[1] "ofn"        "-oTUCEC-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/UCEC-TP/22507145/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/22553827/UCEC-TP.mergedcluster.txt"

nPatients in clinical file=548, in cluster file=548, common to both=548
[1]  12 548
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
15 18 14  7 
 1  2  3  4 
15 18 14  7 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
14 10  7  7 16 
 1  2  3  4  5 
14 10  7  7 16 
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
208 178  99  54 
  1   2   3   4 
208 178  99  54 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
155  80 196 
  1   2   3 
155  80 196 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6  7 
41 82 53 56 86 68 54 
 1  2  3  4  5  6  7 
41 82 53 56 86 68 54 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
110 183  95  52 
  1   2   3   4 
110 183  95  52 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
189 124  94 138 
  1   2   3   4 
189 124  94 138 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
124  53  47  65 109  69  78 
  1   2   3   4   5   6   7 
124  53  47  65 109  69  78 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
165  81 107 138  47 
  1   2   3   4   5 
165  81 107 138  47 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
219 173 146 
  1   2   3 
219 173 146 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
116 101  93  92 
  1   2   3   4 
116 101  93  92 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
163 136 103 
  1   2   3 
163 136 103 
[1] "data2feature, selection=ALL"
 [1] "VITAL_STATUS"                        
 [2] "DAYS_TO_DEATH"                       
 [3] "DAYS_TO_LAST_FOLLOWUP"               
 [4] "TUMOR_TISSUE_SITE"                   
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[10] "DAYS_TO_LAST_KNOWN_ALIVE"            
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RESIDUAL_TUMOR"                      

Input Data has 13 rows and 548 columns.

[1] "Last Follow UP"
Variable 1:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 2:'DAYS_TO_DEATH':	nDistinctValues=89,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 3:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=418,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 4:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "547"       "1"           
freq.contrast "1"         "547"         
both >= 3     "FALSE"     "FALSE"       
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 10:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RESIDUAL_TUMOR':	nDistinctValues=4,	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] "****** SUMMARY ***** "
Output Data has 548 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 13  2
  subtype2 13  5
  subtype3 13  1
  subtype4  5  2
subtype1 subtype2 subtype3 subtype4 
      15       18       14        7 
subtype1 subtype2 subtype3 subtype4 
       2        5        1        2 
$subtype1
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A0LG 
      149.56        37.02        17.85        32.78       129.80        66.25 
TCGA-AP-A0LT TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       49.22        13.58        71.51        35.34        79.46        49.87 
TCGA-AX-A06F TCGA-B5-A0JR TCGA-B5-A0JZ 
       57.47        56.91        71.44 

$subtype2
TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-A5-A0G3 TCGA-A5-A0GH TCGA-AP-A052 
      110.63        57.80        67.66        46.95        74.10        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       23.31        86.07        63.91        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-B5-A0K4 TCGA-BK-A0CC 
      125.42       117.99        37.78        77.39        57.76        35.08 

$subtype3
TCGA-A5-A0GM TCGA-A5-A0GE TCGA-A5-A0GP TCGA-A5-A0GU TCGA-AP-A05P TCGA-AP-A0LH 
       60.53       105.37        46.55        28.27        20.91        36.36 
TCGA-AP-A0LJ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A06J 
       46.72        33.21        29.69        80.55        88.24        30.02 
TCGA-B5-A0K1 TCGA-BK-A0C9 
       36.49        35.90 

$subtype4
TCGA-AP-A05N TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A062 TCGA-B5-A0K0 TCGA-BG-A0LW 
       23.87        82.52        25.08        45.99        48.59        18.61 
TCGA-BG-A0MI 
       23.47 

subtype1 subtype2 subtype3 subtype4 
   13.58    21.99    20.91    18.61 
subtype1 subtype2 subtype3 subtype4 
  149.56   125.42   105.37    82.52 
subtype1 subtype2 subtype3 subtype4 
  56.910   57.780   36.425   25.080 
[1] "13.6 - 149.6 (56.9)" "22.0 - 125.4 (57.8)" "20.9 - 105.4 (36.4)"
[4] "18.6 - 82.5 (25.1)" 
D1V2, binary
          cls
clus        0  1
  subtype1  7  8
  subtype2 13  5
  subtype3 11  3
  subtype4  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    8
  subtype2   13    5
  subtype3   11    3
  subtype4    7    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         7       13       11        7
  YES        8        5        3        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      13
  subtype2                                       8
  subtype3                                      13
  subtype4                                       7
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             0                                 2
  subtype2                             0                                10
  subtype3                             1                                 0
  subtype4                             0                                 0
D1V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       13        8       13        7
  MIXED SEROUS AND ENDOMETRIOID                  0        0        1        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA              2       10        0        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  9  2  1  0
  subtype2 14  1  1  1
  subtype3 13  0  0  0
  subtype4  6  0  0  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        9       14       13        6
  R1        2        1        0        0
  R2        1        1        0        0
  RX        0        1        0        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 13  1
  subtype2  6  4
  subtype3  4  3
  subtype4  7  0
  subtype5 14  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       10        7        7       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        4        3        0        2 
$subtype1
TCGA-A5-A0GM TCGA-AX-A06B TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GH TCGA-AP-A054 
       60.53        67.66       149.56        37.02        74.10        23.31 
TCGA-AP-A056 TCGA-AP-A05P TCGA-AP-A0LD TCGA-AX-A05Y TCGA-AX-A06F TCGA-AX-A0J1 
       86.07        20.91       117.99        88.24        57.47        77.39 
TCGA-B5-A0K4 TCGA-BK-A0CC 
       57.76        35.08 

$subtype2
TCGA-AP-A053 TCGA-AP-A05D TCGA-A5-A0G3 TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H 
      110.63        57.80        46.95        21.99        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AX-A0IW 
       36.89        48.79       125.42        37.78 

$subtype3
TCGA-A5-A0GA TCGA-A5-A0GP TCGA-AP-A0LH TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Z 
       17.85        46.55        36.36        13.58        80.55        71.51 
TCGA-AX-A064 
       49.87 

$subtype4
TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A0LT TCGA-AX-A060 TCGA-AX-A063 TCGA-B5-A0JR 
       32.78       129.80        49.22        35.34        79.46        56.91 
TCGA-B5-A0JZ 
       71.44 

$subtype5
TCGA-A5-A0GE TCGA-A5-A0GU TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LN 
      105.37        28.27        23.87        66.25        46.72        82.52 
TCGA-AP-A0LV TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06J TCGA-B5-A0K0 
       25.08        33.21        29.69        45.99        30.02        48.59 
TCGA-B5-A0K1 TCGA-BG-A0LW TCGA-BG-A0MI TCGA-BK-A0C9 
       36.49        18.61        23.47        35.90 

subtype1 subtype2 subtype3 subtype4 subtype5 
   20.91    21.99    13.58    32.78    18.61 
subtype1 subtype2 subtype3 subtype4 subtype5 
  149.56   125.42    80.55   129.80   105.37 
subtype1 subtype2 subtype3 subtype4 subtype5 
  64.095   47.870   46.550   56.910   34.555 
[1] "20.9 - 149.6 (64.1)" "22.0 - 125.4 (47.9)" "13.6 - 80.5 (46.5)" 
[4] "32.8 - 129.8 (56.9)" "18.6 - 105.4 (34.6)"
D2V2, binary
          cls
clus        0  1
  subtype1 10  4
  subtype2  7  3
  subtype3  5  2
  subtype4  3  4
  subtype5 13  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    4
  subtype2    7    3
  subtype3    5    2
  subtype4    3    4
  subtype5   13    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        10        7        5        3       13
  YES        4        3        2        4        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"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      11
  subtype2                                       1
  subtype3                                       6
  subtype4                                       7
  subtype5                                      16
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             0                                 3
  subtype2                             0                                 9
  subtype3                             1                                 0
  subtype4                             0                                 0
  subtype5                             0                                 0
D2V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       11        1        6        7
  MIXED SEROUS AND ENDOMETRIOID                  0        0        1        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA              3        9        0        0
                                         clus
vv                                        subtype5
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       16
  MIXED SEROUS AND ENDOMETRIOID                  0
  SEROUS ENDOMETRIAL ADENOCARCINOMA              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       R0 R1 R2 RX
  subtype1 11  1  0  1
  subtype2  9  0  1  0
  subtype3  4  1  1  0
  subtype4  4  1  0  0
  subtype5 14  0  0  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       11        9        4        4       14
  R1        1        0        1        1        0
  R2        0        1        1        0        0
  RX        1        0        0        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 153  54
  subtype2 164  14
  subtype3  82  16
  subtype4  48   6
subtype1 subtype2 subtype3 subtype4 
     207      178       98       54 
subtype1 subtype2 subtype3 subtype4 
      54       14       16        6 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D 
       41.06        29.39        20.81        10.19       110.63        57.80 
TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       93.99        67.66        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
        1.38        80.38        27.09        22.06        66.41        12.56 
TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GQ 
        1.81         4.44        47.84        16.93        33.30        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KJ-A3U4 
       10.19        14.40        17.92         5.88        66.77        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GN 
       23.74        39.52       149.56        37.02        65.75        60.53 
TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       36.82        37.91        17.59        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
       66.15        28.64        25.51        14.96        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       14.43        21.14        34.16        18.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       22.26        17.06        21.21        16.87        16.87        20.78 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
       21.99        63.91        45.53        36.89        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A5FX 
       97.71        33.40        31.30        46.78        49.15        36.13 
TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
        0.56        80.55        35.74        37.78        34.65        25.51 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       32.02        25.91        76.83         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW 
       40.80        81.37         2.96        64.93         0.23         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P 
        0.39        55.30        27.29        27.85        75.72        52.04 
TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       77.23        19.56       225.50       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       31.36       136.60        39.35        29.65        34.13        34.95 
TCGA-BG-A0MT TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       21.17        15.45        23.70        22.39        35.08        31.00 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       24.13        16.64         4.80        61.87        92.88        83.64 
TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 
       86.99        29.95         8.55        22.55        39.48        37.32 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       27.42        11.51        29.92        31.07        18.67         3.95 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       14.73        28.08        13.22         0.72        18.25        16.87 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR 
        2.07        58.95         4.27        18.84        17.29        71.61 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
      109.08        25.91        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
      110.10        79.10        10.92        49.15        37.71        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.42        19.40        27.16        46.42        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       16.34        54.15        23.90        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OO 
       22.03        15.81        11.08        12.59        20.05        45.76 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       29.10        27.35        32.52        11.38        14.70        68.38 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       41.56        78.38         1.74        17.75        14.04        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        26.10        18.21        23.24        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        8.19         4.44         0.07 

$subtype2
TCGA-A5-A0GM TCGA-AJ-A3BG TCGA-AP-A0LS TCGA-BG-A220 TCGA-EY-A215 TCGA-FI-A2D5 
       60.53        18.08        95.47        14.27        18.87        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0GD TCGA-A5-A0GH TCGA-A5-A0GP 
       73.32         0.43        10.29       112.54        74.10        46.55 
TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       73.87        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A2QO TCGA-AJ-A3EK TCGA-AJ-A3EL 
       31.99        24.72        34.95        34.36        14.66        22.49 
TCGA-AJ-A3NE TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A054 
       20.65        22.32        12.82         2.70        35.11        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       86.07        48.03        23.87        66.25        46.72        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DM TCGA-AP-A1E0 
       82.52        61.64        49.22        25.08        55.89        60.23 
TCGA-AP-A1E3 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       27.85        13.58        33.21        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 
       79.46        57.47        27.39        60.66        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       77.39        13.28        32.91        73.41        80.25        37.58 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3G8 
       46.49        38.24        17.75        30.74        31.13         1.18 
TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       18.35        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L 
       71.44        36.49       185.79       113.36        54.44        73.64 
TCGA-B5-A11U TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A3FA TCGA-B5-A3FB 
       16.73        16.57        51.45        48.43        96.30        93.50 
TCGA-B5-A3FC TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.84        20.19        63.68        41.52        48.56        23.47 
TCGA-BG-A0MQ TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A 
       59.74        51.06        34.29        56.58        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA 
       15.45         9.57        20.02        20.12        11.31        34.98 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       13.18        10.03         9.86        24.33        85.55        78.21 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       67.99        96.49        97.41       114.90        85.84        81.57 
TCGA-BS-A0V6 TCGA-BS-A0WQ TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
       89.59        66.48         4.87        23.93         1.74        21.99 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B 
       29.88         1.91        29.33        32.58        15.72        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       37.51        36.79        10.65         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17Q TCGA-D1-A17T 
        6.64        18.02         0.99         1.28         1.78         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       22.92         1.41        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DI-A1BU 
       48.79         2.20       100.83        89.33        10.92        39.29 
TCGA-DI-A1BY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       36.62        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KX TCGA-EY-A1GE TCGA-EY-A1GI 
       50.73        35.15        38.07        38.47        24.36        23.34 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-FI-A2D0 TCGA-FI-A2D6 TCGA-PG-A6IB TCGA-PG-A916 
       31.04        14.14        39.88        25.22        21.30        17.16 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       22.65        39.95        23.64        18.28 

