[1] "ofn"        "-oTCHOL-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/CHOL-TP/22489349/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/22541054/CHOL-TP.mergedcluster.txt"

nPatients in clinical file=45, in cluster file=36, common to both=36
[1] 10 36
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
14  9  7  6 
 1  2  3  4 
14  9  7  6 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
14 10 12 
 1  2  3 
14 10 12 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
10  8 12 
 1  2  3 
10  8 12 
[1] "RPPA_CHIERARCHICAL"
[1] 3
1 2 3 4 
6 7 8 9 
1 2 3 4 
6 7 8 9 
[1] "MRNASEQ_CNMF"
[1] 3
1 2 3 4 5 6 
6 4 5 6 9 6 
1 2 3 4 5 6 
6 4 5 6 9 6 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 
4 5 5 9 6 5 2 
1 2 3 4 5 6 
4 5 5 9 6 5 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
10  6 10 10 
 1  2  3  4 
10  6 10 10 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
 8 10  4  5  5  4 
 1  2  3  4  5  6 
 8 10  4  5  5  4 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 3 4 5 
8 6 7 7 8 
1 2 3 4 5 
8 6 7 7 8 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 
6 8 9 7 6 
1 2 3 4 5 
6 8 9 7 6 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "RACE"                                
[16] "ETHNICITY"                           

Input Data has 16 rows and 36 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=18,	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=18,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "33"                  
freq.contrast "33"               "2"                   
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 36 columns, 1 survival variables, and 9 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] "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"    "RACE"             
YEARS_TO_BIRTH, nv=28, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
19 12  5 
[1] "table(vv)"
vv
T1 T2 T3 
19 12  5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
19 12  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
19 12  5 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 9 5
  subtype2 4 5
  subtype3 2 5
  subtype4 3 3
subtype1 subtype2 subtype3 subtype4 
      14        9        7        6 
subtype1 subtype2 subtype3 subtype4 
       5        5        5        3 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-3X-AAVE 
       11.15        13.22         0.33        12.66        23.31        21.37 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA33 TCGA-W5-AA38 TCGA-YR-A95A TCGA-ZD-A8I3 
       35.41         1.64        47.64        48.36         0.85         5.56 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

$subtype2
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA36 
       14.63        38.70        50.70        30.38         8.91        46.09 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y5 
        5.59        26.56        40.41 

$subtype3
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Z 
       40.11        24.36        13.81        63.75        21.04        53.06 
TCGA-W5-AA34 
       18.25 

$subtype4
TCGA-ZH-A8Y8 TCGA-W5-AA2G TCGA-W5-AA2U TCGA-W5-AA30 TCGA-WD-A7RX TCGA-ZH-A8Y2 
       19.79        64.96        20.61        37.91         0.69        23.05 

subtype1 subtype2 subtype3 subtype4 
    0.33     5.59    13.81     0.69 
subtype1 subtype2 subtype3 subtype4 
   48.36    50.70    63.75    64.96 
subtype1 subtype2 subtype3 subtype4 
   12.94    30.38    24.36    21.83 
[1] "0.3 - 48.4 (12.9)"  "5.6 - 50.7 (30.4)"  "13.8 - 63.8 (24.4)"
[4] "0.7 - 65.0 (21.8)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       7        3         1        1         1         1
  subtype2       2        3         0        1         1         2
  subtype3       5        2         0        0         0         0
  subtype4       5        1         0        0         0         0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          7        2        5        5
  STAGE II         3        3        2        1
  STAGE III        1        0        0        0
  STAGE IV         1        1        0        0
  STAGE IVA        1        1        0        0
  STAGE IVB        1        2        0        0
[1] 6 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
  subtype1  7  4  3
  subtype2  2  5  2
  subtype3  5  2  0
  subtype4  5  1  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        7        2        5        5
  T2        4        5        2        1
  T3        3        2        0        0
[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"
D1V5, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2  5  3
  subtype3  7  0
  subtype4  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2    5    3
  subtype3    7    0
  subtype4    4    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       10        5        7        4
  1        2        3        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"
D1V6, binary
          cls
clus        0  1
  subtype1 11  2
  subtype2  5  3
  subtype3  7  0
  subtype4  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    2
  subtype2    5    3
  subtype3    7    0
  subtype4    5    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       11        5        7        5
  1        2        3        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"
D1V7, binary
          cls
clus       0 1
  subtype1 7 7
  subtype2 6 3
  subtype3 3 4
  subtype4 4 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    7
  subtype2    6    3
  subtype3    3    4
  subtype4    4    2
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7        6        3        4
  MALE          7        3        4        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"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          2                                   2
  subtype2                          0                                   2
  subtype3                          0                                   0
  subtype4                          0                                   0
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                               10
  subtype2                                7
  subtype3                                7
  subtype4                                6
D1V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 2        0        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        2        2        0        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC          10        7        7        6
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 RX
  subtype1 12  2  0
  subtype2  6  1  2
  subtype3  5  2  0
  subtype4  5  0  1
D1V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       12        6        5        5
  R1        2        1        2        0
  RX        0        2        0        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    10
  subtype2     0                         0     9
  subtype3     0                         0     7
  subtype4     0                         1     5
D1V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        0        0
  BLACK OR AFRICAN AMERICAN        1        0        0        1
  WHITE                           10        9        7        5
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 9 5
  subtype2 4 6
  subtype3 5 7
subtype1 subtype2 subtype3 
      14       10       12 
subtype1 subtype2 subtype3 
       5        6        7 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-3X-AAVC TCGA-3X-AAVE 
       11.15        13.22         0.33        19.79        23.31        21.37 
TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W5-AA2X TCGA-W5-AA33 TCGA-W5-AA39 TCGA-WD-A7RX 
       35.41        50.70         8.91        47.64         5.59         0.69 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

