[1] "ofn"        "-oTTGCT-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/TGCT-TP/15092576/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/15111345/TGCT-TP.mergedcluster.txt"

nPatients in clinical file=133, in cluster file=150, common to both=133
[1]  10 133
[1] "CN_CNMF"
[1] 3
 1  2  3 
44 43 46 
 1  2  3 
44 43 46 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
53 45 35 
 1  2  3 
53 45 35 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
47 11 27 18 
 1  2  3  4 
47 11 27 18 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
49 19 35 
 1  2  3 
49 19 35 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
68 36 29 
 1  2  3 
68 36 29 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
42 26 10 17  8 20 10 
 1  2  3  4  5  6  7 
42 26 10 17  8 20 10 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
51 53 29 
 1  2  3 
51 53 29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
68 36 29 
 1  2  3 
68 36 29 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
67 34 32 
 1  2  3 
67 34 32 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
36 32 36 29 
 1  2  3  4 
36 32 36 29 
[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 133 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=4,	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=127,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B430.15.0 B430.16.0
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "FALSE"  
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 133 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"     "RACE"                 
[7] "ETHNICITY"            
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
75 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
75 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
75 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
75 51  6 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
46 11  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   46    13 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
46 11  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 46

$Class1_nSamples
[1] 13

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   46    13 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 42  2
  subtype2 43  0
  subtype3 44  2
subtype1 subtype2 subtype3 
      44       43       46 
subtype1 subtype2 subtype3 
       2        0        2 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO 
       20.32        38.30       122.40        17.16         9.57        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGJ 
       36.13        40.01        52.37        71.24        63.22        75.09 
TCGA-2G-AAGP TCGA-2G-AAGZ TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKH 
      120.62        60.16        98.53        59.74        91.43       161.72 
TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        0.13         7.00         0.10        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-WZ-A7V4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       33.07        23.90         4.90         5.06         6.87        18.38 
TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90S 
       12.07        16.87        67.66        41.69         8.32        31.92 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E 
       58.88        40.96         8.15        37.02        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       11.34        46.88 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH 
       30.35        59.70       102.35       154.59       191.31        36.99 
TCGA-2G-AAGA TCGA-2G-AAGO TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH3 
       68.22       115.00       170.33        80.94        60.26        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2X-A9D5 
       61.84        59.80       176.15         6.08       122.50         2.73 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        3.52        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V5 
       16.31         3.52        36.79        41.52         3.65         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
        0.82        40.01        65.98         0.46        53.03        93.93 
TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-ZM-AA0B 
        7.89         0.43         6.90        54.35        21.96        27.55 
TCGA-ZM-AA0N 
       10.85 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG6 
       14.14        14.56        14.86        40.70        36.89        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.32        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09       108.16        59.64       106.39        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAKG 
      128.94        61.45        59.84       125.69        59.80       212.65 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AAAL 
       95.67       229.22       184.41       131.21        70.59         4.83 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-X3-A8G4 
        9.63        10.26        17.23        37.18        24.26        28.14 
TCGA-XE-AANI TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       34.22         8.88        50.96        12.92        20.12        57.90 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA06 
        0.56         5.29         7.96        39.35 

