[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/15076818/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/15087707/CHOL-TP.mergedcluster.txt"

nPatients in clinical file=36, in cluster file=36, common to both=36
[1] 10 36
[1] "CN_CNMF"
[1] 3
 1  2 
19 17 
 1  2 
19 17 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
13 10 13 
 1  2  3 
13 10 13 
[1] "RPPA_CNMF"
[1] 3
 1  2 
11 19 
 1  2 
11 19 
[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 
12 15  9 
 1  2  3 
12 15  9 
[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 
 9  6 10 11 
 1  2  3  4 
 9  6 10 11 
[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 
15 21 
 1  2 
15 21 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 
6 3 3 9 5 5 5 
1 2 3 4 5 6 7 
6 3 3 9 5 5 5 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 36 columns.

[1] "Batch" "15"   
[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=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'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"               
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
[7] "RACE"                 
YEARS_TO_BIRTH, nv=28, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 12  7
  subtype2  6 11
subtype1 subtype2 
      19       17 
subtype1 subtype2 
       7       11 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        13.22        23.31        10.16        64.96        20.88 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA31 TCGA-W5-AA33 
        1.64        48.82        30.38         8.91         0.33        35.18 
TCGA-W5-AA38 TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       31.69         0.85         5.56        12.66        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

$subtype2
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2T 
       14.63        20.02         6.77        63.75        21.04        40.11 
TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 
       20.61         5.10        35.47        18.25        46.09         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       18.05         0.69        23.05        24.36        33.37 

subtype1 subtype2 
    0.33     0.69 
subtype1 subtype2 
   64.96    63.75 
subtype1 subtype2 
   13.22    20.61 
[1] "0.3 - 65.0 (13.2)" "0.7 - 63.8 (20.6)"
[1] "hr=" "1.4"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1      10        3         1        1         2         2
  subtype2       9        6         0        1         0         1
D1V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I         10        9
  STAGE II         3        6
  STAGE III        1        0
  STAGE IV         1        1
  STAGE IVA        2        0
  STAGE IVB        2        1
[1] 6 2
[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 10  6  3
  subtype2  9  6  2
D1V4, multiclass
    clus
vv   subtype1 subtype2
  T1       10        9
  T2        6        6
  T3        3        2
[1] 3 2
[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 13  4
  subtype2 13  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    4
  subtype2   13    1
   clus
vv  subtype1 subtype2
  0       13       13
  1        4        1
[1] 2 2
[1] FALSE
D1V6, binary
          cls
clus        0  1
  subtype1 15  3
  subtype2 13  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    3
  subtype2   13    2
   clus
vv  subtype1 subtype2
  0       15       13
  1        3        2
[1] 2 2
[1] FALSE
D1V7, binary
          cls
clus        0  1
  subtype1 10  9
  subtype2 10  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    9
  subtype2   10    7
        clus
vv       subtype1 subtype2
  FEMALE       10       10
  MALE          9        7
[1] 2 2
[1] FALSE
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    15
  subtype2     0                         1    16
D1V8, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            3        0
  BLACK OR AFRICAN AMERICAN        1        1
  WHITE                           15       16
[1] 3 2
[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 4
  subtype2 3 7
  subtype3 6 7
subtype1 subtype2 subtype3 
      13       10       13 
subtype1 subtype2 subtype3 
       4        7        7 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R 
       11.15        13.22        23.31        10.16        20.88        48.82 
TCGA-W5-AA2X TCGA-W5-AA31 TCGA-W5-AA33 TCGA-WD-A7RX TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        8.91         0.33        35.18         0.69        17.06        13.45 
TCGA-ZU-A8S4 
       13.22 

$subtype2
TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 
       14.63        64.96        21.04        18.25        46.09        31.69 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y2 
        5.59        18.05         0.85        23.05 

$subtype3
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U 
       20.02         6.77        63.75         1.64        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 
       30.38         5.10        35.47         5.56        12.66        24.36 
TCGA-ZH-A8Y5 
       33.37 