$subtype3
TCGA-AX-A06D TCGA-D1-A0ZO TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A549 TCGA-A5-A0G1 
       12.26        19.79         6.21        22.78        19.89       106.88 
TCGA-A5-A0GE TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-AJ-A23O TCGA-AJ-A2QL 
      105.37        54.02        23.21        68.65        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BK TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       35.15        33.90        15.62        15.35        15.95        14.76 
TCGA-AJ-A8CW TCGA-AP-A0LD TCGA-AP-A0LH TCGA-AP-A0LQ TCGA-AP-A1DH TCGA-AP-A1DK 
        0.13       117.99        36.36        80.78        71.67        90.97 
TCGA-AP-A1DV TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06J TCGA-AX-A0IS TCGA-AX-A1C9 
        6.71        29.69        88.24        30.02        61.08        26.37 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3GB TCGA-B5-A0K0 
       34.09        85.48        34.32         0.20        14.47        48.59 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       72.62        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A1MW 
       88.34        61.68        85.78        19.50        18.41        14.70 
TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M9 
       18.61        19.33        20.94        35.21        71.24        74.63 
TCGA-BG-A0MA TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VW 
       10.72        43.30        43.04        20.28        15.42        52.01 
TCGA-BG-A0VZ TCGA-BG-A0YU TCGA-BG-A186 TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BS-A0T9 
       52.64        14.83        13.78        35.90        35.90        46.95 
TCGA-BS-A0TG TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-D1-A0ZU 
       77.95        82.39        73.25        59.51        63.58        28.67 
TCGA-D1-A15W TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16R TCGA-D1-A17D TCGA-D1-A17H 
       30.08         0.66        36.10         0.69        30.44        28.01 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A2G6 TCGA-DI-A1C3 
       10.22         1.51        11.15        24.30         8.48        24.30 
TCGA-EC-A1QX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GX 
        7.36        51.09        14.99        23.34        33.34        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-FI-A2D4 TCGA-PG-A917 TCGA-QS-A5YQ TCGA-QS-A744 
       19.33        22.82         7.99         6.97        24.95        14.83 
TCGA-SJ-A6ZI TCGA-SL-A6JA 
       20.75         0.23 

$subtype4
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-BG-A0MS TCGA-BG-A0VT TCGA-A5-A0G9 
       88.18        30.15        16.83        61.87        51.55        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GU TCGA-A5-A1OJ TCGA-A5-A7WJ 
       17.85        32.78       123.68        28.27        33.07        11.21 
TCGA-AJ-A3NC TCGA-AP-A051 TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LL 
       36.99       129.80        12.62        20.91       110.37        83.97 
TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A064 TCGA-B5-A0JR 
       35.54        45.86        51.12        21.90        49.87        56.91 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MZ TCGA-B5-A3FH TCGA-B5-A5OC 
       32.09        73.28        17.36        52.54        27.65        41.06 
TCGA-BG-A0W1 TCGA-BK-A13B TCGA-BK-A13C TCGA-BS-A0U7 TCGA-BS-A0UT TCGA-D1-A0ZN 
       52.83        31.76        24.99        30.74        72.72        16.83 
TCGA-D1-A0ZR TCGA-D1-A160 TCGA-D1-A16O TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B 
        0.56         3.68        33.63        30.15         1.58         7.00 
TCGA-D1-A17L TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-EO-A3AS TCGA-EY-A1GD 
       26.37        15.88        27.16        16.31        34.39        53.88 
TCGA-EY-A1GF TCGA-EY-A1GO TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A5W2 TCGA-FI-A2D2 
       27.16        19.27        16.11        32.78        16.96        77.33 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.43     0.13     0.56 
subtype1 subtype2 subtype3 subtype4 
  225.50   185.79   117.99   129.80 
subtype1 subtype2 subtype3 subtype4 
  27.420   33.750   28.340   31.925 
[1] "0.1 - 225.5 (27.4)" "0.4 - 185.8 (33.8)" "0.1 - 118.0 (28.3)"
[4] "0.6 - 129.8 (31.9)"
D3V2, binary
          cls
clus         0   1
  subtype1 107  86
  subtype2  95  77
  subtype3  54  41
  subtype4  34  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107   86
  subtype2   95   77
  subtype3   54   41
  subtype4   34   20
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       107       95       54       34
  YES       86       77       41       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"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      88
  subtype2                                     169
  subtype3                                      95
  subtype4                                      52
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            12                               108
  subtype2                             7                                 2
  subtype3                             2                                 2
  subtype4                             1                                 1
D3V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       88      169       95       52
  MIXED SEROUS AND ENDOMETRIOID                 12        7        2        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA            108        2        2        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 132   9  11  19
  subtype2 122  11   2  16
  subtype3  75   2   2   3
  subtype4  42   0   1   2
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      132      122       75       42
  R1        9       11        2        0
  R2       11        2        2        1
  RX       19       16        3        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 120  33
  subtype2  65  15
  subtype3 171  25
subtype1 subtype2 subtype3 
     153       80      196 
subtype1 subtype2 subtype3 
      33       15       25 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06D TCGA-AX-A2H8 
       41.06        20.81        10.19        93.99        12.26        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       27.88         1.38        27.09        12.56        14.27         1.81 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-FI-A2CX 
       16.93        33.30         6.21        10.19        14.40        66.77 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0GG TCGA-A5-A0GQ 
       36.00        23.74        39.52       106.88       123.68        73.87 
TCGA-A5-A0GR TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 
       36.82        31.99        31.99        36.33       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EL 
       28.64        25.51        14.96        18.12         1.64        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3NE TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       22.26        20.65        15.35        16.87        16.87        20.78 
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A1DK TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AX-A0IZ 
       48.03        27.12        90.97        27.85        21.90        43.82 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       32.91        34.65        25.51        32.02        25.91        76.83 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HG TCGA-AX-A2HK 
       37.58         4.77        30.12        71.24        38.24         2.96 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       31.13         0.20         0.20         0.26         0.30         1.18 
TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11O TCGA-B5-A11X TCGA-B5-A1MR 
        0.39        27.85        75.72        85.78        19.59       225.50 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3S1 
       50.89        11.87        31.36        96.30        93.50        29.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A139 
       41.06        34.95        15.45        23.70        35.08        31.00 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0UL TCGA-BS-A0V8 TCGA-D1-A0ZS TCGA-D1-A101 
       24.13        92.88        81.57        83.64         4.87         1.74 
TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A168 TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       39.48        29.88        36.10        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17B TCGA-D1-A17K TCGA-D1-A1NU 
       29.92        18.67        14.73         7.00        28.08        13.22 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KY 
        3.95        48.79        17.29         2.20       109.08        10.92 
TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LZ TCGA-E6-A2P8 
       39.29        35.38         9.37        12.39        79.10         2.37 
TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A3AV TCGA-EO-A3AZ 
        7.36        10.92        66.90        57.60        35.15        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO 
       26.96        22.26        16.34        54.15        23.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 
       18.84        22.03        15.81        20.05        45.76        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       32.52        11.38        14.70        68.38        39.88        77.33 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       25.22        59.01         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB 
       78.38         1.74        17.75        13.28         9.47        21.30 
TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       22.59         8.19         0.07 

$subtype2
TCGA-AJ-A2QM TCGA-AX-A1CP TCGA-AX-A1CR TCGA-4E-A92E TCGA-A5-A7WK TCGA-AJ-A23M 
       29.39        36.39        23.05         0.43        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3NF TCGA-AJ-A3OK TCGA-AJ-A8CT TCGA-AP-A1DQ 
       14.43        34.16        21.21        15.95         2.70        46.78 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A2H7 TCGA-AX-A2HH 
       51.12         0.56        60.66        26.37        40.80        17.75 
TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-B5-A11M TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11U 
       64.93         0.30        44.78        52.04        77.23        16.73 
TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OD 
       16.57       102.31       136.60        39.35        27.65        34.13 
TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A 
       51.06        52.83        56.58        14.83        13.78        14.01 
TCGA-BG-A3PP TCGA-BK-A6W4 TCGA-BS-A0V7 TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZV 
       22.39         9.86        63.58        29.95         0.56        23.93 
TCGA-D1-A0ZZ TCGA-D1-A162 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16X TCGA-D1-A16Y 
       22.55        37.64        36.36        37.51         3.65        17.49 
TCGA-D1-A17C TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A2G7 
        0.99        26.37         1.51         0.72        18.25        58.95 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KV TCGA-DI-A1C3 TCGA-DI-A2QU 
        4.27        18.84        71.61        89.33        24.30        31.10 
TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3L0 
      110.10        37.71        51.42        19.40        34.39        51.09 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2OQ TCGA-FI-A2EU TCGA-FI-A2F9 
       32.71        17.62        12.59        29.10        96.69        59.28 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QF-A5YS 
       14.04        26.10        18.21        23.24        38.70        22.65 
TCGA-QS-A5YQ TCGA-QS-A8F1 
       24.95         4.44 

$subtype3
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AP-A0LS TCGA-BG-A0VT TCGA-D1-A0ZO 
       30.15        16.83        18.08        95.47        51.55        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 
        4.44        47.84        22.78        17.88        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-5S-A9Q8 TCGA-A5-A0VO 
       19.89         5.88        13.84        73.32        10.29        28.77 
TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK 
       33.07        24.72        34.95        11.21        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       19.79        35.15        34.36        18.90        33.90        14.66 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       17.06        36.99        15.62        14.76        22.32        12.82 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A05O TCGA-AP-A1DH TCGA-AP-A1DM TCGA-AP-A1DO 
       35.11         0.13        12.62        71.67        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A5FX 
       35.54        49.15         6.71        60.23        45.86        36.13 
TCGA-AX-A06H TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1CE TCGA-AX-A1CI 
       27.39        61.08        40.11        13.28        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HJ 
       73.41        80.25        81.37        34.32        46.49        30.74 
TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.23         0.56        43.82        20.52        18.35        14.47 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       55.30        59.24        58.75        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11S 
       88.34        54.44        73.64        61.68        32.09        73.28 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A1MV TCGA-B5-A1MW 
       19.56        19.50        18.41        17.36        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-BG-A0MA TCGA-BG-A0MH TCGA-BG-A0MK 
       48.43        52.54        71.84        10.72        63.45        43.30 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A187 TCGA-BG-A18B TCGA-BG-A222 
       52.01        34.29        52.64        14.73        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C 
       20.02        20.12        11.31        34.98        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0UA 
       16.64        13.18        10.03        46.95        96.49       114.90 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       59.51        89.59        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZU TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       28.67        21.99        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16F TCGA-D1-A16N 
       32.58         0.66        15.72        37.32         2.63        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A174 TCGA-D1-A175 
       33.63        10.65         0.69         3.95        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       30.15        18.02         1.58        30.44         1.28        28.01 
TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-DF-A2KU TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
        8.48        15.88       100.83        27.16        25.91        16.31 
TCGA-DI-A1BY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G 
       36.62        23.38        58.95        45.57        16.04        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A3AU 
       49.15        61.74        61.55        46.26        51.52        50.73 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       38.07        46.42        38.47        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GT TCGA-EY-A1GU 
       27.16        23.34        23.34        33.34        16.11        32.78 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A548 
       11.08        37.05        19.33        22.82        31.04        14.14 
TCGA-EY-A5W2 TCGA-FI-A2D4 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YT TCGA-QS-A5YR 
       16.96         7.99        17.16         6.97        39.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        20.75        18.28         0.23 

subtype1 subtype2 subtype3 
    0.07     0.30     0.13 
subtype1 subtype2 subtype3 
  225.50   136.60   185.79 
subtype1 subtype2 subtype3 
  27.090   26.235   24.330 
[1] "0.1 - 225.5 (27.1)" "0.3 - 136.6 (26.2)" "0.1 - 185.8 (24.3)"
D4V2, binary
          cls
clus         0   1
  subtype1  69  69
  subtype2  45  31
  subtype3 108  84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   69
  subtype2   45   31
  subtype3  108   84
     clus
vv    subtype1 subtype2 subtype3
  NO        69       45      108
  YES       69       31       84
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      74
  subtype2                                      46
  subtype3                                     192
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            10                                71
  subtype2                             7                                27
  subtype3                             4                                 0
D4V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       74       46      192
  MIXED SEROUS AND ENDOMETRIOID                 10        7        4
  SEROUS ENDOMETRIAL ADENOCARCINOMA             71       27        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 100   8   8  13
  subtype2  45   5   2  12
  subtype3 139   6   2  14
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      100       45      139
  R1        8        5        6
  R2        8        2        2
  RX       13       12       14
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 35  6
  subtype2 76  6
  subtype3 47  6
  subtype4 42 14
  subtype5 65 19
  subtype6 58 10
  subtype7 40 14
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      41       82       53       56       84       68       54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        6        6       14       19       10       14 
$subtype1
TCGA-4E-A92E TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GN TCGA-AJ-A3OL 
        0.43        17.85       112.54       123.68        60.53        14.76 
TCGA-AP-A1DR TCGA-AX-A05S TCGA-AX-A060 TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-B5-A0JU 
       49.15        13.58        35.34         0.20         1.18        59.24 
TCGA-B5-A0K1 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MH TCGA-BK-A0C9 TCGA-BK-A6W3 
       36.49        71.24        74.63        63.45        35.90        10.03 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0V4 TCGA-D1-A0ZZ TCGA-D1-A15W 
       61.87        67.99        30.74        59.51        22.55        30.08 
TCGA-D1-A160 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16O 
        3.68        36.10        37.32        37.51         2.63        33.63 
TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A17H TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A1NS 
        3.95        30.15        28.01        10.22         1.78         1.41 
TCGA-D1-A1O5 TCGA-D1-A3DA TCGA-EY-A5W2 TCGA-QF-A5YS TCGA-QS-A744 
       15.06        15.88        16.96        22.65        14.83 