subtype1 subtype2 subtype3 
    0.10     0.16     0.56 
subtype1 subtype2 subtype3 
  161.72   191.31   229.22 
subtype1 subtype2 subtype3 
   34.34    36.79    59.46 
[1] "0.1 - 161.7 (34.3)" "0.2 - 191.3 (36.8)" "0.6 - 229.2 (59.5)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1       4       15        5        1         4         0         1
  subtype2      10        6        4        0         2         1         0
  subtype3       5        4        2        4         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          1          1          1       10
  subtype2         1          0          0          1       15
  subtype3         1          0          5          3       21
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           4       10        5
  STAGE IA         15        6        4
  STAGE IB          5        4        2
  STAGE II          1        0        4
  STAGE IIA         4        2        0
  STAGE IIB         0        1        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        1        0        0
  STAGE IIIB        1        0        5
  STAGE IIIC        1        1        3
  STAGE IS         10       15       21
[1] 12  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 27 14  2
  subtype2 24 18  1
  subtype3 24 19  3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       27       24       24
  T2       14       18       19
  T3        2        1        3
[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       N0 N1+N2
  subtype1 13     5
  subtype2 13     3
  subtype3 20     5
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          13       13       20
  N1+N2        5        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 37  1
  subtype2 38  0
  subtype3 39  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    1
  subtype2   38    0
  subtype3   39    3
   clus
vv  subtype1 subtype2 subtype3
  0       37       38       39
  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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    38
  subtype2     1                         1    38
  subtype3     1                         2    42
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           38       38       42
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  4 37
  subtype3  5 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   37
  subtype2    4   37
  subtype3    5   37
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        4        5
  NOT HISPANIC OR LATINO       37       37       37
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 51  2
  subtype2 43  2
  subtype3 35  0
subtype1 subtype2 subtype3 
      53       45       35 
subtype1 subtype2 subtype3 
       2        2        0 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAHA 
      154.59       191.31        36.99        63.32        60.26        98.53 
TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
       59.74        91.43         6.08         2.73         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A9 
        0.10         4.83        13.58        16.31        10.26        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 
       37.68        24.99        35.61        23.90        41.52         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-AANJ TCGA-XE-AANV 
        5.06         0.16         0.82        18.38        65.98        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF 
       93.93        12.07         7.89        16.87        67.66        41.69 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90S TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        8.32         6.90        31.92        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       14.14        17.16         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        61.71        63.22        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       79.76        75.09       108.16       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 
       59.28       124.57        61.45        60.16        59.84        59.90 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 
       70.59        17.23        37.18        33.07         4.90        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANR TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       28.14         6.87         0.46        12.92        20.12        57.90 
TCGA-YU-A90Y TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        40.96         8.15 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
       67.96        92.09        59.64       128.94       170.33        80.94 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAL5 
      125.69        61.84        59.80        59.80       176.15       184.41 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A84W 
        3.52        20.68        18.15         9.14         1.38         9.63 
TCGA-SO-A8JP TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-XE-AAOL 
        3.52        40.01        34.22         8.88        50.96         0.43 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       54.35        21.96         5.29        58.88         7.96 

subtype1 subtype2 subtype3 
    0.10     0.46     0.43 
subtype1 subtype2 subtype3 
  191.31   229.22   184.41 
subtype1 subtype2 subtype3 
   27.55    59.84    50.96 
[1] "0.1 - 191.3 (27.6)" "0.5 - 229.2 (59.8)" "0.4 - 184.4 (51.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1       9       18        5        0         1         1         1
  subtype2       4        3        4        3         5         0         0
  subtype3       6        4        2        2         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          0       15
  subtype2         1          1          4          2       16
  subtype3         1          0          1          3       15
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9        4        6
  STAGE IA         18        3        4
  STAGE IB          5        4        2
  STAGE II          0        3        2
  STAGE IIA         1        5        0
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        4        1
  STAGE IIIC        0        2        3
  STAGE IS         15       16       15
[1] 12  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 34 16  2
  subtype2 18 26  1
  subtype3 23  9  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       34       18       23
  T2       16       26        9
  T3        2        1        3
[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       N0 N1+N2
  subtype1 15     3
  subtype2 17     9
  subtype3 14     1
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          15       17       14
  N1+N2        3        9        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"
D2V6, binary
          cls
clus        0  1
  subtype1 48  0
  subtype2 38  2
  subtype3 28  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    0
  subtype2   38    2
  subtype3   28    2
   clus
vv  subtype1 subtype2 subtype3
  0       48       38       28
  1        0        2        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    48
  subtype2     0                         3    42
  subtype3     1                         2    28
D2V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        1        3        2
  WHITE                           48       42       28
[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"
D2V8, binary
          cls
clus        0  1
  subtype1  4 48
  subtype2  3 37
  subtype3  4 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   48
  subtype2    3   37
  subtype3    4   26
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        4
  NOT HISPANIC OR LATINO       48       37       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 46  1
  subtype2 11  0
  subtype3 26  1
  subtype4 16  2
subtype1 subtype2 subtype3 subtype4 
      47       11       27       18 
subtype1 subtype2 subtype3 subtype4 
       1        0        1        2 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       60.26        59.90        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
       59.80       176.15         6.08         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS 
        7.00         0.10        20.68        18.15         9.14        16.31 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-XE-A8H5 
        3.52        36.79        37.68        23.90        41.52        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W 
       41.69         0.43         8.32         6.90        54.35        21.96 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        5.29        37.02        27.55        17.39        16.41 

$subtype2
TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFY TCGA-2G-AAG8 TCGA-2G-AAG9 
      191.31        14.14        17.16        36.13        63.22        63.32 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGZ TCGA-XE-AAOD TCGA-YU-A90S 
      115.00       120.62        60.16        67.66        31.92 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGC 
       14.56        36.89        52.37        71.24        72.20        72.85 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGV 
       79.76        67.96        92.09        59.64        59.28       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-2G-AALP 
      170.33        80.94       125.69       212.65       184.41        70.59 
TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
       10.26         4.90        28.14        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94I TCGA-YU-AA61 
       50.96         7.96         8.15 

