[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/15094079/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/15120652/UCEC-TP.mergedcluster.txt"

nPatients in clinical file=537, in cluster file=547, common to both=536
[1]  12 536
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
14 18 12 10 
 1  2  3  4 
14 18 12 10 
[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   5 
164 299  19   9  37 
  1   2   3   4   5 
164 299  19   9  37 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
162  87 171 
  1   2   3 
162  87 171 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6 
42 39 40 12 41 26 
 1  2  3  4  5  6 
42 39 40 12 41 26 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
70 67 44 19 
 1  2  3  4 
70 67 44 19 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
230 151 153 
  1   2   3 
230 151 153 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
122  51  46  63 107  68  77 
  1   2   3   4   5   6   7 
122  51  46  63 107  68  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
218 148 161 
  1   2   3 
218 148 161 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
214  56 142 115 
  1   2   3   4 
214  56 142 115 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
165  92 134 
  1   2   3 
165  92 134 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
140 114 137 
  1   2   3 
140 114 137 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 536 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=429,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "535"       "1"           
freq.contrast "1"         "535"         
both >= 3     "FALSE"     "FALSE"       
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'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 8:'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 9:'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 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=35,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 536 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "HISTOLOGICAL_TYPE"                     
[3] "RADIATIONS_RADIATION_REGIMENINDICATION"
[4] "COMPLETENESS_OF_RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 12  2
  subtype2 14  4
  subtype3 11  1
  subtype4  8  2
subtype1 subtype2 subtype3 subtype4 
      14       18       12       10 
subtype1 subtype2 subtype3 subtype4 
       2        4        1        2 
$subtype1
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A0LT 
      149.56        37.02        17.85        32.78        83.67        49.22 
TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       13.58        46.45        35.34        66.58        34.98        51.09 
TCGA-B5-A0JR TCGA-B5-A0JZ 
       56.91        28.64 

$subtype2
TCGA-A5-A0G3 TCGA-A5-A0GH TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       46.95        74.10        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
       63.91        57.80        45.53        36.89        48.79       125.42 
TCGA-AP-A0LD TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-B5-A0K4 TCGA-BK-A0CC 
      117.99        53.92        37.78        65.88        17.88        10.22 

$subtype3
TCGA-A5-A0GE TCGA-A5-A0GP TCGA-AP-A05P TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AX-A05T 
      105.37        46.55        20.91        36.36        31.73        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A06J TCGA-B5-A0K1 TCGA-BK-A0C9 
       29.69        68.35        72.03        30.02        30.51        35.90 

$subtype4
TCGA-A5-A0GM TCGA-A5-A0GU TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LN TCGA-AP-A0LV 
       60.53        28.27        23.87        63.16        82.52        25.08 
TCGA-AX-A062 TCGA-B5-A0K0 TCGA-BG-A0LW TCGA-BG-A0MI 
       45.99        28.34        18.61        23.47 

subtype1 subtype2 subtype3 subtype4 
   13.58     5.95    19.82    18.61 
subtype1 subtype2 subtype3 subtype4 
  149.56   125.42   105.37    82.52 
subtype1 subtype2 subtype3 subtype4 
  41.735   47.870   33.815   28.305 
[1] "13.6 - 149.6 (41.7)" "6.0 - 125.4 (47.9)"  "19.8 - 105.4 (33.8)"
[4] "18.6 - 82.5 (28.3)" 
D1V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      12
  subtype2                                       8
  subtype3                                      11
  subtype4                                      10
          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       12        8       11       10
  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"
D1V4, binary
          cls
clus        0  1
  subtype1  8  6
  subtype2 12  6
  subtype3  3  9
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2   12    6
  subtype3    3    9
  subtype4    2    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8       12        3        2
  YES        6        6        9        8
[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       R0 R1 R2 RX
  subtype1  8  2  1  0
  subtype2 14  1  1  1
  subtype3 10  1  0  0
  subtype4  9  0  0  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        8       14       10        9
  R1        2        1        1        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         1
  subtype2                                0     0                         4
  subtype3                                1     3                         0
  subtype4                                0     0                         1
          vv
clus       WHITE
  subtype1    10
  subtype2    13
  subtype3     8
  subtype4     9
D1V6, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   1        0        3        0
  BLACK OR AFRICAN AMERICAN               1        4        0        1
  WHITE                                  10       13        8        9
[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"
D1V7, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 1 6
  subtype3 0 9
  subtype4 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    1    6
  subtype3    0    9
  subtype4    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        0        0
  NOT HISPANIC OR LATINO        6        6        9        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 13  1
  subtype2  7  3
  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        3        3        0        2 
$subtype1
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GH TCGA-A5-A0GM TCGA-AP-A054 TCGA-AP-A056 
      149.56        37.02        74.10        60.53        23.31        86.07 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AX-A05Y TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A0J1 
       20.91       117.99        72.03        53.92        51.09        65.88 
TCGA-B5-A0K4 TCGA-BK-A0CC 
       17.88        10.22 

$subtype2
TCGA-A5-A0G3 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       46.95        21.99         5.95        63.91        57.80        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        68.35        46.45 
TCGA-AX-A064 
       34.98 

$subtype4
TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A0LT TCGA-AX-A060 TCGA-AX-A063 TCGA-B5-A0JR 
       32.78        83.67        49.22        35.34        66.58        56.91 
TCGA-B5-A0JZ 
       28.64 

$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        63.16        31.73        82.52 
TCGA-AP-A0LV TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06J TCGA-B5-A0K0 
       25.08        19.82        29.69        45.99        30.02        28.34 
TCGA-B5-A0K1 TCGA-BG-A0LW TCGA-BG-A0MI TCGA-BK-A0C9 
       30.51        18.61        23.47        35.90 

