[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/19775566/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/20140863/TGCT-TP.mergedcluster.txt"

nPatients in clinical file=134, in cluster file=150, common to both=134
[1]  10 134
[1] "CN_CNMF"
[1] 3
 1  2  3 
44 43 47 
 1  2  3 
44 43 47 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
54 45 35 
 1  2  3 
54 45 35 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
44  7  8 29 16 
 1  2  3  4  5 
44  7  8 29 16 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
50 19 35 
 1  2  3 
50 19 35 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
69 36 29 
 1  2  3 
69 36 29 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
42 27 10 17  8 20 10 
 1  2  3  4  5  6  7 
42 27 10 17  8 20 10 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
51 54 29 
 1  2  3 
51 54 29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
69 36 29 
 1  2  3 
69 36 29 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
68 34 32 
 1  2  3 
68 34 32 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
36 33 36 29 
 1  2  3  4 
36 33 36 29 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 134 columns.

[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=131,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=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:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 134 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "RADIATION_THERAPY"          
[7] "KARNOFSKY_PERFORMANCE_SCORE" "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
76 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
76 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
76 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
76 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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=3, 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 45  2
subtype1 subtype2 subtype3 
      44       43       47 
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        46.13       128.58        24.66        16.54        22.52 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGJ 
       36.13        50.27        52.37        75.58        75.25        96.59 
TCGA-2G-AAGP TCGA-2G-AAGZ TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKH 
      132.10       172.04       110.10       182.10       211.89       225.60 
TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
       19.96        17.03         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        15.48        31.92 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E 
       71.24        51.72        28.41        37.02        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH 
       41.39        76.11       114.77       154.59       203.28        45.21 
TCGA-2G-AAGA TCGA-2G-AAGO TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH3 
       80.19       132.36       181.28       175.20       180.07        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2X-A9D5 
       73.91       232.80       186.31        17.82       208.44        14.30 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       14.33        22.95        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        17.75        36.79        41.52        24.76         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        55.92        93.93 
TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-ZM-AA0B 
        7.89         0.43         9.24        64.57        36.59        27.55 
TCGA-ZM-AA0N 
       20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG6 
       22.19        14.56        14.86        45.67        44.48        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       81.37        73.45        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09       119.05       127.92       120.20       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAKG 
      148.83       161.06       199.23       204.16        59.80       216.92 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AAAL 
      230.89       229.22       244.50       131.21        86.96        15.88 
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-A9SE TCGA-XE-AANI TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-XY-A8S2 TCGA-XY-A8S3 
       23.28        34.22         8.88        50.96        22.09        27.72 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA06 
       68.02         0.56        28.47        17.62        49.25 

subtype1 subtype2 subtype3 
    0.10     0.16     0.56 
subtype1 subtype2 subtype3 
   225.6    232.8    244.5 
subtype1 subtype2 subtype3 
   34.34    40.01    68.02 
[1] "0.1 - 225.6 (34.3)" "0.2 - 232.8 (40.0)" "0.6 - 244.5 (68.0)"
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        5        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        5
  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 25 19  3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       27       24       25
  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 40  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    1
  subtype2   38    0
  subtype3   40    3
   clus
vv  subtype1 subtype2 subtype3
  0       37       38       40
  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"
D1V7, binary
          cls
clus        0  1
  subtype1 37  6
  subtype2 28 11
  subtype3 45  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    6
  subtype2   28   11
  subtype3   45    2
     clus
vv    subtype1 subtype2 subtype3
  NO        37       28       45
  YES        6       11        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"
D1V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    38
  subtype2     1                         1    38
  subtype3     1                         2    43
D1V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           38       38       43
[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"
D1V10, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  4 37
  subtype3  6 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   37
  subtype2    4   37
  subtype3    6   37
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        4        6
  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 52  2
  subtype2 43  2
  subtype3 35  0
subtype1 subtype2 subtype3 
      54       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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAHA 
      154.59       203.28        45.21        73.45       180.07       110.10 
TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      182.10       211.89        17.82        14.30        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A9 
        0.10        15.88        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        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANJ 
        5.06         0.16         0.82        18.38        23.28        65.98 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       55.92        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90S TCGA-ZM-AA05 TCGA-ZM-AA06 
       41.69        15.48         9.24        31.92        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        26.66        22.39        57.07        20.84 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       22.19        24.66        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        81.37        75.25        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       89.88        96.59       119.05       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 
      158.33       144.85       161.06       172.04       199.23        59.90 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 
       86.96        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        22.09        27.72        68.02 
TCGA-YU-A90Y TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        51.72        28.41 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
       85.84        92.09       127.92       148.83       181.28       175.20 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAL5 
      204.16        73.91        59.80       232.80       186.31       244.50 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A84W 
       14.33        22.95        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 
       17.75        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 
       64.57        36.59        28.47        71.24        17.62 