$subtype4
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAGJ TCGA-2G-AAGK 
        9.57        14.86        40.01        61.71        75.09       108.16 
TCGA-2G-AAGN TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      106.39       124.57        61.45       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-XE-A8H1 TCGA-YU-A90P TCGA-YU-A90Y 
      131.21        37.18        24.26         6.87        57.90         0.56 

subtype1 subtype2 subtype3 subtype4 
    0.10    14.14     4.90     0.56 
subtype1 subtype2 subtype3 subtype4 
  176.15   191.31   212.65   229.22 
subtype1 subtype2 subtype3 subtype4 
   27.55    63.22    59.64    61.58 
[1] "0.1 - 176.2 (27.6)"  "14.1 - 191.3 (63.2)" "4.9 - 212.7 (59.6)" 
[4] "0.6 - 229.2 (61.6)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1      11       13        4        0         0         1         0
  subtype2       0        1        4        0         2         0         0
  subtype3       3        3        0        2         0         0         1
  subtype4       0        3        0        3         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1          0          0          2       15
  subtype2          1          1          0        2
  subtype3          0          2          1       14
  subtype4          0          2          1        7
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          11        0        3        0
  STAGE IA         13        1        3        3
  STAGE IB          4        4        0        0
  STAGE II          0        0        2        3
  STAGE IIA         0        2        0        1
  STAGE IIC         1        0        0        0
  STAGE III         0        0        1        0
  STAGE IIIA        0        1        0        0
  STAGE IIIB        0        1        2        2
  STAGE IIIC        2        0        1        1
  STAGE IS         15        2       14        7
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 31 16  0
  subtype2  2  9  0
  subtype3 21  4  2
  subtype4  6 11  1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       31        2       21        6
  T2       16        9        4       11
  T3        0        0        2        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       N0 N1+N2
  subtype1 16     0
  subtype2  5     4
  subtype3 12     2
  subtype4  7     3
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          16        5       12        7
  N1+N2        0        4        2        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"
D3V6, binary
          cls
clus        0  1
  subtype1 43  0
  subtype2  9  1
  subtype3 21  3
  subtype4 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    0
  subtype2    9    1
  subtype3   21    3
  subtype4   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       43        9       21       16
  1        0        1        3        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    39
  subtype2     0                         0    11
  subtype3     1                         0    25
  subtype4     0                         2    16
D3V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        1        0
  BLACK OR AFRICAN AMERICAN        2        0        0        2
  WHITE                           39       11       25       16
[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"
D3V8, binary
          cls
clus        0  1
  subtype1  5 39
  subtype2  0 10
  subtype3  3 21
  subtype4  1 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   39
  subtype2    0   10
  subtype3    3   21
  subtype4    1   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        0        3        1
  NOT HISPANIC OR LATINO       39       10       21       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 48  1
  subtype2 19  0
  subtype3 32  3
subtype1 subtype2 subtype3 
      49       19       35 
subtype1 subtype2 subtype3 
       1        0        3 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
      191.31        63.32        60.26        59.90        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 
       59.74        59.80        59.80       176.15         6.08         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX 
        0.13         3.52         7.00         0.10        20.68        18.15 
TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE 
        9.14        16.31         3.52        36.79        37.68        23.90 
TCGA-W4-A7U2 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       41.52        40.01        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 
       12.07         7.89        41.69         0.43         8.32         6.90 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       31.92        21.96         5.29        37.02        27.55        17.39 
TCGA-ZM-AA0E 
       16.41 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGG 
       14.14        17.16        71.24        72.20        63.22        67.96 
TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ 
       92.09       115.00       120.62       128.94       170.33        60.16 
TCGA-2G-AALP TCGA-W4-A7U3 TCGA-XE-A8H1 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A94I 
       70.59         4.90         6.87         8.88        67.66         7.96 
TCGA-YU-AA61 
        8.15 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.56         9.57        14.86        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       52.37        61.71        72.85        79.76        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
       59.64       106.39        59.28       124.57        61.45        80.94 
TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      125.69       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-SN-A84X TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-AANI 
      131.21        10.26        37.18        24.26        28.14        34.22 
TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90Y 
       16.87        50.96        57.90        54.35         0.56 