subtype1 subtype2 subtype3 subtype4 subtype5 
   10.22     5.95    13.58    28.64    18.61 
subtype1 subtype2 subtype3 subtype4 subtype5 
  149.56   125.42    68.35    83.67   105.37 
subtype1 subtype2 subtype3 subtype4 subtype5 
  57.225   46.240   36.360   49.220   29.855 
[1] "10.2 - 149.6 (57.2)" "6.0 - 125.4 (46.2)"  "13.6 - 68.3 (36.4)" 
[4] "28.6 - 83.7 (49.2)"  "18.6 - 105.4 (29.9)"
D2V2, continuous
          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"
D2V4, binary
          cls
clus        0  1
  subtype1  7  7
  subtype2  7  3
  subtype3  2  5
  subtype4  5  2
  subtype5  4 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    7
  subtype2    7    3
  subtype3    2    5
  subtype4    5    2
  subtype5    4   12
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7        7        2        5        4
  YES        7        3        5        2       12
[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       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 13  1  0  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       11        9        4        4       13
  R1        1        0        1        1        1
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         2
  subtype2                                0     0                         3
  subtype3                                0     1                         0
  subtype4                                1     0                         0
  subtype5                                1     1                         1
          vv
clus       WHITE
  subtype1     9
  subtype2     7
  subtype3     5
  subtype4     6
  subtype5    13
D2V6, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        1
  ASIAN                                   2        0        1        0        1
  BLACK OR AFRICAN AMERICAN               2        3        0        0        1
  WHITE                                   9        7        5        6       13
[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"
D2V7, binary
          cls
clus       0 1
  subtype1 1 9
  subtype2 0 2
  subtype3 1 5
  subtype4 0 2
  subtype5 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    0    2
  subtype3    1    5
  subtype4    0    2
  subtype5    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        1        0        0
  NOT HISPANIC OR LATINO        9        2        5        2        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 126  37
  subtype2 276  22
  subtype3  16   3
  subtype4   9   0
  subtype5  30   7
subtype1 subtype2 subtype3 subtype4 subtype5 
     163      298       19        9       37 
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       22        3        0        7 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        36.69        37.02        65.75        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       14.43         0.39        29.39        34.16         1.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS 
        1.64        22.26        20.81        21.21        10.19        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
       16.87        20.78        21.99         5.95        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
       45.53        36.89        48.79       125.42         3.39        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU 
       46.78        21.90        36.13         0.56        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP 
       37.78        16.96        13.55        20.28        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF 
       11.08         4.77        30.12        71.24        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
        2.96        64.93         0.56        43.82        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        0.30         0.26         0.30         0.39        80.38        27.29 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       17.85         4.11        75.72       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
       12.79        33.11        29.65        34.13        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       36.49        12.56         6.81        10.22        10.16        24.13 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G 
       67.20        49.55        29.95        22.55        39.48        27.42 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       11.51        31.07        18.67        14.73        28.08        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH 
        0.72        18.25         2.07        44.88         4.27         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       16.93        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       48.36        27.32        10.92        49.15        37.71        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       19.40        34.39        27.16        26.96        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV 
        4.54        23.90         6.90        17.62        15.09        15.81 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ 
       11.08        12.59        10.19        14.40        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D 
       27.35        13.84        11.38        17.92        14.70         5.88 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       41.06        39.95        96.69        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       18.21        23.24        23.97        12.92         7.00         4.44 
TCGA-SL-A6J9 
        0.07 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       10.29       106.88        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP 
      105.37        87.32        74.10        57.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       38.37        28.27        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BG 
        5.33         5.16        10.26        19.79        34.36         0.76 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       14.66        22.49        36.99        20.65        15.35        15.95 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
       22.32        12.82         2.70        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
        8.22        23.87        12.20        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       60.36        55.89        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       10.42        27.85        16.24        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       31.13         0.23         0.20         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.64        28.34        30.51        25.91        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       43.96        40.50        16.73        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       191.84        14.40        14.70        11.70        15.29 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       96.30        78.81        62.14        14.27        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.19        35.21        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU 
       48.56        23.47        43.30        43.04        39.32        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 
       13.78        14.73        14.01        15.45        14.27         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.02        20.12        11.31        34.98         6.21        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.99        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0V4 
       97.41        88.34        85.84        82.39        81.57        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        0.56         4.87        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 
       29.88         1.91         3.68        29.33        32.58        15.72 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.01        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        2.33        22.92         1.41        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DA TCGA-DF-A2KV TCGA-DF-A2KY 
        1.05         3.95         3.52         0.26        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX 
       27.16        16.31        39.29        36.62        24.30        23.38 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37         6.67        16.04         7.36        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EO-A3AV 
       61.55        66.90        46.26        57.60        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       17.19        17.88        14.53        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GT 
       27.16        23.34        23.34        22.78        13.97        16.11 
TCGA-EY-A1GU TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A548 
       12.43        19.33        18.87        22.82        31.04        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 
       16.96        40.01        39.88        13.84         8.98        28.96 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.07        18.28         0.23 

$subtype3
TCGA-A5-A0G2 TCGA-A5-A0GV TCGA-A5-A2K3 TCGA-AJ-A2QN TCGA-AX-A05W TCGA-AX-A3FZ 
      149.56        20.81        46.32         2.40        68.35         0.20 
TCGA-B5-A0JT TCGA-B5-A11P TCGA-B5-A3F9 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A18C 
       43.13        36.82       116.25        30.81        24.39        15.45 
TCGA-BG-A2AE TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT TCGA-D1-A169 TCGA-D1-A16V 
       23.70         4.80        61.87        72.72        37.32         3.95 
TCGA-EY-A1G7 
        6.21 

$subtype4
TCGA-A5-A0GN TCGA-AP-A1DO TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-D1-A0ZQ 
       60.53        31.30        21.17        15.42        52.83         8.55 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A2OO 
       19.27        18.84        45.76 

$subtype5
TCGA-A5-A0R7 TCGA-A5-A3LO TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3NG TCGA-AJ-A3OL 
       17.59         7.33         1.68        17.06        15.62        14.76 
TCGA-AJ-A8CW TCGA-AP-A0LO TCGA-AX-A2H7 TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11Q 
        0.13        33.40        40.80        17.88         8.71        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       33.50        27.35        19.56        19.33        20.94        34.98 
TCGA-BG-A221 TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0UV TCGA-D1-A0ZU TCGA-D1-A102 
        1.81        35.90        16.64        73.25        28.67         4.44 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-E6-A1M0 
        0.66        36.10        11.15        41.42         8.48        17.06 
TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GQ TCGA-EY-A1GX TCGA-EY-A549 TCGA-FI-A2D4 
       51.52        24.89        17.88         6.48        19.89         7.99 
TCGA-QS-A744 
       14.83 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.20     0.20     8.55     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
  125.42   191.84   149.56    60.53    73.25 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.210   24.805   30.810   21.170   17.880 
[1] "0.1 - 125.4 (21.2)" "0.2 - 191.8 (24.8)" "0.2 - 149.6 (30.8)"
[4] "8.6 - 60.5 (21.2)"  "0.1 - 73.2 (17.9)" 
D3V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      48
  subtype2                                     286
  subtype3                                      17
  subtype4                                       8
  subtype5                                      36
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            11                               105
  subtype2                             8                                 5
  subtype3                             0                                 2
  subtype4                             1                                 0
  subtype5                             1                                 0
D3V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       48      286       17        8
  MIXED SEROUS AND ENDOMETRIOID                 11        8        0        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA            105        5        2        0
                                         clus
vv                                        subtype5
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       36
  MIXED SEROUS AND ENDOMETRIOID                  1
  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"
D3V4, binary
          cls
clus         0   1
  subtype1  32 132
  subtype2  95 204
  subtype3   2  17
  subtype4   3   6
  subtype5   9  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  132
  subtype2   95  204
  subtype3    2   17
  subtype4    3    6
  subtype5    9   28
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        32       95        2        3        9
  YES      132      204       17        6       28
[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        R0  R1  R2  RX
  subtype1 103   9  10  14
  subtype2 211  14   5  19
  subtype3  12   0   1   1
  subtype4   9   0   0   0
  subtype5  28   0   1   1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      103      211       12        9       28
  R1        9       14        0        0        0
  R2       10        5        1        0        1
  RX       14       19        1        0        1
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        50
  subtype2                                3    15                        43
  subtype3                                0     3                         1
  subtype4                                0     0                         1
  subtype5                                0     0                         6
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         3    95
  subtype2                                         5   219
  subtype3                                         0    15
  subtype4                                         0     8
  subtype5                                         1    29
D3V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 1        3        0        0
  ASIAN                                            2       15        3        0
  BLACK OR AFRICAN AMERICAN                       50       43        1        1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        3        5        0        0
  WHITE                                           95      219       15        8
                                           clus
vv                                          subtype5
  AMERICAN INDIAN OR ALASKA NATIVE                 0
  ASIAN                                            0
  BLACK OR AFRICAN AMERICAN                        6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           29
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1   6 112
  subtype2   8 201
  subtype3   0  15
  subtype4   0   9
  subtype5   0  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  112
  subtype2    8  201
  subtype3    0   15
  subtype4    0    9
  subtype5    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            6        8        0        0        0
  NOT HISPANIC OR LATINO      112      201       15        9       30
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 132  28
  subtype2  78   9
  subtype3 154  17
subtype1 subtype2 subtype3 
     160       87      171 
subtype1 subtype2 subtype3 
      28        9       17 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0GR TCGA-A5-A1OF TCGA-A5-A1OG 
       41.06        36.69       106.88        36.82         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M 
       36.33        91.04        46.32        28.64        14.96         1.18 
TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA 
       29.39         1.12         1.64        22.49        22.26        20.81 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A3TW 
       20.65        21.21        10.19        15.35        16.87        16.87 
TCGA-AP-A059 TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A1DK TCGA-AP-A1E4 TCGA-AP-A3K1 
        8.22         3.39        27.12        60.36        16.24        21.90 
TCGA-AP-A5FX TCGA-AX-A06D TCGA-AX-A0IZ TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       36.13        12.26        43.82        19.20        16.96        13.55 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 
       20.28        12.43        76.83        25.12        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       30.12        71.24        61.18        19.36        26.33        17.75 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 
        2.96        31.13         0.20         0.20         1.38         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        0.30         1.18         0.39        17.85         4.11        75.72 
TCGA-B5-A11X TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FA 
       19.59       191.84        50.89        11.87        12.79        96.30 
TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0YV 
       78.81        29.65        41.06        34.13        34.95        12.56 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A139 
       15.45        14.27         1.81        23.70        10.22        10.16 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZZ 
       24.13        67.20        49.55        29.95         4.87        22.55 
TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       39.48        29.88        36.10        27.42        11.51        29.92 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       18.67        14.73        28.08        13.22         0.72        18.25 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KY 
        3.95         3.52         4.27         4.11        16.93        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        48.36         2.37 
TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22X 
       27.32         7.36        10.92        37.71        66.90        57.60 
TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        27.16        26.96        22.26        16.34         6.21 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
        4.54        23.90         6.90        19.27        18.84        15.09 
TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ 
       15.81        10.19        14.40        20.05        45.76        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2CY 
       27.35        13.84        11.38        14.70        40.01        41.06 
TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       39.95         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A6IB 
        2.43        23.74        13.28         9.47        26.10        15.45 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       12.92         7.00         4.44         0.07 