$subtype2
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA34 TCGA-W5-AA36 
       14.63        38.70        64.96        21.04        18.25        46.09 
TCGA-W5-AA38 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y2 
       48.36        26.56         0.85        23.05 

$subtype3
TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2Q 
       40.11        12.66        24.36        13.81        63.75         1.64 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-ZD-A8I3 TCGA-ZH-A8Y5 
       20.61        30.38        53.06        37.91         5.56        40.41 

subtype1 subtype2 subtype3 
    0.33     0.85     1.64 
subtype1 subtype2 subtype3 
   50.70    64.96    63.75 
subtype1 subtype2 subtype3 
  15.140   24.805   27.370 
[1] "0.3 - 50.7 (15.1)" "0.8 - 65.0 (24.8)" "1.6 - 63.8 (27.4)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       8        3         1        0         0         2
  subtype2       6        2         0        2         0         0
  subtype3       5        4         0        0         2         1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          8        6        5
  STAGE II         3        2        4
  STAGE III        1        0        0
  STAGE IV         0        2        0
  STAGE IVA        0        0        2
  STAGE IVB        2        0        1
[1] 6 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
  subtype1  8  4  2
  subtype2  6  3  1
  subtype3  5  5  2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        6        5
  T2        4        3        5
  T3        2        1        2
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2  7  0
  subtype3  9  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2    7    0
  subtype3    9    3
   clus
vv  subtype1 subtype2 subtype3
  0       10        7        9
  1        2        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2  7  2
  subtype3 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2    7    2
  subtype3   11    1
   clus
vv  subtype1 subtype2 subtype3
  0       10        7       11
  1        2        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus       0 1
  subtype1 6 8
  subtype2 8 2
  subtype3 6 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    8
  subtype2    8    2
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6        8        6
  MALE          8        2        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          2                                   2
  subtype2                          0                                   2
  subtype3                          0                                   0
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                               10
  subtype2                                8
  subtype3                               12
D2V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  CHOLANGIOCARCINOMA; DISTAL                 2        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        2        2        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC          10        8       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"
          vv
clus       R0 R1 RX
  subtype1 11  0  3
  subtype2  8  2  0
  subtype3  9  3  0
D2V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       11        8        9
  R1        0        2        3
  RX        3        0        0
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    11
  subtype2     0                         1     9
  subtype3     1                         0    11
D2V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        1
  BLACK OR AFRICAN AMERICAN        1        1        0
  WHITE                           11        9       11
[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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 7
  subtype2 5 3
  subtype3 7 5
subtype1 subtype2 subtype3 
      10        8       12 
subtype1 subtype2 subtype3 
       7        3        5 
$subtype1
TCGA-3X-AAV9 TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-W5-AA2H TCGA-W5-AA2I 
       11.15         0.33        12.66        23.31        35.41        63.75 
TCGA-W5-AA2X TCGA-W5-AA34 TCGA-WD-A7RX TCGA-ZD-A8I3 
        8.91        18.25         0.69         5.56 

$subtype2
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA33 
       19.79        14.63        64.96        50.70        20.61        47.64 
TCGA-W5-AA39 TCGA-ZH-A8Y6 
        5.59        17.06 

$subtype3
TCGA-4G-AAZT TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 
       13.81        21.04         1.64        30.38        53.06        37.91 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       46.09        48.36        26.56         0.85        23.05        40.41 