subtype1 subtype2 subtype3 
    0.10     4.90     0.56 
subtype1 subtype2 subtype3 
  191.31   170.33   229.22 
subtype1 subtype2 subtype3 
   30.35    67.66    59.28 
[1] "0.1 - 191.3 (30.4)" "4.9 - 170.3 (67.7)" "0.6 - 229.2 (59.3)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1      11       14        3        0         0         1         0
  subtype2       0        3        4        1         1         0         0
  subtype3       3        3        1        4         2         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1          0          1          2       16
  subtype2          1          1          1        6
  subtype3          0          3          1       16
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          11        0        3
  STAGE IA         14        3        3
  STAGE IB          3        4        1
  STAGE II          0        1        4
  STAGE IIA         0        1        2
  STAGE IIC         1        0        0
  STAGE III         0        0        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        1        3
  STAGE IIIC        2        1        1
  STAGE IS         16        6       16
[1] 11  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 33 16  0
  subtype2 10  8  1
  subtype3 17 16  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       33       10       17
  T2       16        8       16
  T3        0        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"
          vv
clus       N0 N1+N2
  subtype1 17     1
  subtype2  8     3
  subtype3 15     5
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          17        8       15
  N1+N2        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 45  0
  subtype2 13  3
  subtype3 31  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    0
  subtype2   13    3
  subtype3   31    1
   clus
vv  subtype1 subtype2 subtype3
  0       45       13       31
  1        0        3        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    42
  subtype2     0                         0    18
  subtype3     1                         2    31
D4V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        2        0        2
  WHITE                           42       18       31
[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"
D4V8, binary
          cls
clus        0  1
  subtype1  5 41
  subtype2  2 14
  subtype3  2 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   41
  subtype2    2   14
  subtype3    2   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        2
  NOT HISPANIC OR LATINO       41       14       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 67  1
  subtype2 33  3
  subtype3 29  0
subtype1 subtype2 subtype3 
      68       36       29 
subtype1 subtype2 subtype3 
       1        3        0 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       191.31        36.99        63.32        60.26        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      176.15         6.08         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
        1.38        16.31         3.52        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       35.61        23.90        41.52         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        0.82        18.38        40.01        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL 
       93.93        12.07         7.89        67.66        41.69         0.43 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
        8.32         6.90        54.35        31.92        21.96         5.29 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       14.14        17.16         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        61.71        63.22        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW 
       79.76        75.09       108.16       106.39       115.00        61.45 
TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       60.16       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      131.21        70.59        17.23        37.18        33.07        24.26 
TCGA-XE-A8H1 TCGA-XE-AAOB TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
        6.87        16.87        12.92        20.12        57.90         0.56 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       67.96        92.09        59.64       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 
      128.94       170.33        80.94        59.84       125.69       184.41 
TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOC 
        9.63        10.26         4.90        28.14        34.22         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        58.88         7.96        40.96         8.15 

subtype1 subtype2 subtype3 
    0.10     0.56     4.90 
subtype1 subtype2 subtype3 
  191.31   229.22   184.41 
subtype1 subtype2 subtype3 
  26.270   60.805   58.880 
[1] "0.1 - 191.3 (26.3)" "0.6 - 229.2 (60.8)" "4.9 - 184.4 (58.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      15       19        7        0         1         1         1
  subtype2       2        3        4        3         4         0         0
  subtype3       2        3        0        2         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          2       18
  subtype2         1          1          3          1       13
  subtype3         1          0          2          2       15
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          15        2        2
  STAGE IA         19        3        3
  STAGE IB          7        4        0
  STAGE II          0        3        2
  STAGE IIA         1        4        1
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        1        2
  STAGE IS         18       13       15
[1] 12  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 42 23  2
  subtype2 13 22  1
  subtype3 20  6  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       13       20
  T2       23       22        6
  T3        2        1        3
[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       N0 N1+N2
  subtype1 20     3
  subtype2 15     7
  subtype3 11     3
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          20       15       11
  N1+N2        3        7        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"
D5V6, binary
          cls
clus        0  1
  subtype1 60  0
  subtype2 32  2
  subtype3 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    0
  subtype2   32    2
  subtype3   22    2
   clus
vv  subtype1 subtype2 subtype3
  0       60       32       22
  1        0        2        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    59
  subtype2     0                         2    34
  subtype3     1                         1    25
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           59       34       25
[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"
D5V8, binary
          cls
clus        0  1
  subtype1  5 59
  subtype2  2 32
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   59
  subtype2    2   32
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        4
  NOT HISPANIC OR LATINO       59       32       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 41  1
  subtype2 26  0
  subtype3  8  2
  subtype4 17  0
  subtype5  8  0
  subtype6 19  1
  subtype7 10  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      42       26       10       17        8       20       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       1        0        2        0        0        1        0 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAFE TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
       20.32        38.30       154.59        63.32        60.26        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       61.84        98.53        59.74        59.80        91.43         6.08 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-SB-A76C TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-WZ-A7V4 
       20.68         1.38        37.68        24.99        35.61         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO4 
        0.16         0.82        18.38         0.46        53.03        12.07 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 
       67.66        41.69         8.32        54.35        31.92         5.29 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        17.39        16.41        11.34        46.88 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       30.35        59.70       102.35       122.40       191.31        36.99 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
       59.80       176.15        18.15         9.14        13.58        16.31 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-XE-A8H5 
        3.52        36.79        23.90        41.52         3.65        40.01 
TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90W 
       65.98        93.93         7.89         0.43         6.90        21.96 
TCGA-ZM-AA0B TCGA-ZM-AA0N 
       27.55        10.85 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAGC TCGA-2G-AAGK TCGA-2G-AAGS TCGA-2G-AAKG TCGA-2G-AALP 
       14.14        72.85       108.16        59.28       212.65        70.59 
TCGA-X3-A8G4 TCGA-XE-AAOB TCGA-XY-A8S3 TCGA-YU-A90Y 
       28.14        16.87        20.12         0.56 