$subtype2
TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A3LO TCGA-AJ-A23N 
       87.32        38.37         9.60         8.02         7.33        14.43 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3OK TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        0.39        34.16        15.95        12.82        20.78         2.70 
TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A1CJ 
       46.78        27.85         0.56        60.66        15.25        54.12 
TCGA-AX-A1CP TCGA-AX-A2H7 TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-B5-A11M TCGA-B5-A11O 
       36.39        40.80        64.93         0.30        44.78        40.50 
TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11Y TCGA-B5-A121 
       36.82        33.50        27.35        16.73        18.41        16.57 
TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0VV TCGA-BG-A0VX 
      102.31       116.25        33.11        14.27        26.66        34.29 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A3PP 
       52.83        56.58        14.83        13.78        14.01         6.81 
TCGA-BK-A56F TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0UL TCGA-BS-A0V7 TCGA-D1-A0ZR 
       13.18         9.86        46.95        81.57        63.58         0.56 
TCGA-D1-A0ZV TCGA-D1-A15W TCGA-D1-A162 TCGA-D1-A165 TCGA-D1-A16B TCGA-D1-A16D 
       23.93        30.08        37.64         0.66        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       36.79        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17S TCGA-D1-A1O5 
        7.00         0.99        26.37         1.51        24.30        15.06 
TCGA-D1-A2G7 TCGA-DF-A2KV TCGA-DI-A0WH TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU 
       44.88        89.33        16.31        36.62        24.30        31.10 
TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3L0 TCGA-EY-A1GR 
      110.10        51.42        19.40        34.39        24.89        17.62 
TCGA-EY-A210 TCGA-FI-A2D0 TCGA-FI-A2F9 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
       12.59        39.88        29.23        18.21        23.24        23.97 
TCGA-QF-A5YS TCGA-QS-A5YQ TCGA-SJ-A6ZJ 
       18.84        12.92        18.28 

$subtype3
TCGA-5S-A9Q8 TCGA-A5-A0VO TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL 
       10.29        11.97         5.33         5.16        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
        2.40        34.36         0.76        18.90         1.68        14.66 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A8CW 
       17.06        36.99        15.62        14.76        22.32         0.13 
TCGA-AP-A05O TCGA-AP-A0LS TCGA-AP-A1DH TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       12.20        63.06        71.67        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AX-A06H TCGA-AX-A0IS 
       49.15         6.71        30.90        10.42        27.39        35.01 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2HA 
       40.11        13.28        20.05        72.56        67.50        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HJ TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX 
       34.32        46.49        30.74         0.23         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JX 
       20.52        18.35        14.47        43.13        48.76        44.71 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A1MV 
       43.96        32.09        19.56        19.50        17.36        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-BG-A0MA TCGA-BG-A0MH 
       14.70        11.70        15.29        62.14        10.72        63.45 
TCGA-BG-A0MK TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A187 TCGA-BG-A18B 
       43.30        24.39        16.34        52.64        14.73        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B 
        9.57        20.02        20.12        11.31        34.98        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0V4 
       24.99        16.64        10.03        96.49        88.34        59.51 
TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       62.79        63.16        66.48        16.83        19.79         8.55 
TCGA-D1-A0ZU TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15Z TCGA-D1-A160 
       28.67         1.74         4.44        21.99         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16F TCGA-D1-A16N 
       29.33        32.58        15.72        37.32         2.63        31.07 
TCGA-D1-A16V TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.95        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R 
       30.44         1.28        28.01        10.22         1.78        11.15 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        2.33        22.92         1.41        16.87        18.02         2.07 
TCGA-D1-A1O7 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-E6-A1LX 
        1.05        41.42         8.48         0.26        27.16        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
       17.06         6.67        16.04        16.80        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B0 
       61.55        46.26        51.52        26.43        17.19        17.88 
TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.53        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        22.78        13.97        17.88        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       11.08         6.48        19.33        18.87        22.82        31.04 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2D4 
       17.92        14.14        19.89        16.96         5.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YT TCGA-QS-A5YR 
       13.84        28.96        11.24         6.97        39.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SL-A6JA 
       14.83        14.07         0.23 

subtype1 subtype2 subtype3 
    0.07     0.30     0.13 
subtype1 subtype2 subtype3 
  191.84   116.25   185.79 
subtype1 subtype2 subtype3 
  18.755   24.300   18.900 
[1] "0.1 - 191.8 (18.8)" "0.3 - 116.2 (24.3)" "0.1 - 185.8 (18.9)"
D4V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      66
  subtype2                                      69
  subtype3                                     168
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            15                                81
  subtype2                             2                                16
  subtype3                             3                                 0
D4V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       66       69      168
  MIXED SEROUS AND ENDOMETRIOID                 15        2        3
  SEROUS ENDOMETRIAL ADENOCARCINOMA             81       16        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"
D4V4, binary
          cls
clus         0   1
  subtype1  37 125
  subtype2  13  74
  subtype3  40 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37  125
  subtype2   13   74
  subtype3   40  131
     clus
vv    subtype1 subtype2 subtype3
  NO        37       13       40
  YES      125       74      131
[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        R0  R1  R2  RX
  subtype1 102  10   8  12
  subtype2  54   3   4  12
  subtype3 121   6   1  10
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      102       54      121
  R1       10        3        6
  R2        8        4        1
  RX       12       12       10
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        42
  subtype2                                0     2                        20
  subtype3                                1     4                        31
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         3   101
  subtype2                                         4    57
  subtype3                                         0   128
D4V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        1
  ASIAN                                            2        2        4
  BLACK OR AFRICAN AMERICAN                       42       20       31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        3        4        0
  WHITE                                          101       57      128
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1   6 114
  subtype2   1  64
  subtype3   4 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  114
  subtype2    1   64
  subtype3    4  126
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        1        4
  NOT HISPANIC OR LATINO      114       64      126
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 38  4
  subtype2 33  6
  subtype3 39  1
  subtype4  8  4
  subtype5 39  2
  subtype6 23  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      42       39       40       12       41       26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        6        1        4        2        3 
$subtype1
TCGA-A5-A0G1 TCGA-A5-A0GE TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0R8 TCGA-A5-A0RA 
      106.88       105.37        38.37        36.82        19.59        29.06 
TCGA-A5-A0VP TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LM 
       42.35         8.22        36.89         3.39        97.71        27.12 
TCGA-AX-A05Z TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06L TCGA-B5-A0K2 TCGA-B5-A0K4 
       46.45        34.98        12.26        60.66        25.91        17.88 
TCGA-B5-A11I TCGA-B5-A11U TCGA-B5-A11Y TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0MG 
       75.72        16.73        18.41        19.33        20.94        48.56 
TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0T9 TCGA-BS-A0U9 TCGA-D1-A0ZR 
       34.98        10.22        10.16        46.95        67.20         0.56 
TCGA-D1-A101 TCGA-D1-A15X TCGA-D1-A163 TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
        1.74        29.88        32.58        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16X TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17N 
       27.42        29.92         3.65         7.00        30.44         1.51 