subtype1 subtype2 subtype3 
    0.33     0.85     1.64 
subtype1 subtype2 subtype3 
   48.82    64.96    63.75 
subtype1 subtype2 subtype3 
  13.220   19.645   20.610 
[1] "0.3 - 48.8 (13.2)" "0.8 - 65.0 (19.6)" "1.6 - 63.8 (20.6)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       8        2         1        0         0         2
  subtype2       6        2         0        2         0         0
  subtype3       5        5         0        0         2         1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          8        6        5
  STAGE II         2        2        5
  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  3  2
  subtype2  6  3  1
  subtype3  5  6  2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        6        5
  T2        3        3        6
  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  9  2
  subtype2  7  0
  subtype3 10  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    2
  subtype2    7    0
  subtype3   10    3
   clus
vv  subtype1 subtype2 subtype3
  0        9        7       10
  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  9  2
  subtype2  7  2
  subtype3 12  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    2
  subtype2    7    2
  subtype3   12    1
   clus
vv  subtype1 subtype2 subtype3
  0        9        7       12
  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 7
  subtype2 7 3
  subtype3 7 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    7
  subtype2    7    3
  subtype3    7    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6        7        7
  MALE          7        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    10
  subtype2     0                         1     9
  subtype3     1                         0    12
D2V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        1
  BLACK OR AFRICAN AMERICAN        1        1        0
  WHITE                           10        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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  6  5
  subtype2  9 10
subtype1 subtype2 
      11       19 
subtype1 subtype2 
       5       10 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W5-AA2X 
       11.15        14.63        64.96        20.88        48.82         8.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA39 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       35.18        18.25         5.59        17.06        13.45 

$subtype2
TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2U 
       23.31         6.77        63.75        21.04         1.64        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA36 TCGA-W5-AA38 
       30.38         5.10        35.47         0.33        46.09        31.69 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
       18.05         0.69         0.85         5.56        12.66        23.05 
TCGA-ZH-A8Y5 
       33.37 

subtype1 subtype2 
    5.59     0.33 
subtype1 subtype2 
   64.96    63.75 
subtype1 subtype2 
   17.06    20.61 
[1] "5.6 - 65.0 (17.1)" "0.3 - 63.8 (20.6)"
[1] "hr=" "1.3"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       7        2         1        0         0         1
  subtype2      10        4         0        2         2         1
D3V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          7       10
  STAGE II         2        4
  STAGE III        1        0
  STAGE IV         0        2
  STAGE IVA        0        2
  STAGE IVB        1        1
[1] 6 2
[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  3  1
  subtype2 10  6  3
D3V4, multiclass
    clus
vv   subtype1 subtype2
  T1        7       10
  T2        3        6
  T3        1        3
[1] 3 2
[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  9  1
  subtype2 13  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2   13    3
   clus
vv  subtype1 subtype2
  0        9       13
  1        1        3
[1] 2 2
[1] FALSE
D3V6, binary
          cls
clus        0  1
  subtype1 10  1
  subtype2 14  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    1
  subtype2   14    3
   clus
vv  subtype1 subtype2
  0       10       14
  1        1        3
[1] 2 2
[1] FALSE
D3V7, binary
          cls
clus        0  1
  subtype1  6  5
  subtype2 11  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    5
  subtype2   11    8
        clus
vv       subtype1 subtype2
  FEMALE        6       11
  MALE          5        8
[1] 2 2
[1] FALSE
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1     9
  subtype2     1                         1    17
D3V8, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            1        1
  BLACK OR AFRICAN AMERICAN        1        1
  WHITE                            9       17
[1] 3 2
[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-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2X TCGA-W5-AA34 TCGA-ZH-A8Y1 
       11.15        20.88        63.75         8.91        18.25        12.66 

$subtype2
TCGA-3X-AAVA TCGA-W5-AA2G TCGA-W5-AA2R TCGA-W5-AA33 TCGA-W5-AA39 TCGA-ZH-A8Y6 
       14.63        64.96        48.82        35.18         5.59        17.06 
TCGA-ZH-A8Y8 
       13.45 

$subtype3
TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA38 TCGA-WD-A7RX 
       23.31         6.77        20.61        35.47        31.69         0.69 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        5.56        23.05 

$subtype4
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA36 
       21.04         1.64        30.38         5.10         0.33        46.09 
TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y5 
       18.05         0.85        33.37 

subtype1 subtype2 subtype3 subtype4 
    8.91     5.59     0.69     0.33 
subtype1 subtype2 subtype3 subtype4 
   63.75    64.96    35.47    46.09 
subtype1 subtype2 subtype3 subtype4 
  15.455   17.060   21.830   18.050 
[1] "8.9 - 63.8 (15.5)" "5.6 - 65.0 (17.1)" "0.7 - 35.5 (21.8)"
[4] "0.3 - 46.1 (18.1)"
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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     5
  subtype2     0                         1     6
  subtype3     1                         1     6
  subtype4     0                         0     9
D4V8, 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 7 5
  subtype2 7 8
  subtype3 4 5
subtype1 subtype2 subtype3 
      12       15        9 
subtype1 subtype2 subtype3 
       5        8        5 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2H 
       11.15        14.63        13.22        23.31        10.16        20.88 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W6-AA0S TCGA-ZU-A8S4 
       48.82        20.61         8.91        35.47        18.05        13.22 