subtype1 subtype2 subtype3 
    0.10     0.46     0.43 
subtype1 subtype2 subtype3 
  211.89   230.89   244.50 
subtype1 subtype2 subtype3 
  27.715   75.250   50.960 
[1] "0.1 - 211.9 (27.7)" "0.5 - 230.9 (75.2)" "0.4 - 244.5 (51.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1       9       19        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         19        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 35 16  2
  subtype2 18 26  1
  subtype3 23  9  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       35       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 49  0
  subtype2 38  2
  subtype3 28  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    0
  subtype2   38    2
  subtype3   28    2
   clus
vv  subtype1 subtype2 subtype3
  0       49       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"
D2V7, binary
          cls
clus        0  1
  subtype1 37 14
  subtype2 44  0
  subtype3 29  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   14
  subtype2   44    0
  subtype3   29    5
     clus
vv    subtype1 subtype2 subtype3
  NO        37       44       29
  YES       14        0        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"
D2V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    49
  subtype2     0                         3    42
  subtype3     1                         2    28
D2V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        1        3        2
  WHITE                           49       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"
D2V10, binary
          cls
clus        0  1
  subtype1  5 48
  subtype2  3 37
  subtype3  4 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   48
  subtype2    3   37
  subtype3    4   26
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        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 43  1
  subtype2  7  0
  subtype3  8  0
  subtype4 27  2
  subtype5 15  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      44        7        8       29       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        0        0        2        1 
$subtype1
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL 
      180.07        59.90        73.91       110.10        59.80       232.80 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      186.31        17.82        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SO-A8JP 
        0.10        22.95        18.15         9.14        16.31        17.75 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-XE-A8H5 TCGA-XE-AANJ 
       36.79        37.68        23.90        41.52        40.01        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOF 
        0.46        55.92        93.93        12.07         7.89        41.69 
TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA0B 
        0.43         9.24        64.57        36.59        28.47        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E 
       27.88        26.66 

$subtype2
TCGA-2G-AAFG TCGA-2G-AAFY TCGA-2G-AAG9 TCGA-2G-AAHC TCGA-XY-A89B TCGA-YU-A90S 
      203.28        36.13        73.45       182.10        15.48        31.92 
TCGA-ZM-AA05 
       37.02 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGO TCGA-2G-AAGP 
       22.19        24.66        75.58        75.25       132.36       132.10 
TCGA-2G-AAGZ TCGA-XE-AAOD 
      172.04        67.66 

$subtype4
TCGA-2G-AAFJ TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAGC TCGA-2G-AAGF 
       14.56        44.48        52.37        73.35        84.99        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGV 
       85.84        92.09       119.05       127.92       158.33       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       204.16       216.92       244.50        86.96 
TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AAOB 
       10.26         4.90        28.14        23.28        34.22        16.87 
TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA61 
        8.88        50.96         0.56        17.62        28.41 