$subtype2
TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GH TCGA-A5-A0GV TCGA-A5-A0GW 
      149.56        46.95        37.02        74.10        20.81        23.21 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       19.96        17.59        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LT TCGA-AX-A06B 
       63.91        57.80       117.99       110.37        49.22        53.92 
TCGA-AX-A06F TCGA-AX-A0J0 TCGA-B5-A0JN TCGA-B5-A0JY TCGA-B5-A0K3 TCGA-B5-A11E 
       51.09        40.11        80.38        32.55        27.29         8.71 
TCGA-B5-A11H TCGA-B5-A11X TCGA-BG-A0RY TCGA-BG-A0YV TCGA-BG-A18C TCGA-BS-A0TA 
       88.34        19.59        15.42        12.56        15.45        23.47 
TCGA-BS-A0TJ TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A177 
       67.99        15.72        36.10        31.07        18.67        18.02 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R 
       14.73        28.08        11.15 

$subtype3
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-AX-A05W TCGA-AX-A063 
       83.51        32.78        65.75        60.53        68.35        66.58 
TCGA-AX-A06J TCGA-AX-A0J1 TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A11F TCGA-B5-A11N 
       30.02        65.88        28.64        30.51       185.79        43.96 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11W TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M9 
       32.09        27.35        19.50        20.19        38.37        28.27 
TCGA-BG-A0MC TCGA-BG-A0MH TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0W1 TCGA-BG-A0YU 
       41.52        63.45        30.81        21.17        52.83        14.83 
TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0U7 
       13.78        14.01        15.45         6.21        24.99        30.74 
TCGA-BS-A0U8 TCGA-D1-A0ZZ TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A16O TCGA-D1-A175 
       97.41        22.55        30.08         3.68        33.63         6.64 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17Q 
       28.01        26.37        10.22         1.78 

$subtype4
TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GG TCGA-AP-A0LP TCGA-AX-A05S TCGA-AX-A05Y 
       17.85       112.54        87.32        61.64        13.58        72.03 
TCGA-AX-A060 TCGA-BG-A0M4 TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-D1-A16V 
       35.34        34.98        35.90        85.55        85.84         3.95 

$subtype5
TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0R9 TCGA-A5-A0VQ TCGA-AP-A051 
       57.53        60.53        28.27        24.62        15.95        83.67 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
       23.87        12.20        20.91        63.16        31.73        83.97 
TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A0IS 
       82.52        25.08        19.82        29.69        45.99        35.01 
TCGA-B5-A0K0 TCGA-B5-A0K7 TCGA-B5-A11G TCGA-B5-A11V TCGA-B5-A11Z TCGA-B5-A121 
       28.34        17.10       113.36        19.56        17.36        16.57 
TCGA-BG-A0M3 TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BS-A0TI TCGA-BS-A0UJ 
       35.21        20.28        24.39        26.66        61.87        82.39 
TCGA-BS-A0V7 TCGA-D1-A15Z TCGA-D1-A165 TCGA-D1-A16B TCGA-D1-A16Q TCGA-D1-A16Y 
       63.58         1.91         0.66        36.36        10.65        17.49 
TCGA-D1-A176 TCGA-D1-A17C TCGA-D1-A17S TCGA-D1-A17T TCGA-DI-A0WH 
       30.15         0.99        24.30         2.33        16.31 

$subtype6
TCGA-A5-A0GX TCGA-A5-A0VO TCGA-AP-A05H TCGA-AP-A0LH TCGA-AX-A0IW TCGA-AX-A0IZ 
       68.65        11.97        45.53        36.36        37.78        43.82 
TCGA-B5-A0JT TCGA-B5-A0K9 TCGA-BG-A0LW TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A187 
       43.13        11.01        18.61        22.06        36.49        14.73 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A103 
       78.21        77.95        29.95        28.67         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16R 
       39.48        29.33        37.64        37.32        11.51         0.69 
TCGA-D1-A17F TCGA-D1-A17U 
        1.28        22.92 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.56     5.95     1.78     3.95     0.66     0.69 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  106.88   149.56   185.79   112.54   113.36    78.21 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   29.47    28.08    30.05    48.77    25.08    29.64 
[1] "0.6 - 106.9 (29.5)" "6.0 - 149.6 (28.1)" "1.8 - 185.8 (30.0)"
[4] "4.0 - 112.5 (48.8)" "0.7 - 113.4 (25.1)" "0.7 - 78.2 (29.6)" 
D5V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      35
  subtype2                                      28
  subtype3                                      39
  subtype4                                      12
  subtype5                                      41
  subtype6                                      19
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             1                                 6
  subtype2                             0                                11
  subtype3                             1                                 0
  subtype4                             0                                 0
  subtype5                             0                                 0
  subtype6                             1                                 6
D5V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       35       28       39       12
  MIXED SEROUS AND ENDOMETRIOID                  1        0        1        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA              6       11        0        0
                                         clus
vv                                        subtype5 subtype6
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       41       19
  MIXED SEROUS AND ENDOMETRIOID                  0        1
  SEROUS ENDOMETRIAL ADENOCARCINOMA              0        6
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus        0  1
  subtype1 20 22
  subtype2 19 20
  subtype3 13 27
  subtype4  4  8
  subtype5 13 28
  subtype6 11 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   22
  subtype2   19   20
  subtype3   13   27
  subtype4    4    8
  subtype5   13   28
  subtype6   11   15
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        20       19       13        4       13       11
  YES       22       20       27        8       28       15
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 24  3  3  6
  subtype2 29  1  1  2
  subtype3 26  0  0  5
  subtype4 10  1  1  0
  subtype5 32  2  0  1
  subtype6 22  0  0  2
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       24       29       26       10       32       22
  R1        3        1        0        1        2        0
  R2        3        1        0        1        0        0
  RX        6        2        5        0        1        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         6
  subtype2                                0     3                         6
  subtype3                                0     0                         2
  subtype4                                1     2                         1
  subtype5                                1     2                         3
  subtype6                                0     1                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         2    30
  subtype2                                         1    28
  subtype3                                         0    38
  subtype4                                         0     8
  subtype5                                         1    33
  subtype6                                         0    25
D5V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        0        1
  ASIAN                                            1        3        0        2
  BLACK OR AFRICAN AMERICAN                        6        6        2        1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        2        1        0        0
  WHITE                                           30       28       38        8
                                           clus
vv                                          subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0
  ASIAN                                            2        1
  BLACK OR AFRICAN AMERICAN                        3        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0
  WHITE                                           33       25
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  2 29
  subtype2  2 21
  subtype3  0 30
  subtype4  0 10
  subtype5  1 23
  subtype6  0 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   29
  subtype2    2   21
  subtype3    0   30
  subtype4    0   10
  subtype5    1   23
  subtype6    0   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        2        0        0        1        0
  NOT HISPANIC OR LATINO       29       21       30       10       23       22
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 59 11
  subtype2 63  4
  subtype3 40  4
  subtype4 18  1
subtype1 subtype2 subtype3 subtype4 
      70       67       44       19 
subtype1 subtype2 subtype3 subtype4 
      11        4        4        1 
$subtype1
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GH 
      106.88       149.56        46.95        37.02       105.37        74.10 
TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0VP TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       38.37        19.59        42.35        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LI 
       86.07        63.91        36.89       117.99         3.39        97.71 
TCGA-AP-A0LT TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       49.22        13.58        19.82        34.98        12.26        51.09 
TCGA-AX-A06L TCGA-AX-A0J0 TCGA-B5-A0JN TCGA-B5-A0JY TCGA-B5-A0K3 TCGA-B5-A0K7 
       60.66        40.11        80.38        32.55        27.29        17.10 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11X TCGA-B5-A11Y TCGA-BG-A0M0 TCGA-BG-A0M6 
       88.34        75.72        19.59        18.41        19.33        22.06 
TCGA-BG-A0MG TCGA-BG-A0YV TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0T9 
       48.56        12.56        34.98        10.22        10.16        46.95 
TCGA-BS-A0TA TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A0ZR TCGA-D1-A0ZZ TCGA-D1-A101 
       23.47        67.20        63.58         0.56        22.55         1.74 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16D 
       30.08        29.88        32.58        15.72        36.10        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16Q TCGA-D1-A16S 
       36.79         2.63        27.42        29.92        10.65        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17B 
        3.65        17.49        30.15        18.02        14.73         7.00 
TCGA-D1-A17C TCGA-D1-A17N TCGA-D1-A17S TCGA-D1-A17T 
        0.99         1.51        24.30         2.33 