$subtype4
TCGA-2G-AAFJ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGG TCGA-2G-AAGI 
       14.56        52.37        71.24        72.20        67.96        92.09 
TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAL5 
      120.62       128.94       170.33        80.94        59.84       184.41 
TCGA-SN-A84W TCGA-SN-A84X TCGA-XE-AANI TCGA-XE-AAOC TCGA-YU-A94D 
        9.63        10.26        34.22         8.88        58.88 

$subtype5
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGZ 
       17.16         9.57        16.50        63.22        68.22        60.16 
TCGA-2G-AAKH TCGA-XE-A8H1 
      161.72         6.87 

$subtype6
TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGF 
       14.86        36.13        40.01        61.71        68.38        79.76 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAKD TCGA-2G-AAKL 
       75.09       106.39       115.00        61.45       122.50        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      229.22       131.21        17.23        37.18        33.07        24.26 
TCGA-XY-A8S2 TCGA-YU-A90P 
       12.92        57.90 

$subtype7
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH4 TCGA-W4-A7U3 
       40.70        36.89        59.64       124.57       125.69         4.90 
TCGA-XE-AAOJ TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96         7.96        40.96         8.15 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.10     0.43     0.56     8.88     6.87    12.92     4.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  154.59   191.31   212.65   184.41   161.72   229.22   125.69 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  22.835   28.950   43.710   67.960   38.660   61.580   40.830 
[1] "0.1 - 154.6 (22.8)"  "0.4 - 191.3 (29.0)"  "0.6 - 212.7 (43.7)" 
[4] "8.9 - 184.4 (68.0)"  "6.9 - 161.7 (38.7)"  "12.9 - 229.2 (61.6)"
[7] "4.9 - 125.7 (40.8)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1       9       12        5        0         1         0         1
  subtype2       6        7        2        0         0         1         0
  subtype3       1        0        1        0         0         0         0
  subtype4       2        2        0        1         1         0         0
  subtype5       0        0        2        1         3         0         0
  subtype6       1        3        1        2         1         0         0
  subtype7       0        1        0        1         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          2        9
  subtype2         0          0          0          0        9
  subtype3         0          0          2          1        5
  subtype4         0          0          1          1        9
  subtype5         0          1          0          0        1
  subtype6         1          0          2          0        8
  subtype7         1          0          0          1        5
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           9        6        1        2        0        1        0
  STAGE IA         12        7        0        2        0        3        1
  STAGE IB          5        2        1        0        2        1        0
  STAGE II          0        0        0        1        1        2        1
  STAGE IIA         1        0        0        1        3        1        0
  STAGE IIB         0        1        0        0        0        0        0
  STAGE IIC         1        0        0        0        0        0        0
  STAGE III         0        0        0        0        0        1        1
  STAGE IIIA        0        0        0        0        1        0        0
  STAGE IIIB        1        0        2        1        0        2        0
  STAGE IIIC        2        0        1        1        0        0        1
  STAGE IS          9        9        5        9        1        8        5
[1] 12  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 21 18  2
  subtype2 21  5  0
  subtype3  6  3  1
  subtype4 11  4  2
  subtype5  3  5  0
  subtype6  6 14  0
  subtype7  7  2  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       21       21        6       11        3        6        7
  T2       18        5        3        4        5       14        2
  T3        2        0        1        2        0        0        1
[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"
          vv
clus       N0 N1+N2
  subtype1 11     2
  subtype2  9     1
  subtype3  5     1
  subtype4  8     2
  subtype5  2     4
  subtype6  9     3
  subtype7  2     0
D6V5, multiclass
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      13       10        6       10        6       12        2 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype3" "subtype4" "subtype5"
[13] "subtype5" "subtype6" "subtype5" "subtype6" "subtype6" "subtype4"
[19] "subtype4" "subtype6" "subtype5" "subtype1" "subtype5" "subtype3"
[25] "subtype6" "subtype6" "subtype4" "subtype4" "subtype6" "subtype3"
[31] "subtype6" "subtype6" "subtype4" "subtype3" "subtype6" "subtype4"
[37] "subtype4" "subtype5" "subtype4" "subtype2" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype3" "subtype4" "subtype6" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype6" "subtype2"
[55] "subtype1" "subtype1" "subtype3"
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          11        9        5        8        2        9
  N1+N2        2        1        1        2        4        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 37  0
  subtype2 23  0
  subtype3  8  1
  subtype4 15  1
  subtype5  7  1
  subtype6 19  0
  subtype7  5  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    0
  subtype2   23    0
  subtype3    8    1
  subtype4   15    1
  subtype5    7    1
  subtype6   19    0
  subtype7    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       37       23        8       15        7       19        5
  1        0        0        1        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    36
  subtype2     1                         1    23
  subtype3     0                         1     9
  subtype4     1                         0    15
  subtype5     0                         0     8
  subtype6     0                         1    19
  subtype7     0                         1     8
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        0        1        0
  BLACK OR AFRICAN AMERICAN        2        1        1        0        0
  WHITE                           36       23        9       15        8
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        1        1
  WHITE                           19        8
[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"
D6V8, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  3 22
  subtype3  0  9
  subtype4  3 13
  subtype5  1  7
  subtype6  1 18
  subtype7  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   37
  subtype2    3   22
  subtype3    0    9
  subtype4    3   13
  subtype5    1    7
  subtype6    1   18
  subtype7    1    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        3        0        3        1        1
  NOT HISPANIC OR LATINO       37       22        9       13        7       18
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 50  1
  subtype2 51  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      51       53       29 
subtype1 subtype2 subtype3 
       1        2        1 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       63.32        60.26        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 
       59.80        91.43       176.15         6.08         2.73         0.13 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        7.00         0.10         4.83        18.15        13.58         1.38 
TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE 
       16.31         3.52        37.68        24.99        35.61        23.90 
TCGA-W4-A7U2 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR 
       41.52         5.06         0.16        18.38        40.01         0.46 
TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A9T9 
       53.03        12.07        67.66        41.69         8.32         6.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0D 
       54.35        31.92        21.96         5.29        37.02        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       16.41        11.34        46.88 