$subtype5
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAGJ TCGA-2G-AAGN 
       16.54        14.86        50.27        81.37        96.59       120.20 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      144.85       161.06       225.60       230.89       229.22       131.21 
TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-XE-A8H1 TCGA-YU-A90P 
       37.18        24.26         6.87        68.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10    15.48    22.19     0.56     6.87 
subtype1 subtype2 subtype3 subtype4 subtype5 
  232.80   203.28   172.04   244.50   230.89 
subtype1 subtype2 subtype3 subtype4 subtype5 
  32.530   37.020   75.415   73.350   88.980 
[1] "0.1 - 232.8 (32.5)"  "15.5 - 203.3 (37.0)" "22.2 - 172.0 (75.4)"
[4] "0.6 - 244.5 (73.3)"  "6.9 - 230.9 (89.0)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1      11       12        4        0         0         0         0
  subtype2       0        2        0        0         1         1         0
  subtype3       0        0        4        0         1         0         0
  subtype4       3        4        0        2         0         0         1
  subtype5       0        3        0        3         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  subtype1          0          0          2       14
  subtype2          0          1          0        2
  subtype3          1          0          0        2
  subtype4          0          2          2       14
  subtype5          0          2          0        6
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          11        0        0        3        0
  STAGE IA         12        2        0        4        3
  STAGE IB          4        0        4        0        0
  STAGE II          0        0        0        2        3
  STAGE IIA         0        1        1        0        1
  STAGE IIC         0        1        0        0        0
  STAGE III         0        0        0        1        0
  STAGE IIIA        0        0        1        0        0
  STAGE IIIB        0        1        0        2        2
  STAGE IIIC        2        0        0        2        0
  STAGE IS         14        2        2       14        6
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 29 15  0
  subtype2  4  3  0
  subtype3  1  7  0
  subtype4 21  5  3
  subtype5  6 10  0
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       29        4        1       21        6
  T2       15        3        7        5       10
  T3        0        0        0        3        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1 16     0
  subtype2  1     2
  subtype3  5     2
  subtype4 12     2
  subtype5  6     3
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          16        1        5       12        6
  N1+N2        0        2        2        2        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 40  0
  subtype2  6  0
  subtype3  7  1
  subtype4 22  3
  subtype5 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    0
  subtype2    6    0
  subtype3    7    1
  subtype4   22    3
  subtype5   15    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       40        6        7       22       15
  1        0        0        1        3        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 29 13
  subtype2  5  2
  subtype3  8  0
  subtype4 28  1
  subtype5 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   13
  subtype2    5    2
  subtype3    8    0
  subtype4   28    1
  subtype5   16    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        29        5        8       28       16
  YES       13        2        0        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    36
  subtype2     0                         0     7
  subtype3     0                         0     8
  subtype4     1                         1    26
  subtype5     0                         1    15
D3V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        0        0        1        0
  BLACK OR AFRICAN AMERICAN        2        0        0        1        1
  WHITE                           36        7        8       26       15
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus        0  1
  subtype1  5 36
  subtype2  0  6
  subtype3  0  8
  subtype4  4 21
  subtype5  1 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   36
  subtype2    0    6
  subtype3    0    8
  subtype4    4   21
  subtype5    1   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        0        0        4        1
  NOT HISPANIC OR LATINO       36        6        8       21       14
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 49  1
  subtype2 19  0
  subtype3 32  3
subtype1 subtype2 subtype3 
      50       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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFG TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
      203.28        73.45       180.07        59.90        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 
      182.10        59.80       232.80       186.31        17.82        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX 
       19.96        14.33        17.03         0.10        22.95        18.15 
TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE 
        9.14        16.31        17.75        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        55.92        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        15.48         9.24 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0B 
       64.57        31.92        36.59        28.47        37.02        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E 
       27.88        26.66 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGG 
       22.19        24.66        75.58        73.35        75.25        85.84 
TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ 
       92.09       132.36       132.10       148.83       181.28       172.04 
TCGA-2G-AALP TCGA-W4-A7U3 TCGA-XE-A8H1 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A94I 
       86.96         4.90         6.87         8.88        67.66        17.62 
TCGA-YU-AA61 
       28.41 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.56        16.54        14.86        36.13        44.48        50.27 
TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       52.37        81.37        84.99        89.88        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
      127.92       120.20       158.33       144.85       161.06       175.20 
TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      204.16       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-SN-A84X TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A9SE 
      131.21        10.26        37.18        24.26        28.14        23.28 
TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-YU-A90P TCGA-YU-A90Y 
       34.22        16.87        50.96        68.02         0.56 

