        0
  STAGE IIIC        1        2        1        0        1
  STAGE IV          3        0        1        0        0
  STAGE IVA         2        2        1        0        1
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  1 10  0
  subtype2  0  0 10  2
  subtype3  1  3 11  1
  subtype4  1  3  2  0
  subtype5  0  0  3  1
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        1        1        0
  T2        1        0        3        3        0
  T3       10       10       11        2        3
  T4        0        2        1        0        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  3  5  2
  subtype2  6  2  4
  subtype3  3  9  4
  subtype4  5  1  0
  subtype5  2  0  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        3        6        3        5        2
  N1        5        2        9        1        0
  N2        2        4        4        0        2
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
          cls
clus        0  1
  subtype1  4  5
  subtype2  8  1
  subtype3 10  2
  subtype4  5  0
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    8    1
  subtype3   10    2
  subtype4    5    0
  subtype5    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        4        8       10        5        3
  1        5        1        2        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1  4  8
  subtype2  8  4
  subtype3  3 13
  subtype4  3  3
  subtype5  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    8
  subtype2    8    4
  subtype3    3   13
  subtype4    3    3
  subtype5    2    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        4        8        3        3        2
  MALE          8        4       13        3        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus        0  1
  subtype1  7  1
  subtype2  8  2
  subtype3 11  2
  subtype4  6  0
  subtype5  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    8    2
  subtype3   11    2
  subtype4    6    0
  subtype5    5    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7        8       11        6        5
  YES        1        2        2        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2 11  0
  subtype3 15  1
  subtype4  6  0
  subtype5  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2   11    0
  subtype3   15    1
  subtype4    6    0
  subtype5    5    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  RECTAL ADENOCARCINOMA                12       11       15        6        5
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  2  1
  subtype2  8  0  0  0
  subtype3 10  1  0  0
  subtype4  5  0  0  1
  subtype5  3  0  0  0
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        5        8       10        5        3
  R1        0        0        1        0        0
  R2        2        0        0        0        0
  RX        1        0        0        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