$subtype2
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-BG-A0MS TCGA-BG-A0VT TCGA-EY-A1GQ TCGA-5S-A9Q8 
       88.18        30.15        61.87        51.55        17.88        10.29 
TCGA-A5-A0G9 TCGA-A5-A0GU TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-A5-A7WJ 
       83.51        28.27        24.62        28.77        15.95        11.21 
TCGA-AJ-A2QL TCGA-AJ-A3OK TCGA-AP-A051 TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG 
       19.79        15.95       129.80        20.91       110.37        66.25 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LV TCGA-AP-A1DO 
       46.72        83.97        82.52        61.64        25.08        31.30 
TCGA-AP-A1DP TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A063 TCGA-AX-A06J TCGA-AX-A0IS 
       35.54        33.21        29.69        79.46        30.02        61.08 
TCGA-AX-A0J1 TCGA-AX-A2HJ TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A11F TCGA-B5-A11Q 
       77.39        30.74        71.44        48.59       185.79        32.09 
TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3FD 
       73.28        17.36        16.57        52.54        71.84        39.35 
TCGA-B5-A3FH TCGA-BG-A0LW TCGA-BG-A0M3 TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0W1 
       27.65        18.61        35.21        21.17        20.28        52.83 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.83        13.78        14.01        15.45        20.12        11.31 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BS-A0TC TCGA-BS-A0U8 TCGA-BS-A0UJ 
       31.76        24.99        16.64        85.55        97.41        82.39 
TCGA-BS-A0V7 TCGA-D1-A15Z TCGA-D1-A165 TCGA-D1-A16Q TCGA-D1-A17D TCGA-D1-A17L 
       63.58         1.91         0.66        10.65        30.44        26.37 
TCGA-D1-A17S TCGA-DI-A0WH TCGA-E6-A2P9 TCGA-EO-A22Y TCGA-EO-A3KX TCGA-EY-A1GC 
       24.30        16.31        45.57        51.52        38.47        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GL TCGA-EY-A1GX TCGA-EY-A1H0 
       53.88        24.36        27.16        33.34        37.05        19.33 
TCGA-EY-A548 TCGA-PG-A916 TCGA-QS-A5YQ TCGA-SJ-A6ZJ 
       14.14        17.16        24.95        18.28 

$subtype3
TCGA-A5-A0GM TCGA-AP-A0LS TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-A5-A0G1 TCGA-A5-A0GB 
       60.53        95.47        22.06        66.41       106.88        32.78 
TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0RA TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 
       65.75        23.21        29.06        31.99        33.07        66.15 
TCGA-AJ-A3EK TCGA-AP-A05O TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AP-A1DM TCGA-AP-A1DV 
       14.66        12.62        27.12        49.22        55.89         6.71 
TCGA-AP-A1E3 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A06F TCGA-AX-A2H5 TCGA-AX-A2HG 
       27.85        36.13        80.55        57.47        71.24        38.24 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11G 
       58.75        69.27        72.62        27.85        59.84       113.36 
TCGA-B5-A11H TCGA-B5-A11P TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A1MW 
       88.34        52.04        19.56        19.50        19.59        14.70 
TCGA-B5-A1MX TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0RY TCGA-BG-A18C TCGA-BK-A0CB 
       48.43        63.68        41.52        15.42        15.45        35.90 
TCGA-BS-A0TA TCGA-BS-A0UF TCGA-D1-A163 TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17K 
       24.33        85.84        32.58         6.64        18.02        28.08 
TCGA-D1-A17R TCGA-D1-A2G6 TCGA-DF-A2KV TCGA-EO-A22R TCGA-EO-A3B0 
       11.15         8.48        89.33        61.74        46.42 

$subtype4
TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A3G3 TCGA-EY-A1G7 TCGA-EY-A547 
       93.99        67.66        12.26         1.38         6.21        17.92 
TCGA-EY-A549 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GR TCGA-A5-A0GV TCGA-A5-A0R6 
       19.89       149.56        37.02        36.82        54.02        37.91 
TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A3OJ TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05N 
       14.96        21.14        15.35        23.31        63.91        23.87 
TCGA-AP-A3K1 TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A2HA TCGA-AX-A3FW TCGA-B5-A0K4 
       21.90        88.24        71.51        81.37         0.56        57.76 
TCGA-B5-A0K7 TCGA-B5-A11N TCGA-B5-A11U TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0LX 
       63.55        61.68        16.73        29.65        34.95        20.19 
TCGA-BG-A0MK TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-BS-A0VI TCGA-D1-A167 TCGA-DI-A2QU 
       43.30        35.08        92.88        86.99        15.72        31.10 
TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A22S TCGA-EO-A3AU TCGA-EO-A3B1 TCGA-EY-A1GI 
      110.10        37.71        61.55        50.73        26.96        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       23.90        32.71        18.84        16.11        32.78        15.81 
TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-FI-A2EY TCGA-FI-A3PX 
       12.59        20.05        29.10        32.52        28.93        78.38 
TCGA-KP-A3W3 TCGA-PG-A914 
       26.10        22.59 

$subtype5
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A2HF TCGA-B5-A0JN 
       29.39        10.19       110.63        57.80        27.88        80.38 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A215 TCGA-KJ-A3U4 
       12.56        14.27        33.30        10.19        18.87        36.00 
TCGA-KP-A3VZ TCGA-A5-A0G3 TCGA-A5-A0GH TCGA-A5-A0R7 TCGA-A5-A2K7 TCGA-A5-A7WK 
       23.74        46.95        74.10        17.59        34.95        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A4ZG 
       20.25        14.43        10.26        34.16        18.12        16.37 
TCGA-AJ-A5DW TCGA-AP-A056 TCGA-AP-A0LD TCGA-AP-A1E0 TCGA-AW-A1PO TCGA-AX-A0J0 
       12.82        86.07       117.99        60.23         0.56        40.11 
TCGA-AX-A2H2 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3FS 
        4.77        34.32        46.49        17.75         2.96         0.23 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G9 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A1MS 
        0.20         0.30        18.35         0.39        27.29       102.31 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A26L TCGA-D1-A16N TCGA-D1-A16S 
       20.02        23.70        22.39        24.13        31.07        18.67 
TCGA-D1-A179 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-DF-A2KS 
       14.73         3.95        48.79        58.95         4.27       109.08 
TCGA-DF-A2KU TCGA-DF-A2KY TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
      100.83        10.92        25.91        35.38         9.37        12.39 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22X 
       23.38        79.10        58.95        10.92        49.15        57.60 
TCGA-EO-A2CH TCGA-EO-A3AY TCGA-EY-A1G8 TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GR 
       19.40        38.07        14.99        23.34        19.27        17.62 
TCGA-EY-A2OM TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW 
       22.82        27.35        14.70        68.38        96.69        59.01 
TCGA-FI-A2EX TCGA-H5-A2HR TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A915 TCGA-SL-A6J9 
        9.34         1.74         9.47        21.30         8.19         0.07 

$subtype6
TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A221 TCGA-D1-A3JP TCGA-EY-A214 TCGA-EY-A72D 
       61.18        27.09         1.81        16.93        14.40         5.88 
TCGA-A5-A0GE TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0VP TCGA-A5-A1OG TCGA-A5-A2K5 
      105.37        73.87        19.59        42.35        31.99        24.72 
TCGA-A5-A3LO TCGA-AJ-A3NC TCGA-AJ-A3NG TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A059 
       25.51        36.99        15.62        16.87        21.99        48.03 
TCGA-AP-A05J TCGA-AP-A0LI TCGA-AP-A1DH TCGA-AP-A1E1 TCGA-AX-A062 TCGA-AX-A064 
       36.89        97.71        71.67        45.86        45.99        49.87 
TCGA-AX-A06L TCGA-AX-A2H7 TCGA-B5-A11I TCGA-B5-A11Y TCGA-B5-A1MV TCGA-B5-A1MY 
       60.66        40.80        75.72        18.41        51.45        11.87 
TCGA-B5-A3FB TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0VV 
       93.50        34.13        19.33        20.94        48.56        51.06 
TCGA-BG-A222 TCGA-BK-A139 TCGA-BS-A0T9 TCGA-BS-A0TD TCGA-D1-A0ZR TCGA-D1-A101 
        9.57        31.00        46.95        78.21         0.56         1.74 
TCGA-D1-A15X TCGA-D1-A16B TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16X 
       29.88        36.36        36.79        27.42        29.92         3.65 
TCGA-D1-A17B TCGA-D1-A17N TCGA-D1-A17T TCGA-D1-A1NY TCGA-D1-A3DH TCGA-DF-A2KZ 
        7.00         1.51         2.33        16.87        18.84        27.16 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22U TCGA-EO-A3AV 
       39.29        36.62         7.36        16.80        46.26        35.15 
TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1GS TCGA-EY-A2OP TCGA-EY-A4KR TCGA-K6-A3WQ 
       22.26        51.09        22.03        31.04        11.38        14.04 
TCGA-QS-A5YR TCGA-SJ-A6ZI 
       23.64        20.75 

$subtype7
TCGA-A5-AB3J TCGA-D1-A102 TCGA-EY-A1GK TCGA-A5-A0GX TCGA-A5-A1OH TCGA-A5-A2K4 
       16.83         4.44        22.78        68.65        36.33        28.64 
TCGA-AJ-A3BK TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A0IW 
       33.90        45.53        36.36        46.78        51.12        37.78 
TCGA-AX-A0IZ TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0K9 TCGA-B5-A11L TCGA-B5-A1MU 
       43.82        43.82        55.30        13.45        73.64        50.89 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A5OC TCGA-BG-A0MA TCGA-BG-A187 TCGA-BK-A0CA 
       31.36        96.30        41.06        10.72        14.73        34.98 
TCGA-BS-A0TG TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A161 
       77.95        29.95        28.67        21.99        39.48        29.33 
TCGA-D1-A162 TCGA-D1-A16I TCGA-D1-A16R TCGA-D1-A16Y TCGA-D1-A17C TCGA-D1-A17F 
       37.64        11.51         0.69        17.49         0.99         1.28 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NZ TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-E6-A2P8 
       22.92        13.22        18.02        17.29         2.20         2.37 
TCGA-EC-A1NJ TCGA-EO-A22T TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GW TCGA-EY-A2OO 
       16.04        66.90        27.16        16.34        11.08        45.76 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6JA 
       13.28        18.21        23.24        38.70         4.44         0.23 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.20     0.66     6.64     0.56     0.07     0.56     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  123.68   185.79   113.36   149.56   117.99   105.37    96.30 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  30.080   30.295   36.130   30.375   21.845   28.650   27.900 
[1] "0.2 - 123.7 (30.1)" "0.7 - 185.8 (30.3)" "6.6 - 113.4 (36.1)"
[4] "0.6 - 149.6 (30.4)" "0.1 - 118.0 (21.8)" "0.6 - 105.4 (28.6)"
[7] "0.2 - 96.3 (27.9)" 
D5V2, binary
          cls
clus        0  1
  subtype1 26 13
  subtype2 43 39
  subtype3 27 24
  subtype4 29 24
  subtype5 42 32
  subtype6 33 35
  subtype7 28 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   13
  subtype2   43   39
  subtype3   27   24
  subtype4   29   24
  subtype5   42   32
  subtype6   33   35
  subtype7   28   25
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        26       43       27       29       42       33       28
  YES       13       39       24       24       32       35       25
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      39
  subtype2                                      81
  subtype3                                      46
  subtype4                                      34
  subtype5                                      46
  subtype6                                      52
  subtype7                                      31
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             2                                 0
  subtype2                             0                                 1
  subtype3                             2                                 5
  subtype4                             3                                19
  subtype5                             3                                37
  subtype6                             2                                14
  subtype7                             5                                18
D5V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       39       81       46       34
  MIXED SEROUS AND ENDOMETRIOID                  2        0        2        3
  SEROUS ENDOMETRIAL ADENOCARCINOMA              0        1        5       19
                                         clus
vv                                        subtype5 subtype6 subtype7
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       46       52       31
  MIXED SEROUS AND ENDOMETRIOID                  3        2        5
  SEROUS ENDOMETRIAL ADENOCARCINOMA             37       14       18
[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       R0 R1 R2 RX
  subtype1 31  1  1  2
  subtype2 61  1  0  6
  subtype3 32  2  0  5
  subtype4 37  3  2  5
  subtype5 58  4  3  9
  subtype6 47  1  4  5
  subtype7 35  2  1  5
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       31       61       32       37       58       47       35
  R1        1        1        2        3        4        1        2
  R2        1        0        0        2        3        4        1
  RX        2        6        5        5        9        5        5
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  98  12
  subtype2 144  37
  subtype3  78  17
  subtype4  43   9
subtype1 subtype2 subtype3 subtype4 
     110      181       95       52 
subtype1 subtype2 subtype3 subtype4 
      12       37       17        9 
$subtype1
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
       88.18        60.53        30.15        61.87        51.55        14.27 
TCGA-D1-A102 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        4.44         0.43        10.29        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0VP TCGA-A5-A0VQ 
      112.54       123.68        60.53        36.82        42.35        15.95 
TCGA-A5-A1OJ TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A3OK TCGA-AP-A0LL TCGA-AP-A0LP 
       33.07        34.95        11.21        15.95        83.97        61.64 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W 
       31.30        35.54        49.15        13.58        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06J TCGA-AX-A0IS 
       88.24        35.34        79.46        49.87        30.02        61.08 
TCGA-AX-A0J1 TCGA-AX-A2H7 TCGA-AX-A2HD TCGA-B5-A0JU TCGA-B5-A0K1 TCGA-B5-A0K7 
       77.39        40.80        46.49        59.24        36.49        63.55 
TCGA-B5-A11F TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A3FH TCGA-BG-A0LW TCGA-BG-A0LX 
      185.79        73.28        17.36        27.65        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MH TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0W1 
       41.52        48.56        63.45        20.28        51.06        52.83 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A222 TCGA-BK-A0C9 TCGA-BK-A13B 
       14.83        13.78        15.45         9.57        35.90        31.76 
TCGA-BK-A6W3 TCGA-BS-A0TC TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UJ 
       10.03        85.55        61.87        30.74        97.41        82.39 
TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-D1-A0ZR TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
       59.51        63.58         0.56        30.08         1.91         3.68 
TCGA-D1-A169 TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16O TCGA-D1-A16V TCGA-D1-A16X 
       37.32        37.51         2.63        33.63         3.95         3.65 
TCGA-D1-A176 TCGA-D1-A17C TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17S 
       30.15         0.99        26.37        10.22         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1O5 TCGA-D1-A3DA TCGA-DI-A1BY 
        2.33        22.92         1.41        15.06        15.88        36.62 
TCGA-E6-A1LX TCGA-E6-A2P9 TCGA-EO-A2CH TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GU 
       23.38        45.57        19.40        24.36        27.16        32.78 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A548 TCGA-EY-A5W2 TCGA-PG-A916 TCGA-QF-A5YS 
       37.05        19.33        14.14        16.96        17.16        22.65 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