subtype1 subtype2 subtype3 
    0.10     4.90     0.56 
subtype1 subtype2 subtype3 
  232.80   181.28   244.50 
subtype1 subtype2 subtype3 
   36.69    75.25    81.37 
[1] "0.1 - 232.8 (36.7)" "4.9 - 181.3 (75.2)" "0.6 - 244.5 (81.4)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1      11       14        4        0         0         1         0
  subtype2       0        3        4        1         1         0         0
  subtype3       3        4        0        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        4
  STAGE IB          4        4        0
  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 17  0
  subtype2 10  8  1
  subtype3 18 15  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       33       10       18
  T2       17        8       15
  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 32  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    0
  subtype2   13    3
  subtype3   32    1
   clus
vv  subtype1 subtype2 subtype3
  0       45       13       32
  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"
D4V7, binary
          cls
clus        0  1
  subtype1 33 15
  subtype2 19  0
  subtype3 34  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   15
  subtype2   19    0
  subtype3   34    1
     clus
vv    subtype1 subtype2 subtype3
  NO        33       19       34
  YES       15        0        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"
D4V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    42
  subtype2     0                         0    18
  subtype3     1                         2    32
D4V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        2        0        2
  WHITE                           42       18       32
[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"
D4V10, binary
          cls
clus        0  1
  subtype1  5 41
  subtype2  2 14
  subtype3  3 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   41
  subtype2    2   14
  subtype3    3   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        3
  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 68  1
  subtype2 33  3
  subtype3 29  0
subtype1 subtype2 subtype3 
      69       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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       203.28        45.21        73.45       180.07        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      186.31        17.82        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR 
        0.82        18.38        40.01        23.28        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF 
       55.92        93.93        12.07         7.89        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        15.48         9.24        64.57        31.92        36.59 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       28.47        37.02        49.25        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       22.19        24.66        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        81.37        75.25        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW 
       89.88        96.59       119.05       120.20       132.36       161.06 
TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      172.04       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      131.21        86.96        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        22.09        27.72        68.02         0.56 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       85.84        92.09       127.92       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 
      148.83       181.28       175.20       199.23       204.16       244.50 
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        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     0.56     4.90 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
   28.47    77.72    71.24 
[1] "0.1 - 232.8 (28.5)" "0.6 - 230.9 (77.7)" "4.9 - 244.5 (71.2)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      15       20        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         20        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 43 23  2
  subtype2 13 22  1
  subtype3 20  6  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       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 61  0
  subtype2 32  2
  subtype3 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61    0
  subtype2   32    2
  subtype3   22    2
   clus
vv  subtype1 subtype2 subtype3
  0       61       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"
D5V7, binary
          cls
clus        0  1
  subtype1 45 19
  subtype2 36  0
  subtype3 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   19
  subtype2   36    0
  subtype3   29    0
     clus
vv    subtype1 subtype2 subtype3
  NO        45       36       29
  YES       19        0        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"
D5V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    60
  subtype2     0                         2    34
  subtype3     1                         1    25
D5V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           60       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"
D5V10, binary
          cls
clus        0  1
  subtype1  6 59
  subtype2  2 32
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   59
  subtype2    2   32
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        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 27  0
  subtype3  8  2
  subtype4 17  0
  subtype5  8  0
  subtype6 19  1
  subtype7 10  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      42       27       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        46.13       154.59        73.45       180.07        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       73.91       110.10       182.10       232.80       211.89        17.82 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       14.30        19.96        14.33        17.03         0.10        15.88 
TCGA-S6-A8JW TCGA-SB-A76C TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-WZ-A7V4 
       22.95         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        55.92        12.07 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 
       67.66        41.69        15.48        64.57        31.92        28.47 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.88        26.66        22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       41.39        76.11       114.77       128.58       203.28        45.21 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
       59.80       186.31        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 
       17.75        36.79        23.90        41.52        24.76        40.01 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 
       23.28        65.98        93.93         7.89         0.43         9.24 
TCGA-YU-A90W TCGA-ZM-AA0B TCGA-ZM-AA0N 
       36.59        27.55        20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAGC TCGA-2G-AAGK TCGA-2G-AAGS TCGA-2G-AAKG TCGA-2G-AALP 
       22.19        84.99       119.05       158.33       216.92        86.96 
TCGA-X3-A8G4 TCGA-XE-AAOB TCGA-XY-A8S3 TCGA-YU-A90Y 
       28.14        16.87        27.72         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        75.58        73.35        85.84        92.09 
TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAL5 
      132.10       148.83       181.28       175.20       199.23       244.50 
TCGA-SN-A84W TCGA-SN-A84X TCGA-XE-AANI TCGA-XE-AAOC TCGA-YU-A94D 
        9.63        10.26        34.22         8.88        71.24 