$subtype2
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      122.40       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 
       14.86        16.50        36.13        40.01        61.71        63.22 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        72.85        68.38        79.76        75.09       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH3 
      106.39       115.00        59.28        61.45        60.16        59.90 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       229.22       131.21 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
        3.52        20.68         9.14        17.23        37.18        36.79 
TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       33.07        24.26         3.65         0.82        28.14         6.87 
TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 
       65.98        93.93         7.89         0.43        12.92        20.12 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       57.90         0.56        39.35        27.55        10.85 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       67.96        92.09        59.64       120.62       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      170.33        80.94        59.84       125.69       184.41        70.59 
TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
        9.63        10.26         4.90        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        58.88         7.96        40.96         8.15 

subtype1 subtype2 subtype3 
    0.10     0.43     4.90 
subtype1 subtype2 subtype3 
  176.15   229.22   184.41 
subtype1 subtype2 subtype3 
   24.99    39.35    58.88 
[1] "0.1 - 176.2 (25.0)" "0.4 - 229.2 (39.4)" "4.9 - 184.4 (58.9)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      11       15        5        0         1         0         1
  subtype2       6        7        6        3         4         1         0
  subtype3       2        3        0        2         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          2       13
  subtype2         1          1          3          1       18
  subtype3         1          0          2          2       15
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          11        6        2
  STAGE IA         15        7        3
  STAGE IB          5        6        0
  STAGE II          0        3        2
  STAGE IIA         1        4        1
  STAGE IIB         0        1        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        1        2
  STAGE IS         13       18       15
[1] 12  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 32 17  1
  subtype2 23 28  2
  subtype3 20  6  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       32       23       20
  T2       17       28        6
  T3        1        2        3
[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       N0 N1+N2
  subtype1 16     2
  subtype2 20     9
  subtype3 10     2
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          16       20       10
  N1+N2        2        9        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"
D7V6, binary
          cls
clus        0  1
  subtype1 44  0
  subtype2 49  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    0
  subtype2   49    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       44       49       21
  1        0        1        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    44
  subtype2     1                         3    49
  subtype3     1                         1    25
D7V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        2        3        1
  WHITE                           44       49       25
[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"
D7V8, binary
          cls
clus        0  1
  subtype1  4 43
  subtype2  3 48
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   43
  subtype2    3   48
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        4
  NOT HISPANIC OR LATINO       43       48       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 67  1
  subtype2 34  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      68       36       29 
subtype1 subtype2 subtype3 
       1        2        1 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       191.31        36.99        63.32        60.26        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      176.15         6.08         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
        1.38        16.31         3.52        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       35.61        23.90        41.52         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        0.82        18.38        40.01        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL 
       93.93        12.07         7.89        67.66        41.69         0.43 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
        8.32         6.90        54.35        31.92        21.96         5.29 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       14.14        17.16         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        61.71        63.22        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       79.76        75.09       108.16       106.39       115.00        59.28 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       61.45        60.16       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      229.22       131.21        17.23        37.18        33.07        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
       28.14         6.87        12.92        20.12        57.90         0.56 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       67.96        92.09        59.64       120.62       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      170.33        80.94        59.84       125.69       184.41        70.59 
TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
        9.63        10.26         4.90        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        58.88         7.96        40.96         8.15 