$subtype2
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       29.39        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       67.66        12.26        27.88         1.38        80.38        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 
       66.41        12.56        16.93        33.30         6.21        10.19 
TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 
       17.92        36.00        23.74       106.88       149.56        46.95 
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0R6 
       37.02        65.75        28.27        54.02        23.21        37.91 
TCGA-A5-A0R9 TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QK 
       24.62        36.33        66.15        18.41        20.25        21.14 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3OJ TCGA-AJ-A3TW TCGA-AJ-A5DW 
       34.16        18.12        14.66        15.35        16.87        12.82 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
      129.80        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       23.87        20.91       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AP-A1DM TCGA-AP-A1DQ 
       46.72        27.12        82.52        25.08        55.89        46.78 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05T 
        6.71        60.23        45.86        51.12        21.90        33.21 
TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC 
       71.51        45.99         4.77        71.24        81.37        34.32 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3GI TCGA-B5-A0JX 
       30.74         2.96         0.23         0.56         0.39        58.75 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E 
       71.44        48.59        72.62        27.29        27.85        59.84 
TCGA-B5-A11G TCGA-B5-A11N TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
      113.36        61.68        52.04        32.09        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA 
       19.50       102.31        50.89        11.87        52.54        96.30 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MT TCGA-BG-A0RY 
       71.84        39.35        29.65        34.95        21.17        15.42 
TCGA-BG-A18C TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BK-A0CB TCGA-BK-A13C 
       15.45        20.02        23.70        20.12        35.90        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TA TCGA-D1-A0ZZ TCGA-D1-A165 TCGA-D1-A167 
       24.13        16.64        24.33        22.55         0.66        15.72 
TCGA-D1-A16B TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17D TCGA-D1-A17K 
       36.36        10.65        18.67        14.73        30.44        28.08 
TCGA-D1-A17R TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KY TCGA-DI-A0WH 
       11.15        58.95        18.84        17.29        10.92        16.31 
TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LZ TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22Y 
       79.10        16.80        10.92        37.71        61.74        51.52 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       50.73        35.15        38.07        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       38.47        54.15        53.88        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       16.11        11.08        12.59        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW 
       32.52        11.38        14.70        68.38        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W1 TCGA-KP-A3W3 
        9.34        28.93        78.38         1.74         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A5YQ TCGA-QS-A8F1 
       18.21        21.30        22.59         8.19        24.95         4.44 
TCGA-SL-A6J9 
        0.07 

$subtype3
TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A221 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
       61.18        27.09         1.81        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GQ TCGA-A5-A0R7 TCGA-A5-A0R8 
        5.88       105.37        74.10        73.87        17.59        19.59 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A3LO TCGA-A5-A3LP 
       31.99        31.99        28.64        24.72        25.51        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A3NC TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A4ZG 
       14.43        10.26        36.99        15.62        14.76        16.37 
TCGA-AP-A052 TCGA-AP-A0LD TCGA-AP-A0LT TCGA-AP-A1DH TCGA-AP-A5FX TCGA-AW-A1PO 
       21.99       117.99        49.22        71.67        36.13         0.56 
TCGA-AX-A06F TCGA-AX-A0J0 TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A3FT TCGA-AX-A3FZ 
       57.47        40.11        38.24        17.75         0.20         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-B5-A0JY TCGA-B5-A0K4 TCGA-B5-A11H 
        0.30         1.18        18.35        69.27        57.76        88.34 
TCGA-B5-A11I TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       75.72        19.59        18.41        51.45        14.70        48.43 
TCGA-B5-A3FB TCGA-B5-A5OD TCGA-BG-A0MK TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CC 
       93.50        34.13        43.30        11.31        22.39        35.08 
TCGA-BK-A139 TCGA-BS-A0T9 TCGA-BS-A0TJ TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0VI 
       31.00        46.95        67.99        92.88        85.84        86.99 
TCGA-D1-A101 TCGA-D1-A15X TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16E TCGA-D1-A16G 
        1.74        29.88        32.58        36.10        36.79        27.42 
TCGA-D1-A16N TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17N TCGA-D1-A1NY 
       31.07         6.64        18.02         7.00         1.51        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KS TCGA-DF-A2KU 
       18.02         3.95        48.79         4.27       109.08       100.83 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-E6-A1M0 TCGA-EC-A1QX TCGA-EO-A1Y7 TCGA-EO-A22S 
       27.16        25.91        58.95         7.36        49.15        61.55 
TCGA-EO-A22X TCGA-EO-A3B1 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GV TCGA-EY-A2OM 
       57.60        26.96        51.09        14.99        15.81        22.82 
TCGA-EY-A2ON TCGA-K6-A3WQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       20.05        14.04        23.64        14.83        20.75 

$subtype4
TCGA-A5-AB3J TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-A5-A0GX TCGA-A5-A0RA TCGA-A5-A0VO 
       16.83        22.78        17.88        68.65        29.06        28.77 
TCGA-AJ-A2QL TCGA-AJ-A3BK TCGA-AP-A05H TCGA-AP-A05O TCGA-AP-A1E3 TCGA-AX-A06L 
       19.79        33.90        45.53        12.62        27.85        60.66 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0K9 TCGA-B5-A11L 
       37.78        43.82        43.82        55.30        13.45        73.64 
TCGA-B5-A121 TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A0MA TCGA-BG-A187 TCGA-BG-A18A 
       16.57        31.36        41.06        10.72        14.73        14.01 
TCGA-BK-A0CA TCGA-BS-A0TD TCGA-BS-A0TG TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A103 
       34.98        78.21        77.95        29.95        28.67        21.99 
TCGA-D1-A15V TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16R 
       39.48        29.33        37.64        11.51        29.92         0.69 
TCGA-D1-A16Y TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A1NU TCGA-D1-A2G6 TCGA-DF-A2KN 
       17.49         1.28        28.01        13.22         8.48         2.20 
TCGA-DF-A2KV TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A3AZ 
       89.33         2.37        16.04        66.90        46.26        27.16 
TCGA-EY-A2OO TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 
       45.76        13.28        23.24        38.70 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.07     0.20     0.69 
subtype1 subtype2 subtype3 subtype4 
  185.79   149.56   117.99    89.33 
subtype1 subtype2 subtype3 subtype4 
   31.53    28.08    26.96    28.72 
[1] "0.2 - 185.8 (31.5)" "0.1 - 149.6 (28.1)" "0.2 - 118.0 (27.0)"
[4] "0.7 - 89.3 (28.7)" 
D6V2, binary
          cls
clus        0  1
  subtype1 69 41
  subtype2 94 77
  subtype3 43 47
  subtype4 22 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   41
  subtype2   94   77
  subtype3   43   47
  subtype4   22   27
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        69       94       43       22
  YES       41       77       47       27
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                     107
  subtype2                                     109
  subtype3                                      75
  subtype4                                      38
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             1                                 2
  subtype2                             7                                67
  subtype3                             5                                15
  subtype4                             4                                10
D6V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      107      109       75       38
  MIXED SEROUS AND ENDOMETRIOID                  1        7        5        4
  SEROUS ENDOMETRIAL ADENOCARCINOMA              2       67       15       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  83   3   2   7
  subtype2 125   6   4  13
  subtype3  58   4   4  11
  subtype4  35   1   1   6
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       83      125       58       35
  R1        3        6        4        1
  R2        2        4        4        1
  RX        7       13       11        6
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 138  50
  subtype2 111  13
  subtype3  80  13
  subtype4 123  15
subtype1 subtype2 subtype3 subtype4 
     188      124       93      138 
subtype1 subtype2 subtype3 subtype4 
      50       13       13       15 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D 
       41.06        29.39        20.81        10.19       110.63        57.80 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A220 TCGA-E6-A8L9 
        1.38        80.38        22.06        12.56        14.27        33.30 
TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KJ-A3U4 
        6.21        10.19        17.92         5.88        66.77        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GH TCGA-A5-A0R6 
       23.74        39.52        46.95        37.02        74.10        37.91 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WK 
       31.99        36.33       118.19        28.64        14.96        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EL 
       20.25        14.43        34.16        18.12         1.64        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       22.26        21.21        15.62        14.76        16.87        16.87 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
       21.99        23.31        63.91        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LI TCGA-AP-A0LM TCGA-AP-A1DK 
       48.79       125.42       117.99        97.71        27.12        90.97 
TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A0IW 
       46.78        51.12        21.90         0.56        35.74        37.78 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       32.91        34.65        25.51        32.02        25.91        76.83 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HH TCGA-AX-A2HK 
        4.77        30.12        71.24        46.49        17.75         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 
       31.13        64.93         0.23         0.20         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A11I 
        0.30         0.39        27.29        57.76        27.85        75.72 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MY TCGA-B5-A1N2 
      225.50       102.31        50.89        14.70        11.87        31.36 
TCGA-B5-A3FA TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AD 
       96.30        29.65        34.13        34.95        15.45        20.02 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 
       23.70        22.39        35.08        31.00        24.13        92.88 
TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZZ TCGA-D1-A15V 
       73.25        83.64        29.95         4.87        22.55        39.48 
TCGA-D1-A167 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A179 TCGA-D1-A17K 
       15.72        11.51        18.67        17.49        14.73        28.08 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       13.22         0.72        18.25         2.07         8.48        58.95 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KU TCGA-DF-A2KY TCGA-DI-A0WH 
        4.27        18.84        17.29       100.83        10.92        16.31 
TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A2P8 
       39.29        35.38         9.37        31.10       110.10         2.37 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       10.92        37.71        57.60        51.42        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM 
       27.16        26.96        22.26        16.34        54.15        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 
       19.27        18.84        17.62        22.03        15.81        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       22.82        20.05        45.76        29.10        27.35        11.38 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       14.70        68.38        77.33        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        17.75        14.04        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       23.24        21.30        38.70        22.59         8.19        14.83 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$subtype2
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-AB3J TCGA-AP-A0LS TCGA-BG-A0MS TCGA-BG-A0VT 
       88.18        60.53        16.83        95.47        61.87        51.55 
TCGA-D1-A102 TCGA-EY-A1GQ TCGA-FI-A2D5 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0GB 
        4.44        17.88        13.84         0.43        10.29        32.78 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       65.75        60.53        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A2K5 TCGA-A5-A3LO 
       17.59        24.62        42.35        15.95        24.72        25.51 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A3NC TCGA-AJ-A5DW TCGA-AJ-A8CW TCGA-AP-A051 
       10.26        21.14        36.99        12.82         0.13       129.80 
TCGA-AP-A05N TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LV 
       23.87       110.37        66.25        83.97        82.52        25.08 
TCGA-AP-A1DH TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AX-A062 TCGA-AX-A063 
       71.67        60.23        45.86        27.85        45.99        79.46 
TCGA-AX-A06H TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1CI TCGA-AX-A1CK 
       27.39        61.08        40.11        77.39        85.48        80.25 
TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HJ TCGA-B5-A0JR TCGA-B5-A0JU 
       37.58        81.37        34.32        30.74        56.91        59.24 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11E 
       86.01        69.27        48.59        64.21        63.55        59.84 
TCGA-B5-A11F TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z 
      185.79        32.09        16.73        19.56        19.59        17.36 
TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 
       52.54        71.84        41.06        18.61        20.19        35.21 
TCGA-BG-A0MA TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VX 
       10.72        23.47        43.04        21.17        20.28        34.29 
TCGA-BG-A186 TCGA-BG-A2L7 TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BS-A0T9 
       13.78        20.12        35.90        31.76        16.64        46.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       61.87        67.99        97.41        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       72.72        63.58        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZU TCGA-D1-A15Z TCGA-D1-A16B TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R 
       28.67         1.91        36.36        31.07        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A175 TCGA-D1-A17C TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1O8 
        3.95         6.64         0.99        10.22        11.15         3.95 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1M0 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U 
       36.62        24.30        58.95        61.74        61.55        46.26 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GI TCGA-EY-A1GL 
       46.42        38.47        14.99        53.88        23.34        33.34 
TCGA-EY-A2OP TCGA-FI-A2D4 TCGA-PG-A917 TCGA-QF-A5YT 
       31.04         7.99         6.97        39.95 

$subtype3
TCGA-AJ-A3BG TCGA-AP-A0LF TCGA-BG-A0M8 TCGA-BG-A221 TCGA-D1-A3JP TCGA-EY-A214 
       18.08        93.99        66.41         1.81        16.93        14.40 
TCGA-EY-A215 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0GA TCGA-A5-A0GR TCGA-A5-A1OF 
       18.87       106.88       149.56        17.85        36.82        31.99 
TCGA-A5-A2K3 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A2QO TCGA-AJ-A3EK TCGA-AJ-A3NE 
       66.15        34.95        11.21        34.36        14.66        20.65 
TCGA-AJ-A3OJ TCGA-AJ-A6NU TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LH TCGA-AP-A0LT 
       15.35        20.78        86.07        48.03        36.36        49.22 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AX-A05S TCGA-AX-A05W 
       55.89        31.30        49.15         6.71        13.58        80.55 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A0IZ TCGA-AX-A1C4 
       71.51        35.34        49.87        57.47        43.82        13.28 
TCGA-AX-A2HG TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-B5-A0JZ TCGA-B5-A0K9 
       38.24         0.20         1.18        18.35        71.44        13.45 
TCGA-B5-A11H TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11Y TCGA-B5-A1MX TCGA-BG-A0M4 
       88.34        73.64        61.68        18.41        48.43        71.24 
TCGA-BG-A0MH TCGA-BG-A0MQ TCGA-BG-A0RY TCGA-BG-A222 TCGA-BG-A3EW TCGA-BK-A6W3 
       63.45        59.74        15.42         9.57        11.31        10.03 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U7 TCGA-BS-A0V4 TCGA-D1-A101 TCGA-D1-A103 
        4.80        77.95        30.74        59.51         1.74        21.99 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16J 
       29.88         3.68        32.58        36.10        27.42        29.92 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A1NY TCGA-D1-A2G0 
       18.02         1.58        28.01        26.37        16.87        48.79 
TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KZ TCGA-DI-A2QT 
       15.88         2.20        71.61       109.08        27.16        12.39 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A22T TCGA-EO-A3AU TCGA-EO-A3AV 
       23.38        79.10         7.36        66.90        50.73        35.15 
TCGA-EO-A3AY TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A3QX TCGA-EY-A5W2 TCGA-FI-A2D0 
       38.07        16.11        32.78        32.52        16.96        39.88 
TCGA-KP-A3W1 TCGA-SJ-A6ZI TCGA-SL-A6JA 
        9.47        20.75         0.23 