$subtype5
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGZ 
       24.66        16.54        22.52        75.25        80.19       172.04 
TCGA-2G-AAKH TCGA-XE-A8H1 
      225.60         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        50.27        81.37        81.47        89.88 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAKD TCGA-2G-AAKL 
       96.59       120.20       132.36       161.06       208.44       230.89 
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 
       22.09        68.02 

$subtype7
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH4 TCGA-W4-A7U3 
       45.67        44.48       127.92       144.85       204.16         4.90 
TCGA-XE-AAOJ TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        17.62        51.72        28.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.10     0.43     0.56     8.88     6.87    14.86     4.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  232.80   203.28   216.92   244.50   225.60   230.89   204.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  28.175   36.590   56.565   75.580   49.955   81.420   48.315 
[1] "0.1 - 232.8 (28.2)"  "0.4 - 203.3 (36.6)"  "0.6 - 216.9 (56.6)" 
[4] "8.9 - 244.5 (75.6)"  "6.9 - 225.6 (50.0)"  "14.9 - 230.9 (81.4)"
[7] "4.9 - 204.2 (48.3)" 
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        8        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        8        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 22  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       22        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 24  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   24    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       24        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"
D6V7, binary
          cls
clus        0  1
  subtype1 31  7
  subtype2 14 12
  subtype3 10  0
  subtype4 17  0
  subtype5  8  0
  subtype6 20  0
  subtype7 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    7
  subtype2   14   12
  subtype3   10    0
  subtype4   17    0
  subtype5    8    0
  subtype6   20    0
  subtype7   10    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        31       14       10       17        8       20       10
  YES        7       12        0        0        0        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    36
  subtype2     1                         1    24
  subtype3     0                         1     9
  subtype4     1                         0    15
  subtype5     0                         0     8
  subtype6     0                         1    19
  subtype7     0                         1     8
D6V9, 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       24        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"
D6V10, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  4 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    4   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        4        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 52  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      51       54       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        41.39        46.13        76.11       114.77       154.59 
TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       73.45       180.07        73.91       110.10       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 
      232.80       211.89       186.31        17.82        14.30        19.96 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
       17.03         0.10        15.88        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        17.75        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 
       55.92        12.07        67.66        41.69        15.48         9.24 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0D 
       64.57        31.92        36.59        28.47        37.02        27.88 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       26.66        22.39        57.07 