subtype1 subtype2 subtype3 
    0.33     5.59     0.85 
subtype1 subtype2 subtype3 
   63.75    64.96    53.06 
subtype1 subtype2 subtype3 
  11.905   20.200   28.470 
[1] "0.3 - 63.8 (11.9)" "5.6 - 65.0 (20.2)" "0.8 - 53.1 (28.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       5        2         1        0         1         1
  subtype2       6        2         0        0         0         0
  subtype3       6        2         0        2         1         1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          5        6        6
  STAGE II         2        2        2
  STAGE III        1        0        0
  STAGE IV         0        0        2
  STAGE IVA        1        0        1
  STAGE IVB        1        0        1
[1] 6 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
  subtype1  5  3  2
  subtype2  6  2  0
  subtype3  6  4  2
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        6        6
  T2        3        2        4
  T3        2        0        2
[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"
D3V5, binary
          cls
clus       0 1
  subtype1 7 2
  subtype2 7 0
  subtype3 8 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2    7    0
  subtype3    8    2
   clus
vv  subtype1 subtype2 subtype3
  0        7        7        8
  1        2        0        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus       0 1
  subtype1 8 1
  subtype2 8 0
  subtype3 8 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2    8    0
  subtype3    8    3
   clus
vv  subtype1 subtype2 subtype3
  0        8        8        8
  1        1        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus       0 1
  subtype1 6 4
  subtype2 5 3
  subtype3 6 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    4
  subtype2    5    3
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6        5        6
  MALE          4        3        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          1                                   2
  subtype2                          0                                   0
  subtype3                          0                                   2
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                7
  subtype2                                8
  subtype3                               10
D3V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3
  CHOLANGIOCARCINOMA; DISTAL                 1        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        2        0        2
  CHOLANGIOCARCINOMA; INTRAHEPATIC           7        8       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"
          vv
clus       R0 R1 RX
  subtype1  7  1  2
  subtype2  7  0  1
  subtype3 10  2  0
D3V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        7        7       10
  R1        1        0        2
  RX        2        1        0
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0     8
  subtype2     0                         1     7
  subtype3     0                         1    11
D3V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        0        1        1
  WHITE                            8        7       11
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 1 5
  subtype2 5 2
  subtype3 4 4
  subtype4 5 4
subtype1 subtype2 subtype3 subtype4 
       6        7        8        9 
subtype1 subtype2 subtype3 subtype4 
       5        2        4        4 
$subtype1
TCGA-3X-AAV9 TCGA-ZH-A8Y1 TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2X TCGA-W5-AA34 
       11.15        12.66        35.41        63.75         8.91        18.25 

$subtype2
TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2R TCGA-W5-AA33 TCGA-W5-AA39 
       19.79        14.63        64.96        50.70        47.64         5.59 
TCGA-ZH-A8Y6 
       17.06 

$subtype3
TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA38 TCGA-WD-A7RX 
       23.31        13.81        20.61        37.91        48.36         0.69 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        5.56        23.05 

$subtype4
TCGA-W5-AA31 TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA36 
        0.33        21.04         1.64        30.38        53.06        46.09 
TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y5 
       26.56         0.85        40.41 

subtype1 subtype2 subtype3 subtype4 
    8.91     5.59     0.69     0.33 
subtype1 subtype2 subtype3 subtype4 
   63.75    64.96    48.36    53.06 
subtype1 subtype2 subtype3 subtype4 
  15.455   19.790   21.830   26.560 
[1] "8.9 - 63.8 (15.5)" "5.6 - 65.0 (19.8)" "0.7 - 48.4 (21.8)"
[4] "0.3 - 53.1 (26.6)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       3        0         1        0         1         1
  subtype2       5        2         0        0         0         0
  subtype3       6        2         0        0         0         0
  subtype4       3        2         0        2         1         1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          3        5        6        3
  STAGE II         0        2        2        2
  STAGE III        1        0        0        0
  STAGE IV         0        0        0        2
  STAGE IVA        1        0        0        1
  STAGE IVB        1        0        0        1
[1] 6 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
  subtype1  3  1  2
  subtype2  5  2  0
  subtype3  6  2  0
  subtype4  3  4  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        5        6        3
  T2        1        2        2        4
  T3        2        0        0        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus       0 1
  subtype1 4 2
  subtype2 6 0
  subtype3 6 0
  subtype4 6 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    6    0
  subtype3    6    0
  subtype4    6    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        4        6        6        6
  1        2        0        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 7 0
  subtype3 7 0
  subtype4 5 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    7    0
  subtype3    7    0
  subtype4    5    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        5        7        7        5
  1        1        0        0        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 4 3
  subtype3 6 2
  subtype4 4 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    4    3
  subtype3    6    2
  subtype4    4    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        4        6        4
  MALE          3        3        2        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          1                                   1
  subtype2                          0                                   0
  subtype3                          0                                   1
  subtype4                          0                                   2
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                4
  subtype2                                7
  subtype3                                7
  subtype4                                7
D4V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 1        0        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1        0        1        2
  CHOLANGIOCARCINOMA; INTRAHEPATIC           4        7        7        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 RX
  subtype1  4  1  1
  subtype2  6  0  1
  subtype3  7  0  1
  subtype4  7  2  0
D4V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        4        6        7        7
  R1        1        0        0        2
  RX        1        1        1        0
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     5
  subtype2     0                         1     6
  subtype3     1                         1     6
  subtype4     0                         0     9
D4V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        0
  BLACK OR AFRICAN AMERICAN        0        1        1        0
  WHITE                            5        6        6        9
[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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 3 3
  subtype2 1 3
  subtype3 4 1
  subtype4 3 3
  subtype5 4 5
  subtype6 3 3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        4        5        6        9        6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        3        1        3        5        3 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2X TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       11.15        13.22        23.31         8.91        17.06         3.22 

$subtype2
TCGA-3X-AAVA TCGA-W5-AA2W TCGA-W5-AA36 TCGA-W6-AA0S 
       14.63        30.38        46.09        26.56 

$subtype3
TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA30 
       21.37        35.41        50.70        20.61        37.91 