subtype1 subtype2 subtype3 
    0.10     0.56     4.90 
subtype1 subtype2 subtype3 
  191.31   229.22   184.41 
subtype1 subtype2 subtype3 
   26.27    59.72    58.88 
[1] "0.1 - 191.3 (26.3)" "0.6 - 229.2 (59.7)" "4.9 - 184.4 (58.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      15       19        7        0         1         1         1
  subtype2       2        3        4        3         4         0         0
  subtype3       2        3        0        2         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          2       18
  subtype2         1          1          3          1       13
  subtype3         1          0          2          2       15
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          15        2        2
  STAGE IA         19        3        3
  STAGE IB          7        4        0
  STAGE II          0        3        2
  STAGE IIA         1        4        1
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        1        2
  STAGE IS         18       13       15
[1] 12  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 42 23  2
  subtype2 13 22  1
  subtype3 20  6  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       13       20
  T2       23       22        6
  T3        2        1        3
[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       N0 N1+N2
  subtype1 20     3
  subtype2 16     8
  subtype3 10     2
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          20       16       10
  N1+N2        3        8        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"
D8V6, binary
          cls
clus        0  1
  subtype1 60  0
  subtype2 33  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    0
  subtype2   33    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       60       33       21
  1        0        1        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    59
  subtype2     0                         2    34
  subtype3     1                         1    25
D8V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           59       34       25
[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"
D8V8, binary
          cls
clus        0  1
  subtype1  5 59
  subtype2  2 32
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   59
  subtype2    2   32
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        4
  NOT HISPANIC OR LATINO       59       32       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 66  1
  subtype2 33  1
  subtype3 30  2
subtype1 subtype2 subtype3 
      67       34       32 
subtype1 subtype2 subtype3 
       1        1        2 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       191.31        36.99        63.32        60.26        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      176.15         6.08         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
        1.38        16.31         3.52        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       35.61        23.90        41.52         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        0.82        18.38        40.01        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B 
       93.93        12.07        67.66        41.69         0.43         8.32 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 
        6.90        54.35        31.92        21.96         5.29        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       14.14        17.16         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF 
       40.01        61.71        63.22        68.22        68.38        79.76 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAGZ 
       75.09       108.16       106.39       115.00        61.45        60.16 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-XE-A8H1 
       70.59        17.23        37.18        33.07        24.26         6.87 
TCGA-XE-AAO6 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
        7.89        12.92        20.12        57.90 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGC TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS 
       72.85        67.96        92.09        59.64       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 
      124.57       128.94       170.33        80.94        59.84       125.69 
TCGA-2G-AAL5 TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI 
      184.41         9.63        10.26         4.90        28.14        34.22 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I 
       16.87         8.88        50.96         0.56        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 
       40.96         8.15 