$subtype2
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      128.58       203.28        45.21        22.19        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 
       14.86        22.52        36.13        50.27        81.37        75.25 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        84.99        81.47        89.88        96.59       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH3 
      120.20       132.36       158.33       161.06       172.04        59.90 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
       14.33        22.95         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        24.76         0.82        28.14         6.87 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A8S2 
       23.28        65.98        93.93         7.89         0.43        22.09 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       27.72        68.02         0.56        49.25        27.55        20.84 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84        92.09       127.92       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       199.23       204.16       244.50        86.96 
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        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     0.43     4.90 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
   31.92    47.23    71.24 
[1] "0.1 - 232.8 (31.9)" "0.4 - 230.9 (47.2)" "4.9 - 244.5 (71.2)"
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        8        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        8        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 24 28  2
  subtype3 20  6  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       32       24       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 50  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    0
  subtype2   50    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       44       50       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"
D7V7, binary
          cls
clus        0  1
  subtype1 33 15
  subtype2 48  4
  subtype3 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   15
  subtype2   48    4
  subtype3   29    0
     clus
vv    subtype1 subtype2 subtype3
  NO        33       48       29
  YES       15        4        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"
D7V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    44
  subtype2     1                         3    50
  subtype3     1                         1    25
D7V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        2        3        1
  WHITE                           44       50       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"
D7V10, binary
          cls
clus        0  1
  subtype1  4 43
  subtype2  4 48
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   43
  subtype2    4   48
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        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 68  1
  subtype2 34  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      69       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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       203.28        45.21        73.45       180.07        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      186.31        17.82        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR 
        0.82        18.38        40.01        23.28        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF 
       55.92        93.93        12.07         7.89        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        15.48         9.24        64.57        31.92        36.59 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       28.47        37.02        49.25        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       22.19        24.66        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        81.37        75.25        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       89.88        96.59       119.05       120.20       132.36       158.33 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      161.06       172.04       208.44       216.92       225.60       230.89 
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        22.09        27.72        68.02         0.56 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84        92.09       127.92       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       199.23       204.16       244.50        86.96 
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        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     0.56     4.90 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
   28.47    77.72    71.24 
[1] "0.1 - 232.8 (28.5)" "0.6 - 230.9 (77.7)" "4.9 - 244.5 (71.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1      15       20        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         20        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 43 23  2
  subtype2 13 22  1
  subtype3 20  6  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       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 61  0
  subtype2 33  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61    0
  subtype2   33    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       61       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"
D8V7, binary
          cls
clus        0  1
  subtype1 45 19
  subtype2 36  0
  subtype3 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   19
  subtype2   36    0
  subtype3   29    0
     clus
vv    subtype1 subtype2 subtype3
  NO        45       36       29
  YES       19        0        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"
D8V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    60
  subtype2     0                         2    34
  subtype3     1                         1    25
D8V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           60       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"
D8V10, binary
          cls
clus        0  1
  subtype1  6 59
  subtype2  2 32
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   59
  subtype2    2   32
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        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 67  1
  subtype2 33  1
  subtype3 30  2
subtype1 subtype2 subtype3 
      68       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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 
      154.59       203.28        45.21        73.45       180.07        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      186.31        17.82        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR 
        0.82        18.38        40.01        23.28        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL 
       55.92        93.93        12.07        67.66        41.69         0.43 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
       15.48         9.24        64.57        31.92        36.59        28.47 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       22.19        24.66        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF 
       50.27        81.37        75.25        80.19        81.47        89.88 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAGZ 
       96.59       119.05       120.20       132.36       161.06       172.04 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-XE-A8H1 
       86.96        17.23        37.18        33.07        24.26         6.87 
TCGA-XE-AAO6 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
        7.89        22.09        27.72        68.02 