$subtype4
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       38.70        13.81        63.75        48.36         5.56        23.05 

$subtype5
TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA33 
        0.33        24.36        19.79        64.96        21.04        47.64 
TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
        5.59         0.69         0.85 

$subtype6
TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-W5-AA2Q TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-ZH-A8Y5 
       40.11        12.66         1.64        53.06        18.25        40.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3.22    14.63    20.61     5.56     0.33     1.64 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   23.31    46.09    50.70    63.75    64.96    53.06 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  12.185   28.470   35.410   30.875   19.790   29.180 
[1] "3.2 - 23.3 (12.2)"  "14.6 - 46.1 (28.5)" "20.6 - 50.7 (35.4)"
[4] "5.6 - 63.8 (30.9)"  "0.3 - 65.0 (19.8)"  "1.6 - 53.1 (29.2)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       4        0         0        0         0         2
  subtype2       1        1         0        1         1         0
  subtype3       3        1         1        0         0         0
  subtype4       4        2         0        0         0         0
  subtype5       6        2         0        1         0         0
  subtype6       1        3         0        0         1         1
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          4        1        3        4        6        1
  STAGE II         0        1        1        2        2        3
  STAGE III        0        0        1        0        0        0
  STAGE IV         0        1        0        0        1        0
  STAGE IVA        0        1        0        0        0        1
  STAGE IVB        2        0        0        0        0        1
[1] 6 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
  subtype1  4  1  1
  subtype2  1  2  1
  subtype3  3  1  1
  subtype4  4  2  0
  subtype5  6  3  0
  subtype6  1  3  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        4        1        3        4        6        1
  T2        1        2        1        2        3        3
  T3        1        1        1        0        0        2
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 2 1
  subtype3 5 0
  subtype4 5 0
  subtype5 7 0
  subtype6 4 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    2    1
  subtype3    5    0
  subtype4    5    0
  subtype5    7    0
  subtype6    4    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        3        2        5        5        7        4
  1        2        1        0        0        0        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"
D5V6, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 2 1
  subtype3 5 0
  subtype4 6 0
  subtype5 7 1
  subtype6 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    2    1
  subtype3    5    0
  subtype4    6    0
  subtype5    7    1
  subtype6    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        3        2        5        6        7        5
  1        2        1        0        0        1        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"
D5V7, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 4 0
  subtype3 3 2
  subtype4 4 2
  subtype5 2 7
  subtype6 4 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    4    0
  subtype3    3    2
  subtype4    4    2
  subtype5    2    7
  subtype6    4    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        3        4        3        4        2        4
  MALE          3        0        2        2        7        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          1                                   2
  subtype2                          0                                   1
  subtype3                          1                                   0
  subtype4                          0                                   0
  subtype5                          0                                   1
  subtype6                          0                                   0
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                3
  subtype2                                3
  subtype3                                4
  subtype4                                6
  subtype5                                8
  subtype6                                6
D5V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 1        0        1        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        2        1        0        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           3        3        4        6
                                     clus
vv                                    subtype5 subtype6
  CHOLANGIOCARCINOMA; DISTAL                 0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           8        6
[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"
          vv
clus       R0 R1 RX
  subtype1  5  0  1
  subtype2  4  0  0
  subtype3  5  0  0
  subtype4  5  1  0
  subtype5  5  2  2
  subtype6  4  2  0
D5V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        5        4        5        5        5        4
  R1        0        0        0        1        2        2
  RX        1        0        0        0        2        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1     4
  subtype2     0                         0     4
  subtype3     1                         0     4
  subtype4     1                         1     4
  subtype5     0                         0     9
  subtype6     0                         0     6
D5V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        1        0
  BLACK OR AFRICAN AMERICAN        1        0        0        1        0
  WHITE                            4        4        4        4        9
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            6
[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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 1 3
  subtype2 4 1
  subtype3 4 1
  subtype4 4 5
  subtype5 1 5
  subtype6 3 2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        5        5        9        6        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        1        1        5        5        2 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2X TCGA-ZU-A8S4 
       11.15        13.22         8.91         3.22 

$subtype2
TCGA-3X-AAVA TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W6-AA0S 
       14.63        21.37        35.41        50.70        26.56 

$subtype3
TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2U TCGA-W5-AA30 
       23.31        38.70        13.81        20.61        37.91 

$subtype4
TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA33 
        0.33        24.36        19.79        64.96        21.04        47.64 
TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
        5.59         0.69         0.85 

$subtype5
TCGA-W5-AA2T TCGA-W5-AA2I TCGA-W5-AA36 TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       40.11        63.75        46.09        48.36         5.56        23.05 