$subtype2
TCGA-A5-A0G9 TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       83.51        65.75        60.53        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       23.21        19.96        17.59        24.62        29.06        15.95 
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       83.67         8.22        57.80        23.87        12.20        20.91 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05U TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A06B 
       82.52        25.08        29.69        46.45        45.99        53.92 
TCGA-AX-A06J TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11G 
       30.02        28.34        25.91        17.88         8.71       113.36 
TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       43.96        32.09        27.35        16.73        19.56        19.50 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M8 
       17.36        16.57        18.61        20.19        20.94        36.49 
TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A187 
       21.17        15.42        24.39        52.83        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18C TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0UJ TCGA-D1-A15Z 
       14.01        15.45         6.21        24.99        82.39         1.91 
TCGA-D1-A165 TCGA-D1-A16B TCGA-D1-A17D TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17R 
        0.66        36.36        30.44        28.08        26.37        11.15 
TCGA-DI-A0WH 
       16.31 

$subtype3
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN 
       17.85        32.78       112.54        87.32        57.53        60.53 
TCGA-AP-A0LP TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A0IS 
       61.64        68.35        72.03        35.34        66.58        35.01 
TCGA-AX-A0J1 TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A11F TCGA-BG-A0M3 TCGA-BG-A0M4 
       65.88        28.64        30.51       185.79        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MH TCGA-BG-A0MS TCGA-BG-A0MU 
       38.37        28.27        41.52        63.45        30.81        20.28 
TCGA-BG-A186 TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0TI TCGA-BS-A0TJ 
       13.78        15.45        35.90        85.55        61.87        67.99 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A169 
       30.74        97.41        85.84         4.44         3.68        37.32 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16V TCGA-D1-A175 TCGA-D1-A17H TCGA-D1-A17M 
       31.07        33.63         3.95         6.64        28.01        10.22 
TCGA-D1-A17Q TCGA-D1-A17U 
        1.78        22.92 

$subtype4
TCGA-A5-A0GX TCGA-A5-A0VO TCGA-AP-A05H TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-B5-A0JT 
       68.65        11.97        45.53        37.78        43.82        43.13 
TCGA-B5-A0K9 TCGA-BG-A0VV TCGA-BS-A0TD TCGA-BS-A0TG TCGA-D1-A0ZP TCGA-D1-A0ZU 
       11.01        26.66        78.21        77.95        29.95        28.67 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A16I TCGA-D1-A16R 
       21.99        39.48        29.33        37.64        11.51         0.69 
TCGA-D1-A17F 
        1.28 

subtype1 subtype2 subtype3 subtype4 
    0.56     0.66     1.78     0.69 
subtype1 subtype2 subtype3 subtype4 
  149.56   113.36   185.79    78.21 
subtype1 subtype2 subtype3 subtype4 
   28.65    25.08    35.11    29.95 
[1] "0.6 - 149.6 (28.6)" "0.7 - 113.4 (25.1)" "1.8 - 185.8 (35.1)"
[4] "0.7 - 78.2 (29.9)" 
D6V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      52
  subtype2                                      64
  subtype3                                      44
  subtype4                                      14
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             2                                16
  subtype2                             1                                 2
  subtype3                             0                                 0
  subtype4                             0                                 5
D6V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       52       64       44       14
  MIXED SEROUS AND ENDOMETRIOID                  2        1        0        0
  SEROUS ENDOMETRIAL ADENOCARCINOMA             16        2        0        5
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 29 41
  subtype2 26 41
  subtype3 17 27
  subtype4  8 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   41
  subtype2   26   41
  subtype3   17   27
  subtype4    8   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        29       26       17        8
  YES       41       41       27       11
[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       R0 R1 R2 RX
  subtype1 43  4  5  9
  subtype2 50  1  0  3
  subtype3 34  2  0  3
  subtype4 16  0  0  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       43       50       34       16
  R1        4        1        2        0
  R2        5        0        0        0
  RX        9        3        3        1
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         9
  subtype2                                1     3                         7
  subtype3                                1     3                         2
  subtype4                                0     1                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         4    54
  subtype2                                         0    52
  subtype3                                         0    38
  subtype4                                         0    18
D6V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        1        0
  ASIAN                                            2        3        3        1
  BLACK OR AFRICAN AMERICAN                        9        7        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        4        0        0        0
  WHITE                                           54       52       38       18
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1  3 46
  subtype2  2 37
  subtype3  0 37
  subtype4  0 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   46
  subtype2    2   37
  subtype3    0   37
  subtype4    0   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        0        0
  NOT HISPANIC OR LATINO       46       37       37       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 183  45
  subtype2 139  12
  subtype3 141  12
subtype1 subtype2 subtype3 
     228      151      153 
subtype1 subtype2 subtype3 
      45       12       12 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 
       41.06        36.69       106.88       149.56        46.95        37.02 
TCGA-A5-A0GH TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       74.10        36.82        19.96        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         5.16        14.96         1.18        14.43 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EL TCGA-AJ-A3EM 
       29.39        34.16         1.12         1.64        22.49        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OL 
       20.81        21.21        15.62        10.19        15.35        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       16.87        16.87        20.78        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       125.42       117.99         3.39        36.36        97.71 
TCGA-AP-A0LM TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO 
       27.12        60.36        46.78        16.24        21.90         0.56 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       53.92        12.26        51.09        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CP 
       16.96        13.55        20.28        12.43        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD 
       11.08         4.77        30.12        71.24        61.18        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.23         0.20         0.20         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K4 
        0.30         1.18         0.39        80.38        27.29        17.88 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11U TCGA-B5-A1MR TCGA-B5-A1MS 
       17.85         8.71        75.72        16.73       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3S1 
       50.89        14.70        11.87        12.79        96.30        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0MT TCGA-BG-A0YV TCGA-BG-A18C 
       34.13        34.95        22.06        21.17        12.56        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
        6.81        10.22        10.16        24.13        16.64         4.80 
TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZS 
       67.20        73.25        63.58        49.55        29.95         4.87 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16G 
       22.55        39.48        29.88        15.72        36.10        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A179 
       11.51        29.92        31.07        18.67        17.49        14.73 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A1O8 
       28.08        13.22         0.72        18.25         2.07         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.52         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KY TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A1NO 
       16.93        10.92        16.31        39.29        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A8L9 
       12.39        31.10       110.10        48.36         2.37        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       10.92        37.71        66.90        57.60        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        35.15        17.19        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       16.34         6.21         4.54         6.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 
       17.62        15.09        16.11        15.81        12.59        10.19 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX 
       13.84        11.38        17.92        14.70         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88        39.95        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.07        28.93        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       45.01         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.97        12.92         7.00        14.83         4.44         0.07 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
       10.29        17.85        32.78        57.53        60.53        60.53 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0VP 
       28.27        20.81        23.21        68.65        17.59        42.35 
TCGA-A5-A0VQ TCGA-A5-A2K5 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A3BG TCGA-AJ-A3EK 
       15.95         5.33         7.33        10.26         0.76        14.66 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A5DW TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A05N 
       36.99        20.65        12.82         0.13        83.67        23.87 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A1DH 
      110.37        63.16        83.97        63.06        49.22        71.67 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       55.89        31.30        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       27.85        13.58        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J1 TCGA-AX-A1C4 
       34.98        27.39        35.01        43.82        65.88        13.28 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A3G9 
       72.56        67.50        25.12        81.37        34.32        18.35 
TCGA-B5-A0JR TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11N 
       13.74        17.10        11.01       185.79        45.90        43.96 
TCGA-B5-A11Q TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MX TCGA-B5-A1MZ 
       32.09        19.56        19.59        17.36        11.70        15.29 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M8 
       62.14        41.06        18.61        20.19        35.21        36.49 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        39.32        30.81        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VX TCGA-BG-A186 TCGA-BG-A3EW TCGA-BK-A0CB TCGA-BK-A13B 
       24.39        34.29        13.78        11.31         6.21        31.76 
TCGA-BK-A6W3 TCGA-BS-A0T9 TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 
       10.03        46.95        77.95        61.87        67.99        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 
       97.41        85.84        82.39        81.57        72.72        59.51 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A101 
       63.16        66.48        16.83         8.55        28.67         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A16B 
        4.44        21.99         1.91         3.68        32.58        36.36 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A177 
       10.65         0.69         3.95        19.53         6.64        18.02 
TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NY 
        0.99        28.01        26.37        10.22        11.15        16.87 
TCGA-DF-A2KZ TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-EC-A1QX 
       27.16        36.62        24.30        23.38        17.06         7.36 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A3AU TCGA-EO-A3B0 TCGA-EO-A3KX 
       61.74        61.55        46.26        26.43        17.88        14.53 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GU 
       14.99        53.88        23.34        13.97        17.88        12.43 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A5W2 TCGA-FI-A2D4 TCGA-PG-A917 TCGA-QF-A5YT 
       14.40        18.87        16.96         7.99         6.97        39.95 
TCGA-SL-A6JA 
        0.23 