$subtype4
TCGA-A5-A1OK TCGA-B5-A0KB TCGA-D1-A0ZO TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A549 
       30.15        27.09        19.79        47.84        22.78        19.89 
TCGA-FI-A2F4 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GP 
       73.32        83.51       112.54       105.37       123.68        46.55 
TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A1OJ TCGA-AJ-A2QL 
       73.87        19.59        29.06        28.77        33.07        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK TCGA-AJ-A5DV 
       35.15        18.90        33.90        17.06        15.95        22.32 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A05O TCGA-AP-A0LJ TCGA-AP-A0LO TCGA-AP-A0LP 
        2.70        35.11        12.62        46.72        33.40        61.64 
TCGA-AP-A1DP TCGA-AP-A5FX TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06J 
       35.54        36.13        33.21        29.69        88.24        30.02 
TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A2H7 TCGA-AX-A3FW 
       60.66        26.37        34.09        73.41        40.80         0.56 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JX 
       43.82        20.52        14.47        86.37        55.30        58.75 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
       36.49        72.62       113.36        54.44        44.78        85.78 
TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A121 TCGA-B5-A1MV 
       52.04        77.23        73.28        19.50        16.57        51.45 
TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 TCGA-BG-A0M2 
      136.60        93.50        39.35        27.65        19.33        20.94 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MK TCGA-BG-A0VV 
       63.68        74.63        41.52        48.56        43.30        51.06 
TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 
       52.01        52.64        52.83        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BK-A56F 
       14.01        15.45        35.90        34.98        24.99        13.18 
TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0UA 
        9.86        24.33        85.55        78.21        96.49       114.90 
TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A15W TCGA-D1-A161 
       86.93        89.59         0.56        23.93        30.08        29.33 
TCGA-D1-A162 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       37.64         0.66        37.32        37.51        36.79         2.63 
TCGA-D1-A16O TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17B TCGA-D1-A17D 
       33.63         3.65        19.53        30.15         7.00        30.44 
TCGA-D1-A17F TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.28         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-DF-A2KV TCGA-DF-A2L0 
        1.41        18.02        15.06         1.05        89.33        25.91 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A3L0 
       45.57        16.04        16.80        49.15        51.52        51.09 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       24.36        27.16        23.34        11.08        37.05        19.33 
TCGA-EY-A548 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       14.14        17.16        22.65        24.95        23.64        18.28 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.13     0.20     0.56 
subtype1 subtype2 subtype3 subtype4 
  225.50   185.79   149.56   136.60 
subtype1 subtype2 subtype3 subtype4 
  25.365   36.130   30.740   31.755 
[1] "0.1 - 225.5 (25.4)" "0.1 - 185.8 (36.1)" "0.2 - 149.6 (30.7)"
[4] "0.6 - 136.6 (31.8)"
D7V2, binary
          cls
clus        0  1
  subtype1 96 78
  subtype2 73 50
  subtype3 40 48
  subtype4 85 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96   78
  subtype2   73   50
  subtype3   40   48
  subtype4   85   50
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        96       73       40       85
  YES       78       50       48       50
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      71
  subtype2                                     124
  subtype3                                      80
  subtype4                                     134
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            15                               103
  subtype2                             0                                 0
  subtype3                             4                                10
  subtype4                             3                                 1
D7V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       71      124       80      134
  MIXED SEROUS AND ENDOMETRIOID                 15        0        4        3
  SEROUS ENDOMETRIAL ADENOCARCINOMA            103        0       10        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 119  13   9  15
  subtype2  96   2   3   5
  subtype3  61   5   4   6
  subtype4  98   2   0  14
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      119       96       61       98
  R1       13        2        5        2
  R2        9        3        4        0
  RX       15        5        6       14
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 91 33
  subtype2 48  5
  subtype3 34 12
  subtype4 61  4
  subtype5 88 20
  subtype6 56 13
  subtype7 74  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     124       53       46       65      108       69       78 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      33        5       12        4       20       13        4 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D 
       41.06        29.39        20.81        10.19       110.63        57.80 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       36.39        23.05        61.18        27.88         1.38        80.38 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A221 TCGA-E6-A8L9 TCGA-EY-A212 TCGA-KJ-A3U4 
       22.06        12.56         1.81        33.30        10.19        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G3 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       23.74        39.52        46.95        37.91        31.99        36.33 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       28.64        14.96        18.41        20.25        14.43        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       18.12         1.64        22.26        21.21        16.87        16.87 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 
       21.99        63.91        45.53        36.89        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A0IU 
      125.42       117.99        46.78        51.12         0.56        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 
       37.78        34.65        25.51        32.02        25.91         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       71.24         2.96        64.93         0.30         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MU 
        0.39        27.29        27.85        75.72       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A3PP 
       11.87        31.36        96.30        29.65        34.13        22.39 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I 
       35.08        24.13        29.95        22.55        39.48        11.51 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       18.67        17.49        14.73        13.22         0.72        18.25 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       58.95        18.84        17.29        35.38         9.37       110.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3B1 
       10.92        37.71        51.42        19.40        34.39        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A210 TCGA-EY-A2OQ 
       22.26        16.34        32.71        19.27        12.59        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       27.35        11.38        14.70        68.38        77.33        96.69 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       13.28        26.10        18.21        23.24        38.70        22.59 
TCGA-PG-A915 TCGA-QF-A5YS TCGA-QS-A8F1 TCGA-SL-A6J9 
        8.19        22.65         4.44         0.07 

$subtype2
TCGA-A5-A0GI TCGA-A5-AB3J TCGA-BG-A0MS TCGA-BG-A0VT TCGA-D1-A102 TCGA-4E-A92E 
       88.18        16.83        61.87        51.55         4.44         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0VQ 
       10.29        60.53        28.27        54.02        68.65        15.95 
TCGA-AJ-A3NC TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05T 
       36.99        66.25        83.97        82.52        25.08        33.21 
TCGA-AX-A0IS TCGA-AX-A1CI TCGA-AX-A1CK TCGA-B5-A0JU TCGA-B5-A0K6 TCGA-B5-A0K7 
       61.08        85.48        80.25        59.24        64.21        63.55 
TCGA-B5-A11F TCGA-B5-A11V TCGA-B5-A11Z TCGA-BG-A0LW TCGA-BG-A0M3 TCGA-BG-A0MI 
      185.79        19.56        17.36        18.61        35.21        23.47 
TCGA-BG-A0MO TCGA-BG-A0MU TCGA-BG-A0VX TCGA-BG-A186 TCGA-BK-A0CB TCGA-BK-A13B 
       43.04        20.28        34.29        13.78        35.90        31.76 
TCGA-BS-A0UJ TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZU TCGA-D1-A15Z 
       82.39        86.99        66.48        16.83        28.67         1.91 
TCGA-D1-A16B TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A17C TCGA-D1-A17M TCGA-D1-A17N 
       36.36        10.65         0.69         0.99        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17T TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-QF-A5YT 
       11.15         2.33        14.99        53.88        39.95 

$subtype3
TCGA-AP-A0LF TCGA-D1-A3JP TCGA-FI-A2CX TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       93.99        16.93        66.77       106.88       149.56        37.02 
TCGA-A5-A0GH TCGA-A5-A0GR TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-AJ-A3OJ 
       74.10        36.82        31.99       118.19        66.15        15.35 
TCGA-AJ-A6NU TCGA-AP-A059 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A2H4 
       20.78        48.03        36.36        97.71        21.90        30.12 
TCGA-AX-A2HG TCGA-AX-A3FT TCGA-B5-A1MR TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BS-A0TA 
       38.24         0.20       225.50        34.95        71.24        24.33 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-D1-A15X TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A2G0 
        4.80        61.87        29.88        27.42        29.92        48.79 
TCGA-DF-A2KN TCGA-DI-A2QT TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A22T TCGA-EO-A3AV 
        2.20        12.39        79.10         7.36        66.90        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A2ON TCGA-FI-A2EW 
       38.07        27.16        22.03        15.81        20.05        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-JU-AAVI TCGA-KP-A3W1 
        9.34        28.93        17.75         9.47 

$subtype4
TCGA-AJ-A3BG TCGA-BG-A0M8 TCGA-EY-A1GQ TCGA-EY-A215 TCGA-FI-A2F4 TCGA-A5-A2K5 
       18.08        66.41        17.88        18.87        73.32        24.72 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A3EK TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A0LE 
       11.21        10.26        14.66         0.13       129.80       110.37 
TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DV TCGA-AP-A1E0 
       27.12        49.22        55.89        31.30         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       45.86        27.85        71.51        35.34        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A2HA TCGA-B5-A0JR 
       57.47        27.39        77.39        13.28        81.37        56.91 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K9 TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A1MX 
       86.01        71.44        13.45        61.68        32.09        48.43 
TCGA-B5-A1MZ TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0MQ TCGA-BS-A0U7 TCGA-BS-A0U8 
       52.54        41.06        20.19        59.74        30.74        97.41 
TCGA-BS-A0UL TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A103 
       81.57        59.51        63.58        83.64         8.55        21.99 
TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17H 
        3.68        32.58        19.53         6.64        18.02        28.01 
TCGA-D1-A17L TCGA-D1-A17Q TCGA-DF-A2KU TCGA-DI-A1BU TCGA-E6-A1LX TCGA-EO-A22R 
       26.37         1.78       100.83        39.29        23.38        61.74 
TCGA-EO-A3B0 TCGA-EY-A1GI TCGA-EY-A1GU TCGA-EY-A5W2 TCGA-SL-A6JA 
       46.42        23.34        32.78        16.96         0.23 

$subtype5
TCGA-AX-A06B TCGA-AX-A06D TCGA-BG-A220 TCGA-EY-A1G7 TCGA-EY-A214 TCGA-EY-A547 
       67.66        12.26        14.27         6.21        14.40        17.92 
TCGA-EY-A72D TCGA-FI-A2D5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GW TCGA-A5-A0R7 
        5.88        13.84        17.85        32.78        23.21        17.59 
TCGA-A5-A0VP TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A3EL TCGA-AJ-A3NE TCGA-AJ-A3NG 
       42.35        34.95        25.51        22.49        20.65        15.62 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05N TCGA-AP-A1DH 
       14.76        12.82        23.31        86.07        23.87        71.67 
TCGA-AP-A1DK TCGA-AP-A1DR TCGA-AX-A062 TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C5 
       90.97        49.15        45.99        43.82        40.11        32.91 
TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HH 
       76.83        37.58        40.80        34.32        46.49        17.75 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-B5-A0JY 
       31.13         0.23         0.20         1.18        18.35        69.27 
TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11X 
       48.59        57.76        59.84        52.04        16.73        19.59 
TCGA-B5-A1MW TCGA-B5-A3FC TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A18C TCGA-BG-A222 
       14.70        71.84        21.17        15.42        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A4ZD TCGA-BS-A0T9 
       20.02        23.70        20.12        11.31        16.64        46.95 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UT TCGA-BS-A0UV 
       77.95        67.99        92.88        85.84        72.72        73.25 
TCGA-D1-A0ZS TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16V 
        4.87        15.72        36.10        37.32        31.07         3.95 
TCGA-D1-A17K TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A3DA 
       28.08        16.87         2.07         3.95         8.48        15.88 
TCGA-D1-A3DG TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        71.61       109.08        10.92        27.16        16.31 
TCGA-DI-A2QU TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X 
       31.10        58.95         2.37        61.55        46.26        57.60 
TCGA-EO-A3AU TCGA-EO-A3KX TCGA-EY-A1GC TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GR 
       50.73        38.47        54.15        33.34        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       16.11        11.08        22.82        45.76        31.04        32.52 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-PG-A6IB TCGA-PG-A917 TCGA-QS-A744 
       39.88         7.99        25.22        21.30         6.97        14.83 

$subtype6
TCGA-A5-A0GM TCGA-AP-A0LS TCGA-B5-A0KB TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0R9 
       60.53        95.47        27.09        65.75        46.55        24.62 
TCGA-A5-A0VO TCGA-A5-A1OJ TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI 
       28.77        33.07        21.14        35.15        34.36        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AP-A0LJ TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AX-A05S 
       33.90        17.06        46.72        33.40        36.13        13.58 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06L TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A2HJ 
       29.69        88.24        60.66        34.09        73.41        30.74 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GB TCGA-B5-A0JT TCGA-B5-A11G TCGA-B5-A11H 
       43.82        20.52        14.47        55.30       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11S TCGA-B5-A11Y TCGA-B5-A1MV TCGA-B5-A3F9 
       54.44        73.64        73.28        18.41        51.45       136.60 
TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0MA 
       93.50        39.35        27.65        19.33        20.94        10.72 
TCGA-BG-A0MH TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BK-A139 
       63.45        52.64        52.83        56.58        14.73        31.00 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-D1-A101 TCGA-D1-A15W TCGA-D1-A165 
       13.18        10.03         9.86         1.74        30.08         0.66 
TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A17A TCGA-D1-A17S TCGA-D1-A1O5 TCGA-DF-A2L0 
       37.51         2.63         1.58        24.30        15.06        25.91 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-EC-A1NJ TCGA-EO-A1Y7 TCGA-EO-A3L0 TCGA-EY-A548 
       36.62        24.30        16.04        49.15        51.09        14.14 
TCGA-QS-A5YQ TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        20.75        18.28 