$subtype6
TCGA-ZH-A8Y1 TCGA-W5-AA2Q TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-ZH-A8Y5 
       12.66         1.64        53.06        18.25        40.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3.22    14.63    13.81     0.33     5.56     1.64 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   13.22    50.70    38.70    64.96    63.75    53.06 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   10.03    26.56    23.31    19.79    43.10    18.25 
[1] "3.2 - 13.2 (10.0)"  "14.6 - 50.7 (26.6)" "13.8 - 38.7 (23.3)"
[4] "0.3 - 65.0 (19.8)"  "5.6 - 63.8 (43.1)"  "1.6 - 53.1 (18.2)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       2        0         0        0         0         2
  subtype2       2        2         1        0         0         0
  subtype3       4        1         0        0         0         0
  subtype4       6        2         0        1         0         0
  subtype5       3        2         0        1         0         0
  subtype6       1        2         0        0         1         1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          2        2        4        6        3        1
  STAGE II         0        2        1        2        2        2
  STAGE III        0        1        0        0        0        0
  STAGE IV         0        0        0        1        1        0
  STAGE IVA        0        0        0        0        0        1
  STAGE IVB        2        0        0        0        0        1
[1] 6 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
  subtype1  2  1  1
  subtype2  2  2  1
  subtype3  4  1  0
  subtype4  6  3  0
  subtype5  3  2  1
  subtype6  1  2  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        2        2        4        6        3        1
  T2        1        2        1        3        2        2
  T3        1        1        0        0        1        2
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 4 0
  subtype3 5 0
  subtype4 7 0
  subtype5 5 0
  subtype6 3 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    4    0
  subtype3    5    0
  subtype4    7    0
  subtype5    5    0
  subtype6    3    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        1        4        5        7        5        3
  1        2        0        0        0        0        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"
D6V6, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 4 0
  subtype3 5 0
  subtype4 7 1
  subtype5 5 1
  subtype6 4 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    4    0
  subtype3    5    0
  subtype4    7    1
  subtype5    5    1
  subtype6    4    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        1        4        5        7        5        4
  1        2        0        0        1        1        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 1 3
  subtype2 4 1
  subtype3 3 2
  subtype4 2 7
  subtype5 5 1
  subtype6 3 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    4    1
  subtype3    3    2
  subtype4    2    7
  subtype5    5    1
  subtype6    3    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        1        4        3        2        5        3
  MALE          3        1        2        7        1        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          1                                   1
  subtype2                          1                                   0
  subtype3                          0                                   1
  subtype4                          0                                   1
  subtype5                          0                                   1
  subtype6                          0                                   0
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                2
  subtype2                                4
  subtype3                                4
  subtype4                                8
  subtype5                                5
  subtype6                                5
D6V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 1        1        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1        0        1        1
  CHOLANGIOCARCINOMA; INTRAHEPATIC           2        4        4        8
                                     clus
vv                                    subtype5 subtype6
  CHOLANGIOCARCINOMA; DISTAL                 0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           5        5
[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"
          vv
clus       R0 R1 RX
  subtype1  3  0  1
  subtype2  5  0  0
  subtype3  4  1  0
  subtype4  5  2  2
  subtype5  6  0  0
  subtype6  3  2  0
D6V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        3        5        4        5        6        3
  R1        0        0        1        2        0        2
  RX        1        0        0        2        0        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     3
  subtype2     1                         0     4
  subtype3     0                         0     5
  subtype4     0                         0     9
  subtype5     1                         1     4
  subtype6     0                         0     5
D6V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        0        1
  WHITE                            3        4        5        9        4
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            5
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 8 2
  subtype2 1 5
  subtype3 5 5
  subtype4 4 6
subtype1 subtype2 subtype3 subtype4 
      10        6       10       10 
subtype1 subtype2 subtype3 subtype4 
       2        5        5        6 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W5-AA2Z 
       11.15        13.22        21.37        35.41        50.70        53.06 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W6-AA0S TCGA-WD-A7RX 
       37.91        47.64        26.56         0.69 

$subtype2
TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA36 TCGA-W5-AA39 TCGA-YR-A95A 
       14.63        64.96        21.04        46.09         5.59         0.85 

$subtype3
TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2Q 
       40.11        12.66        24.36        23.31        13.81         1.64 
TCGA-W5-AA2U TCGA-W5-AA2X TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       20.61         8.91        40.41        17.06 

$subtype4
TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-W5-AA34 
        0.33        19.79        38.70        63.75        30.38        18.25 
TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZU-A8S4 
       48.36         5.56        23.05         3.22 