$subtype3
TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GP 
       83.51       112.54       105.37        87.32        65.75        46.55 
TCGA-A5-A0GQ TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A1OF 
       38.37        19.59        24.62        29.06        11.97         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        9.60         8.02         0.39        19.79         2.40        34.36 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT 
       18.90         1.68        17.06        15.95        22.32         2.70 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       12.20        20.91        31.73        82.52        33.40        61.64 
TCGA-AP-A0LV TCGA-AP-A1DP TCGA-AP-A5FX TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        35.54        36.13        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE 
       72.03        30.02        60.66        19.20        15.25        20.05 
TCGA-AX-A1CJ TCGA-AX-A2H7 TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       54.12        40.80        30.74         0.56        43.82        20.52 
TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 
       14.47        46.75        43.13        44.71        30.51        25.91 
TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
        4.11       113.36        88.34        54.44        44.78        40.50 
TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 
       36.82        33.50        27.35        19.50        18.41        16.57 
TCGA-B5-A1MV TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 
       14.40       116.25        78.81        33.11        14.27        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.94        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ 
       48.56        63.45        43.30        26.66        16.34        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.83        56.58        14.83        14.73        14.01        15.45 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W4 TCGA-BS-A0TA 
       35.90        34.98        24.99        13.18         9.86        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0V6 
       85.55        78.21        96.49        88.34        86.93        62.79 
TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A15W TCGA-D1-A161 TCGA-D1-A162 
       19.79         0.56        23.93        30.08        29.33        37.64 
TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16O 
        0.66        37.32        37.51        36.79         2.63        33.63 
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-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A2G5 TCGA-DF-A2KV TCGA-E6-A2P9 
       18.02        15.06         1.05        41.42        89.33         6.67 
TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE 
       16.04        16.80        49.15        51.52        24.89        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GK TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       27.16        23.34        22.78        11.08         6.48        19.33 
TCGA-EY-A548 TCGA-EY-A549 TCGA-FI-A2F4 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QS-A5YQ 
       14.14        19.89        28.96        11.24        18.84        12.92 
TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       23.64        14.07        18.28 

subtype1 subtype2 subtype3 
    0.07     0.13     0.39 
subtype1 subtype2 subtype3 
  191.84   185.79   116.25 
subtype1 subtype2 subtype3 
  20.085   27.160   24.890 
[1] "0.1 - 191.8 (20.1)" "0.1 - 185.8 (27.2)" "0.4 - 116.2 (24.9)"
D7V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                     102
  subtype2                                     150
  subtype3                                     148
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            16                               112
  subtype2                             1                                 0
  subtype3                             4                                 1
D7V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      102      150      148
  MIXED SEROUS AND ENDOMETRIOID                 16        1        4
  SEROUS ENDOMETRIAL ADENOCARCINOMA            112        0        1
[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"
D7V4, binary
          cls
clus         0   1
  subtype1  54 176
  subtype2  55  96
  subtype3  32 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54  176
  subtype2   55   96
  subtype3   32  121
     clus
vv    subtype1 subtype2 subtype3
  NO        54       55       32
  YES      176       96      121
[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        R0  R1  R2  RX
  subtype1 150  14  11  16
  subtype2 109   6   4   6
  subtype3 107   3   2  13
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      150      109      107
  R1       14        6        3
  R2       11        4        2
  RX       16        6       13
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                        54
  subtype2                                2     7                        20
  subtype3                                1     8                        28
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         6   146
  subtype2                                         2   114
  subtype3                                         1   111
D7V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        2        1
  ASIAN                                            5        7        8
  BLACK OR AFRICAN AMERICAN                       54       20       28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        6        2        1
  WHITE                                          146      114      111
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1   6 163
  subtype2   4  99
  subtype3   4 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  163
  subtype2    4   99
  subtype3    4  108
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        4        4
  NOT HISPANIC OR LATINO      163       99      108
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 96 26
  subtype2 47  4
  subtype3 36  9
  subtype4 61  2
  subtype5 89 17
  subtype6 60  8
  subtype7 74  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     122       51       45       63      106       68       77 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      26        4        9        2       17        8        3 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G3 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       41.06        36.69        46.95        19.96        11.44        36.33 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD 
       28.64        14.96         1.18        14.43        29.39        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
        1.12         1.64        22.26        20.81        21.21        10.19 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
       16.87        16.87        21.99         5.95        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53        36.89        20.91        48.79       125.42       117.99 
TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       46.78        16.24         0.56        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       13.55        20.28        12.43        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G3 
       71.24        61.18        19.36         2.96        64.93         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        0.30         0.26         0.30         0.39        80.38        27.29 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       17.85        75.72       102.31        50.89        11.87        12.79 
TCGA-B5-A3FA TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A221 
       96.30        29.65        34.13        22.06        12.56         1.81 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
        6.81        10.22        24.13        29.95        22.55        39.48 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       11.51        18.67        17.49        14.73        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       18.25        44.88         4.11        35.38         9.37       110.10 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.32        10.92        37.71        51.42        19.40        34.39 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A210 
       26.96        22.26        16.34         6.90        19.27        12.59 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       10.19        29.10        27.35        11.38        14.70        41.06 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       39.95        96.69        25.02        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 
        1.74        14.04         2.43        23.74        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QF-A5YS 
       18.21        23.24        23.97        12.92         7.00        18.84 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       10.29        57.53        60.53        28.27        20.81        68.65 
TCGA-A5-A0VQ TCGA-AJ-A3NC TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LV 
       15.95        36.99        63.16        83.97        82.52        25.08 
TCGA-AX-A05T TCGA-AX-A0IS TCGA-AX-A1CI TCGA-AX-A1CK TCGA-B5-A0JU TCGA-B5-A0K6 
       19.82        35.01        72.56        67.50        48.76        13.74 
TCGA-B5-A0K7 TCGA-B5-A11F TCGA-B5-A11V TCGA-B5-A11Z TCGA-BG-A0LW TCGA-BG-A0M3 
       17.10       185.79        19.56        17.36        18.61        35.21 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VX 
       23.47        43.04        30.81        20.28        24.39        34.29 
TCGA-BG-A186 TCGA-BK-A0CB TCGA-BK-A13B TCGA-BS-A0UJ TCGA-BS-A0VI TCGA-BS-A0WQ 
       13.78         6.21        31.76        82.39        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A15Z TCGA-D1-A16B TCGA-D1-A16Q 
       16.83        28.67         4.44         1.91        36.36        10.65 
TCGA-D1-A16R TCGA-D1-A17C TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17T 
        0.69         0.99        10.22         1.51        11.15         2.33 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-QF-A5YT 
       14.99        53.88        39.95 

$subtype3
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GH TCGA-A5-A0GR TCGA-A5-A1OF 
      106.88       149.56        37.02        74.10        36.82         7.92 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-AJ-A3OJ TCGA-AJ-A6NU TCGA-AP-A059 TCGA-AP-A0LF 
       91.04        46.32        15.35        20.78         8.22         3.39 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A2H4 TCGA-AX-A2HG TCGA-AX-A3FT 
       36.36        97.71        21.90        30.12        26.33         0.20 
TCGA-B5-A1MR TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TI 
      191.84        34.95        34.98        23.47         4.80        61.87 
TCGA-D1-A15X TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A2G0 TCGA-D1-A3JP TCGA-DI-A2QT 
       29.88        27.42        29.92         3.52        16.93        12.39 
TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A22T TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       48.36         7.36        66.90        35.15        17.19        27.16 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A2ON TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX 
       15.09        15.81        20.05        40.01        59.01         9.07 
TCGA-FI-A2EY TCGA-JU-AAVI TCGA-KP-A3W1 
       28.93         7.76         9.47 