$subtype7
TCGA-A5-A1OK TCGA-D1-A0ZO TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A549 TCGA-A5-A0G9 
       30.15        19.79        47.84        22.78        19.89        83.51 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0RA 
      112.54       105.37       123.68        73.87        19.59        29.06 
TCGA-AJ-A2QL TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A05O 
       19.79        15.95        22.32         2.70        35.11        12.62 
TCGA-AP-A0LP TCGA-AP-A1DP TCGA-AX-A05W TCGA-AX-A06J TCGA-AX-A1C9 TCGA-AX-A3FW 
       61.64        35.54        80.55        30.02        26.37         0.56 
TCGA-B5-A0JS TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A11M TCGA-B5-A11O 
       86.37        58.75        36.49        72.62        44.78        85.78 
TCGA-B5-A11R TCGA-B5-A11W TCGA-B5-A121 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       77.23        19.50        16.57        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0YU TCGA-BG-A18A 
       48.56        43.30        51.06        52.01        14.83        14.01 
TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BS-A0TC TCGA-BS-A0TD 
       15.45        35.90        34.98        24.99        85.55        78.21 
TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZR TCGA-D1-A0ZV 
       96.49       114.90        86.93        89.59         0.56        23.93 
TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A16E TCGA-D1-A16O TCGA-D1-A16X TCGA-D1-A176 
       29.33        37.64        36.79        33.63         3.65        30.15 
TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NZ 
        7.00        30.44         1.28        22.92         1.41        18.02 
TCGA-D1-A1O7 TCGA-DF-A2KV TCGA-E6-A2P9 TCGA-EC-A24G TCGA-EO-A22Y TCGA-EY-A1GE 
        1.05        89.33        45.57        16.80        51.52        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-PG-A916 TCGA-QS-A5YR 
       27.16        23.34        37.05        19.33        17.16        23.64 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.43     0.20     0.13     0.20     0.66     0.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  125.42   185.79   225.50   129.80   109.08   136.60   123.68 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  26.005   34.290   33.470   32.780   23.785   31.000   32.035 
[1] "0.1 - 125.4 (26.0)" "0.4 - 185.8 (34.3)" "0.2 - 225.5 (33.5)"
[4] "0.1 - 129.8 (32.8)" "0.2 - 109.1 (23.8)" "0.7 - 136.6 (31.0)"
[7] "0.6 - 123.7 (32.0)"
D8V2, binary
          cls
clus        0  1
  subtype1 59 56
  subtype2 33 20
  subtype3 21 21
  subtype4 32 32
  subtype5 60 42
  subtype6 42 27
  subtype7 47 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   56
  subtype2   33   20
  subtype3   21   21
  subtype4   32   32
  subtype5   60   42
  subtype6   42   27
  subtype7   47   28
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        59       33       21       32       60       42       47
  YES       56       20       21       32       42       27       28
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      24
  subtype2                                      53
  subtype3                                      21
  subtype4                                      63
  subtype5                                     104
  subtype6                                      68
  subtype7                                      76
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            10                                90
  subtype2                             0                                 0
  subtype3                             5                                21
  subtype4                             2                                 0
  subtype5                             3                                 2
  subtype6                             1                                 0
  subtype7                             1                                 1
D8V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       24       53       21       63
  MIXED SEROUS AND ENDOMETRIOID                 10        0        5        2
  SEROUS ENDOMETRIAL ADENOCARCINOMA             90        0       21        0
                                         clus
vv                                        subtype5 subtype6 subtype7
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      104       68       76
  MIXED SEROUS AND ENDOMETRIOID                  3        1        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA              2        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       R0 R1 R2 RX
  subtype1 81  7  3 10
  subtype2 42  1  0  3
  subtype3 32  1  7  4
  subtype4 44  5  1  2
  subtype5 72  7  4  7
  subtype6 44  1  1  6
  subtype7 59  0  0  8
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       81       42       32       44       72       44       59
  R1        7        1        1        5        7        1        0
  R2        3        0        7        1        4        1        0
  RX       10        3        4        2        7        6        8
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 125  39
  subtype2  68  13
  subtype3  89  18
  subtype4 127  11
  subtype5  39   7
subtype1 subtype2 subtype3 subtype4 subtype5 
     164       81      107      138       46 
subtype1 subtype2 subtype3 subtype4 subtype5 
      39       13       18       11        7 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B 
       41.06        29.39        10.19       110.63        93.99        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A221 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 
       22.06        12.56         1.81        33.30         6.21        10.19 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       14.40        17.92         5.88        36.00        23.74        39.52 
TCGA-A5-A0G3 TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 
       46.95        36.82        31.99        36.33       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
       28.64        24.72        25.51        14.96        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       14.43        34.36        34.16        18.12         1.64        22.26 
TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AP-A0L9 
       15.62        16.87        16.87        12.82        20.78       125.42 
TCGA-AP-A0LD TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
      117.99        51.12        21.90        35.74        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HG 
       25.51        76.83         4.77        30.12        71.24        38.24 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K8 
       20.52         0.30         0.26         0.30         0.39        27.85 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A1MY 
       59.84        88.34        75.72       102.31        14.70        11.87 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       96.30        93.50        27.65        29.65        34.13        34.95 
TCGA-BG-A2AD TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       20.02        11.31        22.39        35.08        31.00        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I 
       16.64        92.88        29.95        22.55        39.48        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G0 
       31.07        18.67        28.08        13.22         0.72        48.79 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DI-A1NN TCGA-DI-A1NO 
       71.61       109.08        89.33        10.92        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3AS 
       12.39       110.10        79.10        37.71        19.40        34.39 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3L0 TCGA-EY-A1GC 
       38.07        26.96        22.26        16.34        51.09        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT 
       23.90        32.71        19.27        18.84        22.03        16.11 
TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       15.81        12.59        22.82        20.05        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       27.35        11.38        77.33        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        30.67        59.28        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       17.75        14.04         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 
       21.30        38.70        22.59         8.19        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SL-A6J9 
       20.75         0.07 

$subtype2
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-BG-A0VT TCGA-D1-A102 TCGA-4E-A92E 
       88.18        30.15        16.83        51.55         4.44         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0GN TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0VQ TCGA-A5-A7WJ 
       10.29        60.53        68.65        17.59        15.95        11.21 
TCGA-AJ-A23O TCGA-AJ-A2QN TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3OL TCGA-AJ-A8CW 
       10.26        35.15        36.99        20.65        14.76         0.13 
TCGA-AP-A054 TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LV TCGA-AP-A5FX 
       23.31        83.97        82.52        33.40        25.08        36.13 
TCGA-AW-A1PO TCGA-AX-A0IS TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC 
        0.56        61.08        80.25        37.58        81.37        34.32 
TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K6 
        0.20         1.18        56.91        69.27        48.59        64.21 
TCGA-B5-A11F TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MZ 
      185.79        16.73        19.56        19.59        17.36        52.54 
TCGA-BG-A0LW TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MU TCGA-BG-A0VX TCGA-BG-A0W2 
       18.61        23.47        43.04        20.28        34.29        56.58 
TCGA-BG-A18C TCGA-BK-A13B TCGA-BS-A0T9 TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 
       15.45        31.76        46.95        61.87        96.49        30.74 
TCGA-BS-A0UT TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A15Z TCGA-D1-A16R TCGA-D1-A17M 
       72.72        86.99        16.83         1.91         0.69        10.22 
TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-DI-A0WH TCGA-DI-A1C3 TCGA-E6-A1M0 
       11.15        16.87         8.48        16.31        24.30        58.95 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EY-A1G8 
       61.74        61.55        46.26        57.60        50.73        14.99 
TCGA-EY-A1GD TCGA-EY-A1GL TCGA-EY-A1GR TCGA-EY-A2OO TCGA-EY-A548 TCGA-EY-A5W2 
       53.88        33.34        17.62        45.76        14.14        16.96 
TCGA-PG-A917 TCGA-QF-A5YT TCGA-SL-A6JA 
        6.97        39.95         0.23 

$subtype3
TCGA-A5-A0GM TCGA-AJ-A3BG TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-EY-A215 
       60.53        18.08        80.38        66.41        61.87        18.87 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GA 
       66.77        13.84       106.88       149.56        37.02        17.85 
TCGA-A5-A0GD TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
      112.54        74.10        46.55        28.27        54.02        23.21 
TCGA-A5-A0VO TCGA-A5-A1OF TCGA-AJ-A3EK TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0L8 
       28.77        31.99        14.66       129.80        48.03        48.79 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LQ TCGA-AP-A0LT 
      110.37        66.25        36.36        97.71        80.78        49.22 
TCGA-AP-A1DH TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       71.67        55.89        31.30        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 
       45.86        13.58        29.69        80.55        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A0J0 TCGA-AX-A0J1 
       45.99        79.46        49.87        57.47        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A2HD TCGA-AX-A3G9 
       13.28        32.91        34.09        85.48        46.49        18.35 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K3 TCGA-B5-A0K7 TCGA-B5-A0K9 
       59.24        86.01        71.44        27.29        63.55        13.45 
TCGA-B5-A11N TCGA-B5-A11Y TCGA-B5-A1MR TCGA-B5-A1MX TCGA-BG-A0LX TCGA-BG-A0M3 
       61.68        18.41       225.50        48.43        20.19        35.21 
TCGA-BG-A0M4 TCGA-BG-A0MG TCGA-BG-A0MQ TCGA-BG-A0RY TCGA-BG-A186 TCGA-BG-A222 
       71.24        48.56        59.74        15.42        13.78         9.57 
TCGA-BG-A2AE TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U8 
       23.70        24.33         4.80        77.95        67.99        97.41 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0WQ TCGA-D1-A103 TCGA-D1-A15X 
       85.84        73.25        59.51        66.48        21.99        29.88 
TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16Y 
        3.68        32.58        15.72        36.10        27.42        17.49 
TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A179 TCGA-DF-A2KU TCGA-DF-A2KZ TCGA-E6-A1LX 
        6.64        18.02        14.73       100.83        27.16        23.38 
TCGA-EO-A3AV TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EY-A1GI TCGA-EY-A1GU TCGA-EY-A3QX 
       35.15        46.42        38.47        23.34        32.78        32.52 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.70        68.38        39.88         7.99        25.22 

$subtype4
TCGA-AP-A0LS TCGA-B5-A0KB TCGA-D1-A0ZO TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A549 
       95.47        27.09        19.79        47.84        22.78        19.89 
TCGA-FI-A2F4 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GQ 
       73.32        83.51        32.78       105.37        65.75        73.87 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A1OJ TCGA-AJ-A2QK TCGA-AJ-A2QL 
       24.62        29.06        42.35        33.07        21.14        19.79 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT 
       18.90        33.90        17.06        15.95        22.32         2.70 
TCGA-AJ-A8CV TCGA-AP-A05O TCGA-AP-A0LJ TCGA-AP-A0LP TCGA-AP-A1DK TCGA-AP-A1DP 
       35.11        12.62        46.72        61.64        90.97        35.54 
TCGA-AX-A05T TCGA-AX-A05Y TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A1CJ 
       33.21        88.24        30.02        60.66        26.37        73.41 
TCGA-AX-A2H7 TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3GB TCGA-B5-A0JS 
       40.80        30.74         0.56        43.82        14.47        86.37 
TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A11G 
       55.30        58.75        36.49        72.62        57.76       113.36 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A3F9 TCGA-B5-A3FC 
       73.28        19.50        16.57        51.45       136.60        71.84 
TCGA-B5-A3FD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       39.35        19.33        20.94        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0MT TCGA-BG-A0VV TCGA-BG-A0VW 
       41.52        63.45        43.30        21.17        51.06        52.01 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.64        52.83        14.83        14.73        14.01        15.45 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BS-A0TC 
       35.90        34.98        24.99        13.18        10.03        85.55 
TCGA-BS-A0TD TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZR TCGA-D1-A0ZV 
       78.21        82.39        86.93        89.59         0.56        23.93 
TCGA-D1-A15W TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16B 
       30.08        29.33        37.64         0.66        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V 
       37.51        36.79         2.63        33.63        10.65         3.95 
TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
        3.65        30.15         1.58         7.00        30.44         1.28 
TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       26.37         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        18.02         2.07        15.06         1.05 
TCGA-DF-A2L0 TCGA-DI-A1BY TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 
       25.91        36.62        45.57        16.04        16.80        49.15 
TCGA-EO-A22Y TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GW TCGA-EY-A1GX 
       51.52        24.36        27.16        23.34        11.08        37.05 
TCGA-EY-A1H0 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       19.33        17.16        22.65        24.95        23.64        18.28 