subtype1 subtype2 subtype3 subtype4 
    0.69     0.85     1.64     0.33 
subtype1 subtype2 subtype3 subtype4 
   53.06    64.96    40.41    63.75 
subtype1 subtype2 subtype3 subtype4 
  30.985   17.835   18.835   21.420 
[1] "0.7 - 53.1 (31.0)" "0.8 - 65.0 (17.8)" "1.6 - 40.4 (18.8)"
[4] "0.3 - 63.8 (21.4)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       5        3         1        0         0         1
  subtype2       2        2         0        2         0         0
  subtype3       5        2         0        0         1         2
  subtype4       7        2         0        0         1         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          5        2        5        7
  STAGE II         3        2        2        2
  STAGE III        1        0        0        0
  STAGE IV         0        2        0        0
  STAGE IVA        0        0        1        1
  STAGE IVB        1        0        2        0
[1] 6 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
  subtype1  5  3  2
  subtype2  2  3  1
  subtype3  5  3  2
  subtype4  7  3  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5        2        5        7
  T2        3        3        3        3
  T3        2        1        2        0
[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"
D7V5, binary
          cls
clus       0 1
  subtype1 8 1
  subtype2 4 0
  subtype3 7 3
  subtype4 7 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2    4    0
  subtype3    7    3
  subtype4    7    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        8        4        7        7
  1        1        0        3        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus       0 1
  subtype1 7 1
  subtype2 4 2
  subtype3 8 2
  subtype4 9 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    4    2
  subtype3    8    2
  subtype4    9    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7        4        8        9
  1        1        2        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"
D7V7, binary
          cls
clus       0 1
  subtype1 6 4
  subtype2 3 3
  subtype3 5 5
  subtype4 6 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    4
  subtype2    3    3
  subtype3    5    5
  subtype4    6    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        3        5        6
  MALE          4        3        5        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          2                                   0
  subtype2                          0                                   2
  subtype3                          0                                   2
  subtype4                          0                                   0
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                8
  subtype2                                4
  subtype3                                8
  subtype4                               10
D7V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 2        0        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        0        2        2        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           8        4        8       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 RX
  subtype1  8  1  1
  subtype2  4  1  1
  subtype3  7  2  1
  subtype4  9  1  0
D7V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        8        4        7        9
  R1        1        1        2        1
  RX        1        1        1        0
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0     8
  subtype2     0                         0     6
  subtype3     0                         1     9
  subtype4     1                         1     8
D7V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        1        1
  WHITE                            8        6        9        8
[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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 5 3
  subtype2 6 4
  subtype3 1 3
  subtype4 1 4
  subtype5 2 3
  subtype6 3 1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8       10        4        5        5        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        4        3        4        3        1 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVA TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R 
       11.15        13.22        14.63        21.37        35.41        50.70 
TCGA-W6-AA0S TCGA-ZU-A8S4 
       26.56         3.22 

$subtype2
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2U 
       40.11        24.36        23.31        13.81         1.64        20.61 
TCGA-W5-AA2X TCGA-W5-AA30 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        8.91        37.91        40.41        17.06 

$subtype3
TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-ZD-A8I3 
       38.70        63.75        30.38         5.56 

$subtype4
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA36 TCGA-W5-AA39 TCGA-WD-A7RX 
       64.96        21.04        46.09         5.59         0.69 

$subtype5
TCGA-ZH-A8Y1 TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-W5-AA38 TCGA-ZH-A8Y2 
       12.66        53.06        18.25        48.36        23.05 

$subtype6
TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-W5-AA33 TCGA-YR-A95A 
        0.33        19.79        47.64         0.85 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3.22     1.64     5.56     0.69    12.66     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   50.70    40.41    63.75    64.96    53.06    47.64 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   18.00    21.96    34.54    21.04    23.05    10.32 
[1] "3.2 - 50.7 (18.0)"  "1.6 - 40.4 (22.0)"  "5.6 - 63.8 (34.5)" 
[4] "0.7 - 65.0 (21.0)"  "12.7 - 53.1 (23.1)" "0.3 - 47.6 (10.3)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       4        2         1        0         0         1
  subtype2       6        2         0        0         0         2
  subtype3       1        2         0        0         1         0
  subtype4       2        2         0        1         0         0
  subtype5       3        1         0        0         1         0
  subtype6       3        0         0        1         0         0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          4        6        1        2        3        3
  STAGE II         2        2        2        2        1        0
  STAGE III        1        0        0        0        0        0
  STAGE IV         0        0        0        1        0        1
  STAGE IVA        0        0        1        0        1        0
  STAGE IVB        1        2        0        0        0        0
[1] 6 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
  subtype1  4  2  2
  subtype2  6  3  1
  subtype3  1  3  0
  subtype4  2  2  1
  subtype5  3  1  1
  subtype6  3  1  0
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        4        6        1        2        3        3
  T2        2        3        3        2        1        1
  T3        2        1        0        1        1        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 8 2
  subtype3 3 1
  subtype4 4 0
  subtype5 3 1
  subtype6 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    8    2
  subtype3    3    1
  subtype4    4    0
  subtype5    3    1
  subtype6    3    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        5        8        3        4        3        3
  1        1        2        1        0        1        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 8 2
  subtype3 4 0
  subtype4 3 1
  subtype5 5 0
  subtype6 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    8    2
  subtype3    4    0
  subtype4    3    1
  subtype5    5    0
  subtype6    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        5        8        4        3        5        3
  1        1        2        0        1        0        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus       0 1
  subtype1 5 3
  subtype2 4 6
  subtype3 3 1
  subtype4 3 2
  subtype5 5 0
  subtype6 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    3
  subtype2    4    6
  subtype3    3    1
  subtype4    3    2
  subtype5    5    0
  subtype6    0    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        5        4        3        3        5        0
  MALE          3        6        1        2        0        4
[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       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          2                                   0
  subtype2                          0                                   2
  subtype3                          0                                   0
  subtype4                          0                                   1
  subtype5                          0                                   0
  subtype6                          0                                   1
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                6
  subtype2                                8
  subtype3                                4
  subtype4                                4
  subtype5                                5
  subtype6                                3
D8V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 2        0        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        0        2        0        1
  CHOLANGIOCARCINOMA; INTRAHEPATIC           6        8        4        4
                                     clus
vv                                    subtype5 subtype6
  CHOLANGIOCARCINOMA; DISTAL                 0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        0        1
  CHOLANGIOCARCINOMA; INTRAHEPATIC           5        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 RX
  subtype1  8  0  0
  subtype2  8  1  1
  subtype3  3  1  0
  subtype4  3  0  2
  subtype5  3  2  0
  subtype6  3  1  0
D8V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        8        8        3        3        3        3
  R1        0        1        1        0        2        1
  RX        0        1        0        2        0        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0     6
  subtype2     0                         1     9
  subtype3     1                         0     3
  subtype4     0                         0     5
  subtype5     0                         1     4
  subtype6     0                         0     4
D8V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        1        0        0        1
  WHITE                            6        9        3        5        4
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            4
[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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2      0 1
  subtype1 6 2
  subtype2 2 4
  subtype3 3 4
  subtype4 4 3
  subtype5 3 5
subtype1 subtype2 subtype3 subtype4 subtype5 
       8        6        7        7        8 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        4        4        3        5 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W5-AA2Z TCGA-W5-AA30 
       11.15        13.22        35.41        50.70        53.06        37.91 
TCGA-W5-AA33 TCGA-WD-A7RX 
       47.64         0.69 