$subtype4
TCGA-A5-A2K5 TCGA-AJ-A23O TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A8CW TCGA-AP-A051 
        5.33        10.26         0.76        14.66         0.13        83.67 
TCGA-AP-A0LE TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DV 
      110.37        27.12        49.22        55.89        31.30         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       30.90        10.42        27.85        46.45        35.34        66.58 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A2HA 
       34.98        51.09        27.39        65.88        13.28        81.37 
TCGA-B5-A0JR TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K9 TCGA-B5-A11N TCGA-B5-A11Q 
       56.91        40.67        28.64        11.01        43.96        32.09 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0M8 TCGA-BG-A0MQ 
       11.70        15.29        41.06        20.19        36.49        39.32 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UL TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-BS-A0V8 
       30.74        97.41        81.57        59.51        63.58        49.55 
TCGA-D1-A0ZQ TCGA-D1-A103 TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A174 TCGA-D1-A175 
        8.55        21.99         3.68        32.58        19.53         6.64 
TCGA-D1-A177 TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17Q TCGA-DI-A1BU TCGA-E6-A1LX 
       18.02        28.01        26.37         1.78        39.29        23.38 
TCGA-EO-A22R TCGA-EO-A3B0 TCGA-EY-A1GI TCGA-EY-A1GQ TCGA-EY-A1GU TCGA-EY-A215 
       61.74        17.88        23.34        17.88        12.43        18.87 
TCGA-EY-A5W2 TCGA-FI-A2F4 TCGA-SL-A6JA 
       16.96        28.96         0.23 

$subtype5
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A2K7 
       17.85        32.78        23.21        17.59        42.35         5.16 
TCGA-A5-A3LO TCGA-AJ-A3EL TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A5DW 
        7.33        22.49        20.65        15.62        14.76        12.82 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05N TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DR 
       23.31        86.07        23.87        71.67        60.36        49.15 
TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C5 
       45.99        53.92        12.26        43.82        40.11        19.20 
TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HH 
       76.83        25.12        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        32.55 
TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11X 
       28.34        17.88         8.71        36.82        16.73        19.59 
TCGA-B5-A1MW TCGA-B5-A3FC TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A18C TCGA-BG-A220 
       14.70        62.14        21.17        15.42        15.45        14.27 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A4ZD 
        9.57        20.02        23.70        20.12        11.31        16.64 
TCGA-BS-A0T9 TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UT 
       46.95        77.95        67.99        67.20        85.84        72.72 
TCGA-BS-A0UV TCGA-D1-A0ZS TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N 
       73.25         4.87        15.72        36.10        37.32        31.07 
TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A1O8 TCGA-D1-A2G6 
        3.95        28.08        16.87         2.07         3.95         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A2QU 
        0.26         4.27        10.92        27.16        16.31        31.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU 
       17.06         2.37        61.55        46.26        57.60        26.43 
TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GR 
       14.53         6.21         4.54        13.97        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       16.11        11.08        14.40        22.82        45.76        31.04 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       13.84        17.92         5.88        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-PG-A6IB TCGA-PG-A917 TCGA-QS-A744 
        8.98        15.45         6.97        14.83 

$subtype6
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A1OJ 
       65.75        60.53        46.55        24.62        11.97         9.60 
TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 
        0.39         2.40        34.36        18.90         1.68        17.06 
TCGA-AP-A0LJ TCGA-AP-A0LO TCGA-AP-A0LS TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05U 
       31.73        33.40        63.06        36.13        13.58        29.69 
TCGA-AX-A05Y TCGA-AX-A06L TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A2HJ TCGA-AX-A3FX 
       72.03        60.66        20.05        54.12        30.74        43.82 
TCGA-AX-A3G1 TCGA-AX-A3GB TCGA-B5-A0JT TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11H 
       20.52        14.47        43.13         4.11       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11S TCGA-B5-A11Y TCGA-B5-A1MV TCGA-B5-A3F9 
       54.44        45.90        27.35        18.41        14.40       116.25 
TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0MA 
       78.81        33.11        14.27        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        10.16 
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-DI-A1BY 
       37.51         2.63         1.58        24.30        15.06        36.62 
TCGA-DI-A1C3 TCGA-EC-A1NJ TCGA-EO-A1Y7 TCGA-EO-A3L0 TCGA-EY-A548 TCGA-QS-A5YQ 
       24.30        16.04        49.15        24.89        14.14        12.92 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       14.07        18.28 