subtype1 subtype2 subtype3 
    0.10     6.87     0.56 
subtype1 subtype2 subtype3 
  191.31   229.22   184.41 
subtype1 subtype2 subtype3 
  27.550   60.805   55.625 
[1] "0.1 - 191.3 (27.6)" "6.9 - 229.2 (60.8)" "0.6 - 184.4 (55.6)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      15       18        7        0         1         1         1
  subtype2       2        4        4        3         4         0         0
  subtype3       2        3        0        2         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          1          2       18
  subtype2         1          1          3          0       11
  subtype3         1          0          2          3       17
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          15        2        2
  STAGE IA         18        4        3
  STAGE IB          7        4        0
  STAGE II          0        3        2
  STAGE IIA         1        4        1
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        0        3
  STAGE IS         18       11       17
[1] 12  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 41 23  2
  subtype2 12 22  0
  subtype3 22  6  4
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       41       12       22
  T2       23       22        6
  T3        2        0        4
[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       N0 N1+N2
  subtype1 20     3
  subtype2 14     7
  subtype3 12     3
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          20       14       12
  N1+N2        3        7        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"
D9V6, binary
          cls
clus        0  1
  subtype1 59  0
  subtype2 31  2
  subtype3 24  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    0
  subtype2   31    2
  subtype3   24    2
   clus
vv  subtype1 subtype2 subtype3
  0       59       31       24
  1        0        2        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    58
  subtype2     0                         1    33
  subtype3     1                         2    27
D9V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           58       33       27
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1  5 58
  subtype2  2 31
  subtype3  4 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   58
  subtype2    2   31
  subtype3    4   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        4
  NOT HISPANIC OR LATINO       58       31       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 35  1
  subtype2 32  0
  subtype3 34  2
  subtype4 28  1
subtype1 subtype2 subtype3 subtype4 
      36       32       36       29 
subtype1 subtype2 subtype3 subtype4 
       1        0        2        1 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       154.59       191.31 
TCGA-2G-AAH3 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       59.90        98.53        59.74        59.80        91.43         6.08 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-VF-A8AA 
        0.13         3.52         7.00         0.10         4.83        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 
       24.99        35.61        23.90         5.06         0.16        18.38 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B 
        0.46        53.03        12.07        67.66        41.69         8.32 
TCGA-YU-A90S TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       31.92        37.02        17.39        16.41        11.34        46.88 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH8 
       30.35       122.40        36.99        63.32        60.26        61.84 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       59.80       176.15         2.73        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-W4-A7U2 
       13.58         1.38        16.31         3.52        36.79        41.52 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 
        3.65         0.82        40.01        65.98        93.93         7.89 
TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA06 
        0.43         6.90        54.35        21.96         5.29        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0N 
       27.55        10.85 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       14.14        17.16         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        61.71        63.22        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       79.76        75.09       108.16       106.39       115.00        59.28 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       61.45        60.16       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD 
      229.22       131.21        70.59        17.23        37.18        33.07 
TCGA-W4-A7U4 TCGA-XE-A8H1 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
       24.26         6.87        12.92        20.12        57.90         0.56 

$subtype4
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        40.70        36.89        52.37        71.24        72.20 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       67.96        92.09        59.64       120.62       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-SN-A84W 
      170.33        80.94        59.84       125.69       184.41         9.63 
TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
       10.26         4.90        28.14        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        58.88         7.96        40.96         8.15 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.43     0.56     4.90 
subtype1 subtype2 subtype3 subtype4 
  191.31   176.15   229.22   184.41 
subtype1 subtype2 subtype3 subtype4 
  28.455   24.755   60.805   52.370 
[1] "0.1 - 191.3 (28.5)" "0.4 - 176.2 (24.8)" "0.6 - 229.2 (60.8)"
[4] "4.9 - 184.4 (52.4)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1       9       13        3        0         1         0         1
  subtype2       6        6        4        0         0         1         0
  subtype3       2        3        4        3         4         0         0
  subtype4       2        3        0        2         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1         0          0          0          0        9
  subtype2         0          0          1          2        9
  subtype3         1          1          4          1       12
  subtype4         1          0          1          2       16
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        6        2        2
  STAGE IA         13        6        3        3
  STAGE IB          3        4        4        0
  STAGE II          0        0        3        2
  STAGE IIA         1        0        4        1
  STAGE IIB         0        1        0        0
  STAGE IIC         1        0        0        0
  STAGE III         0        0        1        1
  STAGE IIIA        0        0        1        0
  STAGE IIIB        0        1        4        1
  STAGE IIIC        0        2        1        2
  STAGE IS          9        9       12       16
[1] 12  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 21 13  1
  subtype2 21 10  1
  subtype3 13 22  1
  subtype4 20  6  3
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       21       21       13       20
  T2       13       10       22        6
  T3        1        1        1        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1 14     1
  subtype2  6     2
  subtype3 15     8
  subtype4 11     2
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          14        6       15       11
  N1+N2        1        2        8        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"
D10V6, binary
          cls
clus        0  1
  subtype1 33  0
  subtype2 27  0
  subtype3 32  2
  subtype4 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    0
  subtype2   27    0
  subtype3   32    2
  subtype4   22    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       33       27       32       22
  1        0        0        2        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    32
  subtype2     1                         2    27
  subtype3     0                         2    34
  subtype4     1                         1    25
D10V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        1
  BLACK OR AFRICAN AMERICAN        1        2        2        1
  WHITE                           32       27       34       25
[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"
D10V8, binary
          cls
clus        0  1
  subtype1  2 33
  subtype2  3 26
  subtype3  2 32
  subtype4  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   33
  subtype2    3   26
  subtype3    2   32
  subtype4    4   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        2        4
  NOT HISPANIC OR LATINO       33       26       32       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