$subtype2
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2W 
       20.02         6.77        63.75         1.64        40.11        30.38 
TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y1 
        5.10        18.25        46.09        31.69         5.56        12.66 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       23.05        33.37        17.06 

$subtype3
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA39 TCGA-WD-A7RX 
       64.96        21.04         0.33        35.18         5.59         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
        0.85        24.36        13.45 

subtype1 subtype2 subtype3 
    8.91     1.64     0.33 
subtype1 subtype2 subtype3 
   48.82    63.75    64.96 
subtype1 subtype2 subtype3 
   16.34    20.02    13.45 
[1] "8.9 - 48.8 (16.3)" "1.6 - 63.8 (20.0)" "0.3 - 65.0 (13.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       7        2         1        0         0         2
  subtype2       6        5         0        1         2         1
  subtype3       6        2         0        1         0         0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          7        6        6
  STAGE II         2        5        2
  STAGE III        1        0        0
  STAGE IV         0        1        1
  STAGE IVA        0        2        0
  STAGE IVB        2        1        0
[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  7  3  2
  subtype2  6  6  3
  subtype3  6  3  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7        6        6
  T2        3        6        3
  T3        2        3        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"
D5V5, binary
          cls
clus        0  1
  subtype1  8  2
  subtype2 11  3
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    2
  subtype2   11    3
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0        8       11        7
  1        2        3        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1  8  2
  subtype2 13  2
  subtype3  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    2
  subtype2   13    2
  subtype3    7    1
   clus
vv  subtype1 subtype2 subtype3
  0        8       13        7
  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"
D5V7, binary
          cls
clus        0  1
  subtype1  7  5
  subtype2 11  4
  subtype3  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2   11    4
  subtype3    2    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       11        2
  MALE          5        4        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    10
  subtype2     1                         2    12
  subtype3     0                         0     9
D5V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        0
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                           10       12        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

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        13.22 

$subtype2
TCGA-3X-AAVA TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R TCGA-W6-AA0S 
       14.63        10.16        20.88        48.82        18.05 

$subtype3
TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2U TCGA-W5-AA30 
       23.31        20.02         6.77        20.61        35.47 

$subtype4
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA39 TCGA-WD-A7RX 
       64.96        21.04         0.33        35.18         5.59         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
        0.85        24.36        13.45 

$subtype5
TCGA-W5-AA2I TCGA-W5-AA2T TCGA-W5-AA36 TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       63.75        40.11        46.09        31.69         5.56        23.05 

$subtype6
TCGA-W5-AA2Q TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 
        1.64         5.10        18.25        12.66        33.37 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    8.91    10.16     6.77     0.33     5.56     1.64 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   13.22    48.82    35.47    64.96    63.75    33.37 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  12.185   18.050   20.610   13.450   35.900   12.660 
[1] "8.9 - 13.2 (12.2)"  "10.2 - 48.8 (18.1)" "6.8 - 35.5 (20.6)" 
[4] "0.3 - 65.0 (13.4)"  "5.6 - 63.8 (35.9)"  "1.6 - 33.4 (12.7)" 
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       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
D6V8, 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 7 2
  subtype2 1 5
  subtype3 5 5
  subtype4 5 6
subtype1 subtype2 subtype3 subtype4 
       9        6       10       11 
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-AA30 
       11.15        13.22        10.16        20.88        48.82        35.47 
TCGA-W5-AA33 TCGA-W6-AA0S TCGA-WD-A7RX 
       35.18        18.05         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-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X 
       23.31         6.77         1.64        40.11        20.61         8.91 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       12.66        24.36        33.37        17.06 

$subtype4
TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA34 
       20.02        63.75        30.38         5.10         0.33        18.25 
TCGA-W5-AA38 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       31.69         5.56        23.05        13.45        13.22 