$subtype2
TCGA-3X-AAVA TCGA-W5-AA2O TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W6-AA0S TCGA-ZH-A8Y6 
       14.63        21.04        18.25        46.09        26.56        17.06 

$subtype3
TCGA-ZH-A8Y4 TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA38 
       24.36        23.31        64.96        20.61         8.91        48.36 
TCGA-W5-AA39 
        5.59 

$subtype4
TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-ZH-A8Y2 
       40.11        12.66        21.37        13.81         1.64        23.05 
TCGA-ZH-A8Y5 
       40.41 

$subtype5
TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-YR-A95A 
        0.33        19.79        38.70        63.75        30.38         0.85 
TCGA-ZD-A8I3 TCGA-ZU-A8S4 
        5.56         3.22 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.69    14.63     5.59     1.64     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 
   53.06    46.09    64.96    40.41    63.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
  36.660   19.645   23.310   21.370   12.675 
[1] "0.7 - 53.1 (36.7)"  "14.6 - 46.1 (19.6)" "5.6 - 65.0 (23.3)" 
[4] "1.6 - 40.4 (21.4)"  "0.3 - 63.8 (12.7)" 
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       4        2         1        0         0         1
  subtype2       4        1         0        1         0         0
  subtype3       5        1         0        0         0         1
  subtype4       2        3         0        0         1         1
  subtype5       4        2         0        1         1         0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          4        4        5        2        4
  STAGE II         2        1        1        3        2
  STAGE III        1        0        0        0        0
  STAGE IV         0        1        0        0        1
  STAGE IVA        0        0        0        1        1
  STAGE IVB        1        0        1        1        0
[1] 6 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
  subtype1  4  2  2
  subtype2  4  1  1
  subtype3  5  2  0
  subtype4  2  3  2
  subtype5  4  4  0
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4        4        5        2        4
  T2        2        1        2        3        4
  T3        2        1        0        2        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"
D9V5, binary
          cls
clus       0 1
  subtype1 6 1
  subtype2 5 0
  subtype3 6 1
  subtype4 4 2
  subtype5 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    5    0
  subtype3    6    1
  subtype4    4    2
  subtype5    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        6        5        6        4        5
  1        1        0        1        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"
D9V6, binary
          cls
clus       0 1
  subtype1 6 1
  subtype2 4 1
  subtype3 6 1
  subtype4 6 1
  subtype5 6 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    4    1
  subtype3    6    1
  subtype4    6    1
  subtype5    6    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        6        4        6        6        6
  1        1        1        1        1        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"
D9V7, binary
          cls
clus       0 1
  subtype1 5 3
  subtype2 5 1
  subtype3 4 3
  subtype4 3 4
  subtype5 3 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    3
  subtype2    5    1
  subtype3    4    3
  subtype4    3    4
  subtype5    3    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        5        5        4        3        3
  MALE          3        1        3        4        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       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          2                                   0
  subtype2                          0                                   1
  subtype3                          0                                   2
  subtype4                          0                                   0
  subtype5                          0                                   1
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                6
  subtype2                                5
  subtype3                                5
  subtype4                                7
  subtype5                                7
D9V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 2        0        0        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        0        1        2        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           6        5        5        7
                                     clus
vv                                    subtype5
  CHOLANGIOCARCINOMA; DISTAL                 0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1
  CHOLANGIOCARCINOMA; INTRAHEPATIC           7
[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"
          vv
clus       R0 R1 RX
  subtype1  6  1  1
  subtype2  6  0  0
  subtype3  4  1  2
  subtype4  6  1  0
  subtype5  6  2  0
D9V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        6        6        4        6        6
  R1        1        0        1        1        2
  RX        1        0        2        0        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     7
  subtype2     0                         1     5
  subtype3     0                         0     7
  subtype4     1                         1     5
  subtype5     1                         0     7
D9V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0        1        0
  WHITE                            7        5        7        5        7
[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"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2      0 1
  subtype1 4 2
  subtype2 2 6
  subtype3 7 2
  subtype4 3 4
  subtype5 2 4
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        8        9        7        6 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        6        2        4        4 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVA TCGA-W5-AA2Z TCGA-W6-AA0S TCGA-ZH-A8Y6 
       11.15        13.22        14.63        53.06        26.56        17.06 