$subtype5
TCGA-AJ-A3IA TCGA-D1-A3JP TCGA-EY-A1GQ TCGA-A5-A0GG TCGA-A5-A0R6 TCGA-A5-A0R8 
       20.81        16.93        17.88       123.68        37.91        19.59 
TCGA-A5-A2K7 TCGA-AJ-A3EL TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AP-A05P TCGA-AP-A0LM 
       34.95        22.49        21.21        15.35        20.91        27.12 
TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AX-A06H TCGA-AX-A0IZ TCGA-AX-A1CA TCGA-AX-A1CC 
       46.78        27.85        27.39        43.82        32.02        25.91 
TCGA-B5-A11L TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A2L7 TCGA-BK-A6W4 
       73.64        50.89        31.36        41.06        20.12         9.86 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZS 
      114.90        81.57        63.58        83.64         8.55         4.87 
TCGA-D1-A0ZU TCGA-D1-A101 TCGA-D1-A16J TCGA-D1-A174 TCGA-D1-A17C TCGA-D1-A17H 
       28.67         1.74        29.92        19.53         0.99        28.01 
TCGA-D1-A1O8 TCGA-DI-A1BU TCGA-DI-A2QU TCGA-E6-A2P8 TCGA-EC-A1QX TCGA-EO-A1Y5 
        3.95        39.29        31.10         2.37         7.36        10.92 
TCGA-EO-A22T TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-KP-A3W0 
       66.90        51.42        27.16        13.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.13     3.68     0.56     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  125.42   185.79   225.50   136.60   123.68 
subtype1 subtype2 subtype3 subtype4 subtype5 
  24.015   30.740   40.110   30.295   27.275 
[1] "0.1 - 125.4 (24.0)" "0.1 - 185.8 (30.7)" "3.7 - 225.5 (40.1)"
[4] "0.6 - 136.6 (30.3)" "1.0 - 123.7 (27.3)"
D9V2, binary
          cls
clus        0  1
  subtype1 82 66
  subtype2 49 28
  subtype3 54 53
  subtype4 82 54
  subtype5 20 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   66
  subtype2   49   28
  subtype3   54   53
  subtype4   82   54
  subtype5   20   25
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        82       49       54       82       20
  YES       66       28       53       54       25
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      69
  subtype2                                      79
  subtype3                                      93
  subtype4                                     134
  subtype5                                      32
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            11                                85
  subtype2                             2                                 0
  subtype3                             4                                10
  subtype4                             2                                 2
  subtype5                             3                                12
D9V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       69       79       93      134
  MIXED SEROUS AND ENDOMETRIOID                 11        2        4        2
  SEROUS ENDOMETRIAL ADENOCARCINOMA             85        0       10        2
                                         clus
vv                                        subtype5
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       32
  MIXED SEROUS AND ENDOMETRIOID                  3
  SEROUS ENDOMETRIAL ADENOCARCINOMA             12
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 101  10   8  15
  subtype2  58   2   1   5
  subtype3  73   5   5   7
  subtype4 101   2   0  10
  subtype5  36   3   1   3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      101       58       73      101       36
  R1       10        2        5        2        3
  R2        8        1        5        0        1
  RX       15        5        7       10        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 191  27
  subtype2 125  47
  subtype3 132  14
subtype1 subtype2 subtype3 
     218      172      146 
subtype1 subtype2 subtype3 
      27       47       14 
$subtype1
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-AB3J TCGA-AX-A06B TCGA-AX-A2H8 
       41.06        88.18        60.53        16.83        67.66        61.18 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A1GQ 
       66.41        61.87        51.55        12.56         4.44        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-KP-A3VZ 
       14.40        18.87        17.92         5.88        13.84        23.74 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GU 
        0.43        10.29        65.75        60.53        46.55        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0VQ TCGA-A5-A1OF 
       54.02        23.21        68.65        17.59        15.95        31.99 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QN 
       24.72        34.95        25.51        11.21        10.26        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3EJ TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OL 
       34.36         1.64        36.99        20.65        15.62        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A0L9 
       16.87        12.82         0.13       129.80        23.31       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      117.99       110.37        66.25        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       82.52        33.40        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       55.89        31.30        49.15         6.71        60.23        27.85 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Z 
       36.13         0.56        13.58        33.21        29.69        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A0IS TCGA-AX-A0IZ 
       35.34        45.99        49.87        27.39        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CI TCGA-AX-A1CK 
       40.11        77.39        13.28        32.91        85.48        80.25 
TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HH TCGA-AX-A3FS TCGA-AX-A3FZ 
       37.58        81.37        34.32        17.75         0.23         0.20 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JU TCGA-B5-A0JY 
        1.18        18.35        14.47        56.91        59.24        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11E 
       71.44        48.59        57.76        64.21        63.55        59.84 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11P TCGA-B5-A11U 
      185.79        88.34        73.64        61.68        52.04        16.73 
TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A3FA 
       19.56        19.59        17.36        14.70        48.43        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 
       93.50        71.84        41.06        18.61        20.19        35.21 
TCGA-BG-A0M7 TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0VX 
       63.68        23.47        43.04        59.74        20.28        34.29 
TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       56.58        13.78        15.45         9.57        20.02        20.12 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.00        31.76        16.64        10.03         9.86        46.95 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        61.87        67.99        30.74        97.41        92.88 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V7 
       82.39        81.57        72.72        73.25        59.51        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZU 
       83.64        86.99        66.48        16.83         8.55        28.67 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 
        1.74        21.99         1.91         3.68        32.58        15.72 
TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A177 
       36.10        31.07        10.65         0.69         3.95        18.02 
TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
        0.99        28.01        28.08        10.22         1.51        11.15 
TCGA-D1-A1NY TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-DF-A2KS TCGA-DF-A2KU 
       16.87         3.95         8.48        15.88       109.08       100.83 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU 
       27.16        25.91        16.31        24.30         9.37        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-EC-A1NJ TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U 
       23.38        58.95        16.04        61.74        61.55        46.26 
TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3KX TCGA-EY-A1G8 
       57.60        19.40        50.73        38.07        38.47        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GR TCGA-EY-A1GU 
       54.15        53.88        23.34        33.34        17.62        32.78 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 
       22.82        45.76        31.04        14.14        16.96        39.88 
TCGA-FI-A2D4 TCGA-PG-A6IB TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A744 
        7.99        21.30         6.97        22.65        39.95        14.83 
TCGA-SJ-A6ZI TCGA-SL-A6JA 
       20.75         0.23 

$subtype2
TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF 
       29.39        18.08        20.81        10.19       110.63        93.99 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       36.39        23.05        27.88         1.38        80.38        22.06 
TCGA-BG-A221 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 TCGA-FI-A2CX 
        1.81        16.93        33.30         6.21        10.19        66.77 
TCGA-KJ-A3U4 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 
       36.00        39.52       106.88       149.56        46.95        37.02 
TCGA-A5-A0GA TCGA-A5-A0GH TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       17.85        74.10        36.82        37.91        31.99        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
      118.19        66.15        28.64        14.96        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       14.43        34.16        18.12        14.66        22.49        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A059 TCGA-AP-A05P 
       21.21        15.35        16.87        20.78        48.03        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AP-A3K1 
       48.79        36.36        97.71        46.78        51.12        21.90 
TCGA-AX-A06F TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       57.47        35.74        37.78        34.65        25.51        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HD 
       25.91        76.83         4.77        30.12        71.24        46.49 
TCGA-AX-A2HG TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3G4 
       38.24         2.96        31.13        64.93         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0K9 
        0.26         0.30         0.39        27.29        27.85        13.45 
TCGA-B5-A11I TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       75.72       225.50       102.31        50.89        11.87        31.36 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A2AE TCGA-BG-A3EW 
       29.65        34.13        34.95        71.24        23.70        11.31 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0UF TCGA-D1-A0ZP 
       22.39        35.08        24.13         4.80        85.84        29.95 
TCGA-D1-A0ZS TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A16G TCGA-D1-A16I 
        4.87        22.55        39.48        29.88        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       29.92        18.67        17.49        14.73        13.22         0.72 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       48.79        58.95         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KY TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       71.61        10.92        39.29        35.38        12.39       110.10 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T 
       79.10         2.37         7.36        10.92        37.71        66.90 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       51.42        34.39        35.15        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       22.26        16.34        23.90        32.71        19.27        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ 
       22.03        16.11        15.81        12.59        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 
       27.35        32.52        11.38        14.70        68.38        77.33 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       25.22        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.28        41.56        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
       13.28         9.47        26.10        18.21        23.24        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       22.59         8.19         4.44         0.07 

$subtype3
TCGA-A5-A1OK TCGA-AP-A0LS TCGA-AX-A06D TCGA-B5-A0KB TCGA-D1-A0ZO TCGA-D1-A2G5 
       30.15        95.47        12.26        27.09        19.79        47.84 
TCGA-EY-A1GK TCGA-EY-A549 TCGA-FI-A2F4 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD 
       22.78        19.89        73.32        83.51        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
      105.37       123.68        73.87        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A1OJ TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BI 
       28.77        42.35        33.07        21.14        19.79        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT TCGA-AJ-A8CV 
       33.90        17.06        15.95        22.32         2.70        35.11 
TCGA-AP-A05O TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AX-A05W 
       12.62        61.64        80.78        35.54        45.86        80.55 
TCGA-AX-A05Y TCGA-AX-A063 TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A1CE 
       88.24        79.46        30.02        60.66        26.37        34.09 
TCGA-AX-A1CJ TCGA-AX-A2H7 TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       73.41        40.80        30.74         0.56        43.82        20.52 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.37        55.30        86.01        58.75        36.49        72.62 
TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
      113.36        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MZ 
       73.28        19.50        18.41        16.57        51.45        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M9 
      136.60        39.35        27.65        19.33        20.94        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0MT 
       10.72        41.52        48.56        63.45        43.30        21.17 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU 
       15.42        51.06        52.01        52.64        52.83        14.83 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C 
       14.73        14.01        15.45        35.90        34.98        24.99 
TCGA-BK-A56F TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0UA 
       13.18        24.33        85.55        78.21        96.49       114.90 
TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A15W TCGA-D1-A161 
       86.93        89.59         0.56        23.93        30.08        29.33 
TCGA-D1-A162 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       37.64         0.66        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16O TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        2.63        33.63         3.65        19.53         6.64        30.15 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17L TCGA-D1-A17Q 
        1.58         7.00        30.44         1.28        26.37         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        18.25        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-DF-A2KV TCGA-DI-A1BY TCGA-E6-A2P9 
        2.07        15.06         1.05        89.33        36.62        45.57 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE TCGA-EY-A1GF 
       16.80        49.15        51.52        51.09        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-PG-A916 TCGA-QS-A5YQ 
       23.34        11.08        37.05        19.33        17.16        24.95 
TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       23.64        18.28 

subtype1 subtype2 subtype3 
    0.13     0.07     0.56 
subtype1 subtype2 subtype3 
  185.79   225.50   136.60 
subtype1 subtype2 subtype3 
  31.530   27.225   30.590 
[1] "0.1 - 185.8 (31.5)" "0.1 - 225.5 (27.2)" "0.6 - 136.6 (30.6)"
D10V2, binary
          cls
clus         0   1
  subtype1 124  86
  subtype2  80  80
  subtype3  83  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  124   86
  subtype2   80   80
  subtype3   83   60
     clus
vv    subtype1 subtype2 subtype3
  NO       124       80       83
  YES       86       80       60
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                     207
  subtype2                                      57
  subtype3                                     143
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             6                                 6
  subtype2                            15                               101
  subtype3                             1                                 2
D10V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      207       57      143
  MIXED SEROUS AND ENDOMETRIOID                  6       15        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA              6      101        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        R0  R1  R2  RX
  subtype1 152   9   6  16
  subtype2 112  10   9  13
  subtype3 105   3   0  11
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      152      112      105
  R1        9       10        3
  R2        6        9        0
  RX       16       13       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 88 27
  subtype2 91 10
  subtype3 79 14
  subtype4 74 17
subtype1 subtype2 subtype3 subtype4 
     115      101       93       91 
subtype1 subtype2 subtype3 subtype4 
      27       10       14       17 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A2H8 TCGA-AX-A2HF 
       41.06        29.39        20.81        10.19        61.18        27.88 
TCGA-AX-A3G3 TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A547 
        1.38        12.56        33.30         6.21        10.19        17.92 
TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GB TCGA-A5-A2K4 
        5.88        36.00        23.74        39.52        32.78        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QO 
       24.72        34.95        14.96        18.41        20.25        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NG TCGA-AJ-A3OL 
       34.16        18.12         1.64        22.26        15.62        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CW TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A064 
       16.87        12.82         0.13        51.12         0.56        49.87 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HH 
        4.77        40.80        81.37        34.32        46.49        17.75 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G8 
        0.23         0.20         0.20        20.52         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A1MW 
       18.35         0.39        56.91        27.85       102.31        14.70 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD 
       96.30        93.50        71.84        39.35        29.65        34.13 
TCGA-B5-A5OE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       34.95        20.12        11.31        22.39        35.08        31.00 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A3DA 
       24.13        16.64        10.03        39.48        18.67        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2KY TCGA-DI-A1NO TCGA-DI-A2QT 
        4.27        18.84       109.08        10.92         9.37        12.39 
TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A22S TCGA-EO-A2CH TCGA-EO-A3AY TCGA-EO-A3B1 
      110.10        37.71        61.55        19.40        38.07        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1GO TCGA-EY-A2OM TCGA-EY-A2ON 
       22.26        16.34        38.47        19.27        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       45.76        31.04        27.35        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       96.69        28.93        41.56        78.38         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28         9.47        26.10        18.21        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A917 TCGA-QF-A5YS TCGA-SJ-A6ZI TCGA-SL-A6J9 
       22.59         8.19         6.97        22.65        20.75         0.07 
TCGA-SL-A6JA 
        0.23 

$subtype2
TCGA-AX-A1CP TCGA-B5-A0KB TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1GK 
       36.39        27.09        19.79         4.44        47.84        22.78 
TCGA-4E-A92E TCGA-AJ-A2QL TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        0.43        19.79        18.90        33.90        17.06        36.99 
TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A1DK TCGA-AP-A1DP 
       15.95        22.32         2.70        35.11        90.97        35.54 
TCGA-AP-A1E1 TCGA-AP-A5FX TCGA-AX-A06L TCGA-AX-A1C4 TCGA-AX-A1C9 TCGA-AX-A1CJ 
       45.86        36.13        60.66        13.28        26.37        73.41 
TCGA-AX-A1CK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A11G TCGA-B5-A11M 
       80.25         0.56        43.82        55.30       113.36        44.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Z 
       52.04        32.09        77.23        73.28        19.50        17.36 
TCGA-B5-A121 TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FH TCGA-BG-A0MA TCGA-BG-A0MK 
       16.57        52.54       136.60        27.65        10.72        43.30 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       51.06        52.01        34.29        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BS-A0T9 
       15.45        34.98        31.76        24.99        13.18        46.95 
TCGA-BS-A0V6 TCGA-D1-A15W TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A165 TCGA-D1-A169 
       89.59        30.08        29.33        37.64         0.66        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16N TCGA-D1-A16O 
       36.36        37.51        36.79         2.63        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17B 
       10.65         0.69         3.95         3.65        30.15         7.00 
TCGA-D1-A17D TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       30.44        26.37         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       22.92        18.25        18.02         2.07        15.06         1.05 
TCGA-DF-A2L0 TCGA-DI-A1BY TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EO-A1Y7 
       25.91        36.62        58.95        45.57        16.04        49.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GR TCGA-EY-A1GW 
       24.36        27.16        23.34        23.34        17.62        11.08 
TCGA-EY-A1H0 TCGA-PG-A916 TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       19.33        17.16        24.95        23.64        18.28 