$subtype3
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGC TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS 
       84.99        85.84        92.09       127.92       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 
      144.85       148.83       181.28       175.20       199.23       204.16 
TCGA-2G-AAL5 TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI 
      244.50         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        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 
       51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     6.87     0.56 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
  30.195   77.720   61.805 
[1] "0.1 - 232.8 (30.2)" "6.9 - 230.9 (77.7)" "0.6 - 244.5 (61.8)"
D9V2, 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        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         19        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 42 23  2
  subtype2 12 22  0
  subtype3 22  6  4
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       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 60  0
  subtype2 31  2
  subtype3 24  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    0
  subtype2   31    2
  subtype3   24    2
   clus
vv  subtype1 subtype2 subtype3
  0       60       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"
D9V7, binary
          cls
clus        0  1
  subtype1 45 18
  subtype2 33  1
  subtype3 32  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   18
  subtype2   33    1
  subtype3   32    0
     clus
vv    subtype1 subtype2 subtype3
  NO        45       33       32
  YES       18        1        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"
D9V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    59
  subtype2     0                         1    33
  subtype3     1                         2    27
D9V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           59       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"
D9V10, binary
          cls
clus        0  1
  subtype1  6 58
  subtype2  2 31
  subtype3  4 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   58
  subtype2    2   31
  subtype3    4   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        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 33  0
  subtype3 34  2
  subtype4 28  1
subtype1 subtype2 subtype3 subtype4 
      36       33       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        46.13        76.11       114.77       154.59       203.28 
TCGA-2G-AAH3 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       59.90       110.10       182.10       232.80       211.89        17.82 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-VF-A8AA 
       19.96        14.33        17.03         0.10        15.88        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        55.92        12.07        67.66        41.69        15.48 
TCGA-YU-A90S TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       31.92        37.02        27.88        26.66        22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH8 
       41.39       128.58        45.21        73.45       180.07        73.91 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       59.80       186.31        14.30        22.95        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        17.75        36.79        41.52 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 
       24.76         0.82        40.01        23.28        65.98        93.93 
TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 
        7.89         0.43         9.24        64.57        36.59        28.47 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       49.25        27.55        20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       22.19        24.66        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        81.37        75.25        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       89.88        96.59       119.05       120.20       132.36       158.33 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      161.06       172.04       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD 
      229.22       131.21        86.96        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        22.09        27.72        68.02         0.56 

$subtype4
TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       14.56        45.67        44.48        52.37        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84        92.09       127.92       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-SN-A84W 
      181.28       175.20       199.23       204.16       244.50         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        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.43     0.56     4.90 
subtype1 subtype2 subtype3 subtype4 
  232.80   186.31   230.89   244.50 
subtype1 subtype2 subtype3 subtype4 
   29.90    28.47    80.78    52.37 
[1] "0.1 - 232.8 (29.9)" "0.4 - 186.3 (28.5)" "0.6 - 230.9 (80.8)"
[4] "4.9 - 244.5 (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        7        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        7        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 22 10  1
  subtype3 13 22  1
  subtype4 20  6  3
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       21       22       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 28  0
  subtype3 32  2
  subtype4 22  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    0
  subtype2   28    0
  subtype3   32    2
  subtype4   22    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       33       28       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"
D10V7, binary
          cls
clus        0  1
  subtype1 23 10
  subtype2 22  9
  subtype3 36  0
  subtype4 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   10
  subtype2   22    9
  subtype3   36    0
  subtype4   29    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        23       22       36       29
  YES       10        9        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    32
  subtype2     1                         2    28
  subtype3     0                         2    34
  subtype4     1                         1    25
D10V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        1
  BLACK OR AFRICAN AMERICAN        1        2        2        1
  WHITE                           32       28       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"
D10V10, binary
          cls
clus        0  1
  subtype1  2 33
  subtype2  4 26
  subtype3  2 32
  subtype4  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   33
  subtype2    4   26
  subtype3    2   32
  subtype4    4   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        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"