subtype1 subtype2 subtype3 subtype4 
    0.69     0.85     1.64     0.33 
subtype1 subtype2 subtype3 subtype4 
   48.82    64.96    40.11    63.75 
subtype1 subtype2 subtype3 subtype4 
  18.050   17.835   18.835   18.250 
[1] "0.7 - 48.8 (18.1)" "0.8 - 65.0 (17.8)" "1.6 - 40.1 (18.8)"
[4] "0.3 - 63.8 (18.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       5        2         1        0         0         1
  subtype2       2        2         0        2         0         0
  subtype3       5        2         0        0         1         2
  subtype4       7        3         0        0         1         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          5        2        5        7
  STAGE II         2        2        2        3
  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  2  2
  subtype2  2  3  1
  subtype3  5  3  2
  subtype4  7  4  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5        2        5        7
  T2        2        3        3        4
  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 7 1
  subtype2 4 0
  subtype3 7 3
  subtype4 8 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    4    0
  subtype3    7    3
  subtype4    8    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7        4        7        8
  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  6  1
  subtype2  4  2
  subtype3  8  2
  subtype4 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    4    2
  subtype3    8    2
  subtype4   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        6        4        8       10
  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 5 4
  subtype2 3 3
  subtype3 5 5
  subtype4 7 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    4
  subtype2    3    3
  subtype3    5    5
  subtype4    7    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        5        3        5        7
  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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0     7
  subtype2     0                         0     6
  subtype3     0                         1     9
  subtype4     1                         1     9
D7V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        1        1
  WHITE                            7        6        9        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(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-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R 
       11.15        14.63        13.22        10.16        20.88        48.82 
TCGA-W6-AA0S TCGA-ZU-A8S4 
       18.05        13.22 

$subtype2
TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X 
       23.31         6.77         1.64        40.11        20.61         8.91 
TCGA-W5-AA30 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       35.47        24.36        33.37        17.06 

$subtype3
TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-ZD-A8I3 
       20.02        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-W5-AA2Z TCGA-W5-AA34 TCGA-W5-AA38 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
        5.10        18.25        31.69        12.66        23.05 

$subtype6
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-YR-A95A TCGA-ZH-A8Y8 
        0.33        35.18         0.85        13.45 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   10.16     1.64     5.56     0.69     5.10     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   48.82    40.11    63.75    64.96    31.69    35.18 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  13.925   21.960   25.200   21.040   18.250    7.150 
[1] "10.2 - 48.8 (13.9)" "1.6 - 40.1 (22.0)"  "5.6 - 63.8 (25.2)" 
[4] "0.7 - 65.0 (21.0)"  "5.1 - 31.7 (18.2)"  "0.3 - 35.2 (7.1)"  
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       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
D8V8, 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  7  8
  subtype2 11 10
subtype1 subtype2 
      15       21 
subtype1 subtype2 
       8       10 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-W5-AA2Z 
       11.15        13.22        20.02        63.75        30.38         5.10 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-YR-A95A TCGA-ZD-A8I3 
        0.33        35.18        18.25        31.69         0.85         5.56 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       23.05        13.45        13.22 

$subtype2
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        23.31        10.16         6.77        64.96        20.88 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X 
       21.04         1.64        48.82        40.11        20.61         8.91 
TCGA-W5-AA30 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZH-A8Y1 
       35.47        46.09         5.59        18.05         0.69        12.66 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       24.36        33.37        17.06 

subtype1 subtype2 
    0.33     0.69 
subtype1 subtype2 
   63.75    64.96 
subtype1 subtype2 
   13.45    20.61 
[1] "0.3 - 63.8 (13.4)" "0.7 - 65.0 (20.6)"
[1] "hr=" "1.4"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       9        3         0        1         1         1
  subtype2      10        6         1        1         1         2
D9V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          9       10
  STAGE II         3        6
  STAGE III        0        1
  STAGE IV         1        1
  STAGE IVA        1        1
  STAGE IVB        1        2
[1] 6 2
[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  9  5  1
  subtype2 10  7  4
D9V4, multiclass
    clus
vv   subtype1 subtype2
  T1        9       10
  T2        5        7
  T3        1        4
[1] 3 2
[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 10  2
  subtype2 16  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2   16    3
   clus
vv  subtype1 subtype2
  0       10       16
  1        2        3
[1] 2 2
[1] FALSE
D9V6, binary
          cls
clus        0  1
  subtype1 12  2
  subtype2 16  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    2
  subtype2   16    3
   clus
vv  subtype1 subtype2
  0       12       16
  1        2        3
[1] 2 2
[1] FALSE
D9V7, binary
          cls
clus        0  1
  subtype1  8  7
  subtype2 12  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    7
  subtype2   12    9
        clus
vv       subtype1 subtype2
  FEMALE        8       12
  MALE          7        9
[1] 2 2
[1] FALSE
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    12
  subtype2     1                         1    19
D9V8, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            2        1
  BLACK OR AFRICAN AMERICAN        1        1
  WHITE                           12       19
[1] 3 2
[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 1 2
  subtype3 3 0
  subtype4 3 6
  subtype5 3 2
  subtype6 2 3
  subtype7 2 3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        3        3        9        5        5        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        2        0        6        2        3        3 
$subtype1
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-W5-AA2Z TCGA-W6-AA0S TCGA-ZH-A8Y6 
       11.15        14.63        13.22         5.10        18.05        17.06 