$subtype2
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-3X-AAVC TCGA-W5-AA2I TCGA-W5-AA2X TCGA-W5-AA36 
       40.11        24.36        23.31        63.75         8.91        46.09 
TCGA-W5-AA38 TCGA-ZH-A8Y2 
       48.36        23.05 

$subtype3
TCGA-ZH-A8Y1 TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2R 
       12.66        21.37        13.81        35.41         1.64        50.70 
TCGA-W5-AA2U TCGA-W5-AA30 TCGA-ZH-A8Y5 
       20.61        37.91        40.41 

$subtype4
TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-4G-AAZO TCGA-W5-AA2W TCGA-W5-AA34 TCGA-ZD-A8I3 
        0.33        19.79        38.70        30.38        18.25         5.56 
TCGA-ZU-A8S4 
        3.22 

$subtype5
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA33 TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
       64.96        21.04        47.64         5.59         0.69         0.85 

subtype1 subtype2 subtype3 subtype4 subtype5 
   11.15     8.91     1.64     0.33     0.69 
subtype1 subtype2 subtype3 subtype4 subtype5 
   53.06    63.75    50.70    38.70    64.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.845   32.235   21.370   18.250   13.315 
[1] "11.2 - 53.1 (15.8)" "8.9 - 63.8 (32.2)"  "1.6 - 50.7 (21.4)" 
[4] "0.3 - 38.7 (18.2)"  "0.7 - 65.0 (13.3)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       3        2         0        0         0         1
  subtype2       5        1         0        1         0         1
  subtype3       4        2         1        0         1         1
  subtype4       4        2         0        0         1         0
  subtype5       3        2         0        1         0         0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          3        5        4        4        3
  STAGE II         2        1        2        2        2
  STAGE III        0        0        1        0        0
  STAGE IV         0        1        0        0        1
  STAGE IVA        0        0        1        1        0
  STAGE IVB        1        1        1        0        0
[1] 6 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
  subtype1  3  2  1
  subtype2  5  2  1
  subtype3  4  2  3
  subtype4  4  3  0
  subtype5  3  3  0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3        5        4        4        3
  T2        2        2        2        3        3
  T3        1        1        3        0        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"
D10V5, binary
          cls
clus       0 1
  subtype1 4 1
  subtype2 6 1
  subtype3 7 2
  subtype4 5 1
  subtype5 4 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    6    1
  subtype3    7    2
  subtype4    5    1
  subtype5    4    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        4        6        7        5        4
  1        1        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"
D10V6, binary
          cls
clus       0 1
  subtype1 4 1
  subtype2 6 2
  subtype3 8 1
  subtype4 6 0
  subtype5 4 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    6    2
  subtype3    8    1
  subtype4    6    0
  subtype5    4    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        4        6        8        6        4
  1        1        2        1        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"
D10V7, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 5 3
  subtype3 4 5
  subtype4 4 3
  subtype5 2 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    5    3
  subtype3    4    5
  subtype4    4    3
  subtype5    2    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        5        5        4        4        2
  MALE          1        3        5        3        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       CHOLANGIOCARCINOMA; DISTAL CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  subtype1                          1                                   0
  subtype2                          0                                   3
  subtype3                          1                                   0
  subtype4                          0                                   0
  subtype5                          0                                   1
          vv
clus       CHOLANGIOCARCINOMA; INTRAHEPATIC
  subtype1                                5
  subtype2                                5
  subtype3                                8
  subtype4                                7
  subtype5                                5
D10V8, multiclass
                                     clus
vv                                    subtype1 subtype2 subtype3 subtype4
  CHOLANGIOCARCINOMA; DISTAL                 1        0        1        0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        0        3        0        0
  CHOLANGIOCARCINOMA; INTRAHEPATIC           5        5        8        7
                                     clus
vv                                    subtype5
  CHOLANGIOCARCINOMA; DISTAL                 0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR        1
  CHOLANGIOCARCINOMA; INTRAHEPATIC           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"
          vv
clus       R0 R1 RX
  subtype1  5  1  0
  subtype2  6  1  1
  subtype3  8  1  0
  subtype4  6  1  0
  subtype5  3  1  2
D10V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        5        6        8        6        3
  R1        1        1        1        1        1
  RX        0        1        0        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1     4
  subtype2     0                         1     7
  subtype3     1                         0     8
  subtype4     1                         0     6
  subtype5     0                         0     6
D10V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        1        0
  BLACK OR AFRICAN AMERICAN        1        1        0        0        0
  WHITE                            4        7        8        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"