$subtype3
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-D1-A3JP TCGA-EY-A1GQ TCGA-5S-A9Q8 TCGA-A5-A0GG 
       30.15        16.83        16.93        17.88        10.29       123.68 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A3LO TCGA-AJ-A23N 
       60.53        36.82        36.33        33.07        25.51        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3EL TCGA-AJ-A3NE TCGA-AJ-A3NF 
       10.26        21.14        35.15        22.49        20.65        21.21 
TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A05O TCGA-AP-A0LM TCGA-AP-A1DQ 
       15.35        16.87        20.78        12.62        27.12        46.78 
TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AX-A06H TCGA-AX-A0IZ TCGA-AX-A1C8 TCGA-AX-A1CC 
       60.23        27.85        27.39        43.82        25.51        25.91 
TCGA-AX-A1CN TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3G4 
       37.58        30.74         2.96        31.13        64.93         0.30 
TCGA-AX-A3GB TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A1MV TCGA-B5-A1MY 
       14.47        73.64        85.78        16.73        51.45        11.87 
TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A0MH TCGA-BK-A6W4 TCGA-BS-A0UA TCGA-BS-A0V7 
       31.36        41.06        63.45         9.86       114.90        63.58 
TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A168 TCGA-D1-A174 
       83.64        16.83         8.55         4.87        36.10        19.53 
TCGA-D1-A175 TCGA-D1-A17A TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A1NW TCGA-D1-A1NY 
        6.64         1.58         0.99        28.01         0.72        16.87 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        58.95        17.29         2.20        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A2P8 TCGA-EC-A24G TCGA-EO-A22R 
       39.29        24.30        31.10         2.37        16.80        61.74 
TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        57.60        51.52        51.42        34.39        50.73 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3L0 TCGA-EY-A1GD TCGA-EY-A1GM TCGA-EY-A1GP 
       27.16        46.42        51.09        53.88        32.71        18.84 
TCGA-EY-A1GT TCGA-EY-A210 TCGA-EY-A2OQ TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-PG-A5BC 
       16.11        12.59        29.10        30.67        59.28        23.24 
TCGA-QF-A5YT TCGA-QS-A744 TCGA-QS-A8F1 
       39.95        14.83         4.44 

$subtype4
TCGA-AJ-A3BG TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A1CR TCGA-BG-A221 TCGA-EY-A214 
       18.08        93.99        95.47        23.05         1.81        14.40 
TCGA-EY-A215 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-A5-A0G1 TCGA-A5-A0GQ 
       18.87        66.77        13.84        73.32       106.88        73.87 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A7WJ TCGA-AJ-A3EK 
       31.99        31.99       118.19        66.15        11.21        14.66 
TCGA-AP-A059 TCGA-AP-A1DH TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1DV 
       48.03        71.67        55.89        31.30        49.15         6.71 
TCGA-AP-A3K1 TCGA-AX-A1C5 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       21.90        32.91        32.02        34.09        76.83        85.48 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HG TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A11H 
       30.12        71.24        38.24        59.24        58.75        88.34 
TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MX TCGA-BG-A18C 
       54.44        61.68       225.50        50.89        48.43        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BS-A0V4 TCGA-BS-A0VI TCGA-D1-A15X 
        9.57        20.02        23.70        59.51        86.99        29.88 
TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
        3.68        32.58        15.72        27.42        11.51        29.92 
TCGA-D1-A16Y TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17M 
       17.49        18.02        14.73         1.28        28.08        10.22 
TCGA-D1-A17R TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-DF-A2KR 
       11.15         1.41        13.22         3.95        48.79        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DI-A1NN TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-EC-A1QX 
      100.83        89.33        35.38        23.38        79.10         7.36 
TCGA-EO-A1Y5 TCGA-EO-A22U TCGA-EO-A3AV TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ 
       10.92        46.26        35.15        14.99        54.15        23.90 
TCGA-EY-A1GL TCGA-EY-A1GS TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A3QX TCGA-EY-A4KR 
       33.34        22.03        32.78        15.81        32.52        11.38 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX 
       14.70        16.96        68.38        39.88        59.01         9.34 
TCGA-JU-AAVI 
       17.75 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.43     0.30     1.28 
subtype1 subtype2 subtype3 subtype4 
  110.10   136.60   123.68   225.50 
subtype1 subtype2 subtype3 subtype4 
   22.26    25.91    27.16    31.99 
[1] "0.1 - 110.1 (22.3)" "0.4 - 136.6 (25.9)" "0.3 - 123.7 (27.2)"
[4] "1.3 - 225.5 (32.0)"
D11V2, binary
          cls
clus        0  1
  subtype1 53 48
  subtype2 59 40
  subtype3 43 46
  subtype4 45 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   48
  subtype2   59   40
  subtype3   43   46
  subtype4   45   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        53       59       43       45
  YES       48       40       46       44
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      59
  subtype2                                      96
  subtype3                                      69
  subtype4                                      63
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             6                                51
  subtype2                             2                                 3
  subtype3                             6                                18
  subtype4                             6                                23
D11V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       59       96       69       63
  MIXED SEROUS AND ENDOMETRIOID                  6        2        6        6
  SEROUS ENDOMETRIAL ADENOCARCINOMA             51        3       18       23
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 72  5  4  9
  subtype2 65  4  1 13
  subtype3 70  4  2  4
  subtype4 61  4  5  8
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       72       65       70       61
  R1        5        4        4        4
  R2        4        1        2        5
  RX        9       13        4        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 128  33
  subtype2 121  15
  subtype3  83  20
subtype1 subtype2 subtype3 
     161      136      103 
subtype1 subtype2 subtype3 
      33       15       20 
$subtype1
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AP-A0LS 
       41.06        29.39        18.08        10.19        93.99        95.47 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-BG-A0YV TCGA-BG-A221 TCGA-E6-A8L9 
       23.05        61.18         1.38        12.56         1.81        33.30 
TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A72D TCGA-FI-A2CX 
        6.21        10.19        14.40        18.87         5.88        66.77 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0GB 
       73.32        36.00        23.74        39.52       106.88        32.78 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        31.99       118.19        66.15        28.64        24.72 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.96        11.21        18.41        20.25        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CW 
       18.12         1.64        14.76        16.87        12.82         0.13 
TCGA-AP-A059 TCGA-AP-A1DH TCGA-AP-A1DO TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A3K1 
       48.03        71.67        31.30         6.71        45.86        21.90 
TCGA-AW-A1PO TCGA-AX-A1C5 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A2H2 
        0.56        32.91        32.02        76.83        80.25         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        71.24        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G8 
       17.75         0.23         0.20         0.20         0.26         1.18 
TCGA-AX-A3GI TCGA-B5-A0JU TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11Q TCGA-B5-A1MR 
        0.39        59.24       113.36        88.34        32.09       225.50 
TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
      102.31        14.70        48.43        96.30        93.50        71.84 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       29.65        34.13        34.95        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       23.70        20.12        11.31        35.08        31.00        16.64 
TCGA-BK-A6W3 TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A167 TCGA-D1-A16I TCGA-D1-A16N 
       10.03        39.48        29.88        15.72        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K 
       18.67         3.95        17.49        30.15        14.73        28.08 
TCGA-D1-A17L TCGA-D1-A17Q TCGA-D1-A1NU TCGA-D1-A2G0 TCGA-D1-A3DA TCGA-D1-A3DG 
       26.37         1.78        13.22        48.79        15.88         4.27 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       71.61       100.83        10.92        35.38         9.37        12.39 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22U TCGA-EO-A2CH 
       79.10        58.95        10.92        37.71        46.26        19.40 
TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GC 
       35.15        26.96        16.34        38.47        14.99        54.15 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GU 
       23.34        23.90        19.27        17.62        22.03        32.78 
TCGA-EY-A1GV TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       15.81        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       11.38        68.38        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       59.01         9.34        28.93        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       14.04         9.47        26.10        21.30        22.59         8.19 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
        6.97        22.65        20.75         0.07         0.23 

$subtype2
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-B5-A0KB TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       30.15        16.83        27.09        19.79         4.44        47.84 
TCGA-EY-A1GK TCGA-EY-A547 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0GG TCGA-A5-A0GQ 
       22.78        17.92         0.43        10.29       123.68        73.87 
TCGA-A5-A1OJ TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3BK 
       33.07        21.14        19.79        35.15        18.90        33.90 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NG TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT 
       17.06        36.99        15.62        15.95        22.32         2.70 
TCGA-AJ-A8CV TCGA-AP-A05O TCGA-AP-A1DK TCGA-AP-A1DP TCGA-AP-A1E0 TCGA-AP-A1E3 
       35.11        12.62        90.97        35.54        60.23        27.85 
TCGA-AP-A5FX TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A1C4 TCGA-AX-A1C9 TCGA-AX-A1CE 
       36.13        27.39        60.66        13.28        26.37        34.09 
TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX 
       73.41        37.58        40.80        30.74         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3GB TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A11J TCGA-B5-A11L 
       20.52        14.47        55.30        58.75        54.44        73.64 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W 
       44.78        85.78        52.04        77.23        73.28        19.50 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FD 
       17.36        16.57        51.45        52.54       136.60        39.35 
TCGA-B5-A3FH TCGA-BG-A0MA TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW 
       27.65        10.72        63.45        43.30        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0CA 
       34.29        13.78        14.73        14.01        15.45        34.98 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BS-A0T9 TCGA-BS-A0UA TCGA-BS-A0V6 
       31.76        24.99        13.18        46.95       114.90        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A15W TCGA-D1-A161 TCGA-D1-A162 
       63.58        83.64        16.83        30.08        29.33        37.64 
TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
        0.66        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A17A 
       33.63        10.65         0.69         3.65        19.53         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17N TCGA-D1-A17S 
        7.00         0.99        30.44         1.28         1.51        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 
        2.33        22.92         1.41        18.25        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KV 
       15.06         1.05         3.95         2.20       109.08        89.33 
TCGA-DF-A2L0 TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A2P9 TCGA-EC-A1NJ 
       25.91        36.62        24.30        31.10        45.57        16.04 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE 
       16.80        49.15        66.90        51.52        51.09        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-FI-A2F8 
       27.16        23.34        33.34        11.08        19.33        30.67 
TCGA-PG-A916 TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       17.16        24.95        23.64        18.28 

$subtype3
TCGA-AJ-A3IA TCGA-AX-A1CP TCGA-AX-A2HF TCGA-D1-A3JP TCGA-EY-A1GQ TCGA-FI-A2D5 
       20.81        36.39        27.88        16.93        17.88        13.84 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N 
       60.53        36.82        36.33        34.95        25.51        14.43 
TCGA-AJ-A23O TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NE TCGA-AJ-A3NF 
       10.26        14.66        22.49        22.26        20.65        21.21 
TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A0LM TCGA-AP-A1DM TCGA-AP-A1DQ 
       15.35        16.87        20.78        27.12        55.89        46.78 
TCGA-AP-A1DR TCGA-AP-A1E4 TCGA-AX-A064 TCGA-AX-A0IZ TCGA-AX-A1C8 TCGA-AX-A1CC 
       49.15        51.12        49.87        43.82        25.51        25.91 
TCGA-AX-A1CI TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G9 
       85.48         2.96        31.13        64.93         0.30        18.35 
TCGA-B5-A0JR TCGA-B5-A0K8 TCGA-B5-A11N TCGA-B5-A11U TCGA-B5-A1MU TCGA-B5-A1MY 
       56.91        27.85        61.68        16.73        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A6W4 TCGA-BS-A0V4 
       31.36        41.06        22.39        24.13         9.86        59.51 
TCGA-BS-A0VI TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A168 
       86.99         8.55         4.87         3.68        32.58        36.10 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17H TCGA-D1-A17M 
       27.42        29.92         6.64        18.02        28.01        10.22 
TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH 
       11.15         0.72        16.87         8.48        58.95        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A2QY TCGA-E6-A1LX 
       17.29        27.16        16.31        39.29       110.10        23.38 
TCGA-E6-A2P8 TCGA-EC-A1QX TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22X TCGA-EO-A2CG 
        2.37         7.36        61.74        61.55        57.60        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       34.39        50.73        38.07        27.16        46.42        22.26 
TCGA-EY-A1GD TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A210 TCGA-EY-A2OQ 
       53.88        32.71        18.84        16.11        12.59        29.10 
TCGA-EY-A3QX TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2F9 TCGA-FI-A3PV 
       32.52        14.70        16.96        39.88        59.28        41.56 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QF-A5YT TCGA-QS-A744 
       13.28        18.21        23.24        38.70        39.95        14.83 
TCGA-QS-A8F1 
        4.44 

subtype1 subtype2 subtype3 
    0.07     0.43     0.30 
subtype1 subtype2 subtype3 
   225.5    136.6    110.1 
subtype1 subtype2 subtype3 
  23.740   27.275   25.910 
[1] "0.1 - 225.5 (23.7)" "0.4 - 136.6 (27.3)" "0.3 - 110.1 (25.9)"
D12V2, binary
          cls
clus        0  1
  subtype1 80 67
  subtype2 70 61
  subtype3 50 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80   67
  subtype2   70   61
  subtype3   50   50
     clus
vv    subtype1 subtype2 subtype3
  NO        80       70       50
  YES       67       61       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      92
  subtype2                                     130
  subtype3                                      65
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            11                                60
  subtype2                             3                                 3
  subtype3                             6                                32
D12V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       92      130       65
  MIXED SEROUS AND ENDOMETRIOID                 11        3        6
  SEROUS ENDOMETRIAL ADENOCARCINOMA             60        3       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"
          vv
clus        R0  R1  R2  RX
  subtype1 103   8   9  12
  subtype2  89   5   1  17
  subtype3  76   4   2   5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      103       89       76
  R1        8        5        4
  R2        9        1        2
  RX       12       17        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