$subtype2
TCGA-3X-AAVC TCGA-W5-AA2X TCGA-ZH-A8Y4 
       23.31         8.91        24.36 

$subtype3
TCGA-3X-AAVE TCGA-W5-AA2H TCGA-W5-AA2R 
       10.16        20.88        48.82 

$subtype4
TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2W TCGA-W5-AA31 TCGA-W5-AA34 TCGA-YR-A95A 
       20.02        63.75        30.38         0.33        18.25         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        5.56        13.45        13.22 

$subtype5
TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2U TCGA-W5-AA30 TCGA-ZH-A8Y1 
        6.77         1.64        20.61        35.47        12.66 

$subtype6
TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA33 TCGA-W5-AA39 TCGA-WD-A7RX 
       64.96        21.04        35.18         5.59         0.69 

$subtype7
TCGA-W5-AA2T TCGA-W5-AA36 TCGA-W5-AA38 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       40.11        46.09        31.69        23.05        33.37 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    5.10     8.91    10.16     0.33     1.64     0.69    23.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   18.05    24.36    48.82    63.75    35.47    64.96    46.09 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  13.925   23.310   20.880   13.450   12.660   21.040   33.370 
[1] "5.1 - 18.1 (13.9)"  "8.9 - 24.4 (23.3)"  "10.2 - 48.8 (20.9)"
[4] "0.3 - 63.8 (13.4)"  "1.6 - 35.5 (12.7)"  "0.7 - 65.0 (21.0)" 
[7] "23.1 - 46.1 (33.4)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  subtype1       3        2         0        0         0         1
  subtype2       2        0         0        0         0         1
  subtype3       1        1         1        0         0         0
  subtype4       5        2         0        1         1         0
  subtype5       3        1         0        0         1         0
  subtype6       3        2         0        0         0         0
  subtype7       2        1         0        1         0         1
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          3        2        1        5        3        3        2
  STAGE II         2        0        1        2        1        2        1
  STAGE III        0        0        1        0        0        0        0
  STAGE IV         0        0        0        1        0        0        1
  STAGE IVA        0        0        0        1        1        0        0
  STAGE IVB        1        1        0        0        0        0        1
[1] 6 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
  subtype1  3  2  1
  subtype2  2  1  0
  subtype3  1  1  1
  subtype4  5  4  0
  subtype5  3  1  1
  subtype6  3  2  0
  subtype7  2  1  2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        3        2        1        5        3        3        2
  T2        2        1        1        4        1        2        1
  T3        1        0        1        0        1        0        2
[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"
D10V5, binary
          cls
clus       0 1
  subtype1 4 1
  subtype2 2 1
  subtype3 3 0
  subtype4 6 1
  subtype5 4 1
  subtype6 4 0
  subtype7 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    2    1
  subtype3    3    0
  subtype4    6    1
  subtype5    4    1
  subtype6    4    0
  subtype7    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        4        2        3        6        4        4        3
  1        1        1        0        1        1        0        1
[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"
D10V6, binary
          cls
clus       0 1
  subtype1 4 1
  subtype2 2 1
  subtype3 3 0
  subtype4 7 1
  subtype5 5 0
  subtype6 4 0
  subtype7 3 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    2    1
  subtype3    3    0
  subtype4    7    1
  subtype5    5    0
  subtype6    4    0
  subtype7    3    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        4        2        3        7        5        4        3
  1        1        1        0        1        0        0        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"
D10V7, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 1 2
  subtype3 2 1
  subtype4 4 5
  subtype5 2 3
  subtype6 2 3
  subtype7 4 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    1    2
  subtype3    2    1
  subtype4    4    5
  subtype5    2    3
  subtype6    2    3
  subtype7    4    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        5        1        2        4        2        2        4
  MALE          1        2        1        5        3        3        1
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1     4
  subtype2     0                         0     3
  subtype3     1                         0     2
  subtype4     1                         0     8
  subtype5     0                         0     5
  subtype6     0                         0     5
  subtype7     0                         1     4
D10V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        1        0
  BLACK OR AFRICAN AMERICAN        1        0        0        0        0
  WHITE                            4        3        2        8        5
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            5        4
[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"