$subtype7
TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0R8 
       83.51       112.54       105.37        87.32        38.37        19.59 
TCGA-A5-A0RA TCGA-A5-A1OK TCGA-AJ-A2QL TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT 
       29.06         8.02        19.79        15.95        22.32         2.70 
TCGA-AP-A05O TCGA-AP-A0LP TCGA-AP-A1DP TCGA-AX-A05W TCGA-AX-A06J TCGA-AX-A1C9 
       12.20        61.64        35.54        68.35        30.02        15.25 
TCGA-AX-A3FW TCGA-B5-A0JS TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A11M 
        0.56        46.75        44.71        30.51        25.91        44.78 
TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11W TCGA-B5-A121 TCGA-BG-A0M7 TCGA-BG-A0M9 
       40.50        33.50        19.50        16.57        38.37        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0YU 
       41.52        48.56        43.30        26.66        16.34        14.83 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BS-A0TC 
       14.01        15.45        35.90        34.98        24.99        85.55 
TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZO 
       78.21        96.49        88.34        86.93        62.79        19.79 
TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A16E TCGA-D1-A16O 
        0.56        23.93        29.33        37.64        36.79        33.63 
TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17U 
        3.65        30.15         7.00        30.44         1.28        22.92 
TCGA-D1-A1NS TCGA-D1-A1NZ TCGA-D1-A1O7 TCGA-D1-A2G5 TCGA-DF-A2KV TCGA-E6-A2P9 
        1.41        18.02         1.05        41.42        89.33         6.67 
TCGA-EC-A24G TCGA-EO-A22Y TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GK 
       16.80        51.52        24.36        27.16        23.34        22.78 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A549 TCGA-PG-A916 TCGA-QS-A5YR 
        6.48        19.33        19.89        11.24        23.64 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.69     0.20     0.13     0.20     0.39     0.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  125.42   185.79   191.84   110.37    86.07   116.25   112.54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  20.545   25.080   27.420   28.010   18.595   24.300   27.160 
[1] "0.1 - 125.4 (20.5)" "0.7 - 185.8 (25.1)" "0.2 - 191.8 (27.4)"
[4] "0.1 - 110.4 (28.0)" "0.2 - 86.1 (18.6)"  "0.4 - 116.2 (24.3)"
[7] "0.6 - 112.5 (27.2)"
D8V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      24
  subtype2                                      51
  subtype3                                      20
  subtype4                                      61
  subtype5                                     102
  subtype6                                      67
  subtype7                                      75
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             9                                89
  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       51       20       61
  MIXED SEROUS AND ENDOMETRIOID                  9        0        5        2
  SEROUS ENDOMETRIAL ADENOCARCINOMA             89        0       21        0
                                         clus
vv                                        subtype5 subtype6 subtype7
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      102       67       75
  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"
D8V4, binary
          cls
clus        0  1
  subtype1 26 96
  subtype2 13 38
  subtype3 16 30
  subtype4 26 37
  subtype5 29 78
  subtype6 12 56
  subtype7 19 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   96
  subtype2   13   38
  subtype3   16   30
  subtype4   26   37
  subtype5   29   78
  subtype6   12   56
  subtype7   19   58
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        26       13       16       26       29       12       19
  YES       96       38       30       37       78       56       58
[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       R0 R1 R2 RX
  subtype1 79  7  3 10
  subtype2 39  2  0  3
  subtype3 32  1  7  3
  subtype4 43  5  1  1
  subtype5 72  7  4  5
  subtype6 44  1  1  5
  subtype7 57  0  1  8
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       79       39       32       43       72       44       57
  R1        7        2        1        5        7        1        0
  R2        3        0        7        1        4        1        1
  RX       10        3        3        1        5        5        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        35
  subtype2                                0     2                         8
  subtype3                                1     3                        10
  subtype4                                2     1                         8
  subtype5                                0     4                        15
  subtype6                                1     3                        15
  subtype7                                0     4                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    73
  subtype2                                         0    39
  subtype3                                         1    26
  subtype4                                         3    47
  subtype5                                         4    77
  subtype6                                         0    48
  subtype7                                         0    61
D8V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        1        2
  ASIAN                                            3        2        3        1
  BLACK OR AFRICAN AMERICAN                       35        8       10        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        1        3
  WHITE                                           73       39       26       47
                                           clus
vv                                          subtype5 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE                 0        1        0
  ASIAN                                            4        3        4
  BLACK OR AFRICAN AMERICAN                       15       15       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        4        0        0
  WHITE                                           77       48       61
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1  3 80
  subtype2  1 36
  subtype3  4 33
  subtype4  2 40
  subtype5  3 76
  subtype6  1 45
  subtype7  0 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   80
  subtype2    1   36
  subtype3    4   33
  subtype4    2   40
  subtype5    3   76
  subtype6    1   45
  subtype7    0   60
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        1        4        2        3        1
  NOT HISPANIC OR LATINO       80       36       33       40       76       45
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       60
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 177  39
  subtype2 131  17
  subtype3 151  10
subtype1 subtype2 subtype3 
     216      148      161 
subtype1 subtype2 subtype3 
      39       17       10 
$subtype1
TCGA-2E-A9G8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA 
       41.06       106.88       149.56        46.95        37.02        17.85 
TCGA-A5-A0GH TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A1OF TCGA-A5-A1OG 
       74.10        36.82        23.21        19.96         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A2QO 
        7.33        14.96         1.18        14.43        29.39        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       34.16         1.12         0.76        14.66        22.49        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3QS TCGA-AJ-A3TW 
       20.81        21.21        15.62        15.35        16.87        16.87 
TCGA-AJ-A6NU TCGA-AP-A059 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LH 
       20.78         8.22        48.79       125.42         3.39        36.36 
TCGA-AP-A0LI TCGA-AP-A1DH TCGA-AP-A1DQ TCGA-AP-A1DV TCGA-AP-A1E3 TCGA-AP-A1E4 
       97.71        71.67        46.78         6.71        27.85        16.24 
TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       21.90        53.92        51.09        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR 
       13.55        20.28        12.43        76.83        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HG 
        4.77        30.12        71.24        61.18        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3G1 
       17.75         2.96        31.13        64.93         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-AX-A3GI 
        1.38         0.30         0.26         0.30        18.35         0.39 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11H 
       80.38        27.29        17.88        17.85        11.01        88.34 
TCGA-B5-A11L TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX 
       45.90       191.84       102.31        50.89        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       11.87        12.79        96.30        29.65        34.13        34.95 
TCGA-BG-A0LX TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MG TCGA-BG-A0MT TCGA-BG-A0YV 
       20.19        34.98        22.06        48.56        21.17        12.56 
TCGA-BG-A221 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CC 
        1.81        20.02        23.70        11.31         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TJ TCGA-BS-A0U9 
       10.16        24.13        23.47         4.80        67.99        67.20 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
       85.84        73.25        49.55        29.95        22.55        39.48 
TCGA-D1-A15X TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       29.88        15.72        36.10        27.42        11.51        29.92 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A1NU TCGA-D1-A1NW 
       18.67        14.73         0.99        28.01        13.22         0.72 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
        3.52        44.88         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DI-A1BU TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       10.92        39.29        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 
      110.10        48.36         2.37        27.32         7.36        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AV 
       37.71        66.90        51.42        19.40        34.39        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       17.19        27.16        17.88        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO 
       14.53         6.21         4.54        23.90         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 
       18.84        15.09        16.11        15.81        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       14.40        18.87        20.05        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       11.38        17.92        14.70         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01         9.07        25.02        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
        1.74         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        9.47        26.10        18.21        23.24        15.45        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SL-A6J9 
       12.92         7.00        14.83         4.44        14.07         0.07 

$subtype2
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GV 
       36.69        10.29        57.53        60.53        46.55        20.81 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0VQ TCGA-A5-A1OK TCGA-AJ-A23O TCGA-AJ-A2QN 
       68.65        17.59        15.95         8.02        10.26         2.40 
TCGA-AJ-A3EJ TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A8CW 
        1.64        36.99        20.65        10.19        14.76         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       83.67         5.95        23.31        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LT 
       63.16        83.97        27.12        82.52        33.40        49.22 
TCGA-AP-A0LV TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DR TCGA-AP-A1E0 TCGA-AP-A1E1 
       25.08        55.89        31.30        49.15        30.90        10.42 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05U TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       36.13         0.56        29.69        46.45        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06J TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 
       34.98        12.26        30.02        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN 
       65.88        13.28        19.20        72.56        67.50        25.12 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G8 
       81.37        34.32        46.49         0.23         0.20         1.18 
TCGA-B5-A0JR TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11I TCGA-B5-A11U 
       13.74        17.10         8.71       185.79        75.72        16.73 
TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MZ TCGA-B5-A3FB TCGA-B5-A5OC 
       19.56        19.59        17.36        15.29        78.81        41.06 
TCGA-BG-A0LW TCGA-BG-A0M3 TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       18.61        35.21        23.47        43.04        39.32        30.81 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VX TCGA-BG-A0W2 TCGA-BG-A186 
       20.28        15.42        24.39        34.29        56.58        13.78 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BS-A0T9 
       15.45         9.57        31.76        24.99        16.64        46.95 
TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UT TCGA-BS-A0V4 
       61.87        96.49        30.74        97.41        72.72        59.51 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZS 
       63.58        63.16        66.48        16.83         8.55         4.87 
TCGA-D1-A102 TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A16N TCGA-D1-A16R 
        4.44         1.91         3.68        32.58        31.07         0.69 
TCGA-D1-A16Y TCGA-D1-A177 TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NY 
       17.49        18.02        28.08        10.22        11.15        16.87 
TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1C3 
        3.95         8.48         0.26        27.16        16.31        24.30 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X 
       23.38        17.06        61.74        61.55        46.26        57.60 
TCGA-EO-A3AU TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GR 
       26.43        14.99        53.88        13.97        17.88        17.62 
TCGA-EY-A1GU TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 
       12.43        22.82        45.76        31.04        14.14        16.96 
TCGA-FI-A2EY TCGA-PG-A917 TCGA-QF-A5YT TCGA-SL-A6JA 
       28.93         6.97        39.95         0.23 

$subtype3
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GJ 
       83.51        32.78       112.54       105.37        87.32        65.75 
TCGA-A5-A0GM TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       60.53        38.37        28.27        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A1OJ TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BI 
       11.97        42.35         9.60         0.39        19.79        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
        1.68        17.06        15.95        22.32        12.82         2.70 
TCGA-AP-A05O TCGA-AP-A0LJ TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A1DK 
       12.20        31.73        61.64        80.78        63.06        60.36 
TCGA-AP-A1DP TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A063 
       35.54        13.58        19.82        68.35        72.03        66.58 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A2H7 
       27.39        60.66        15.25        20.05        54.12        40.80 
TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT 
       30.74         0.56        43.82        14.47        46.75        43.13 
TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11J 
       44.71        30.51        25.91         4.11       113.36        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       44.78        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A3F9 
       27.35        19.50        18.41        16.57        14.40       116.25 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M7 
       62.14        33.11        14.27        19.33        20.94        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MH TCGA-BG-A0MK 
       36.49        28.27        10.72        41.52        63.45        43.30 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A187 
       26.66        16.34        52.64        52.83        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2L7 TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A56F 
       14.01        15.45        20.12        35.90        34.98        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0UA 
       10.03         9.86        85.55        78.21        77.95        88.34 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZO TCGA-D1-A0ZR 
       82.39        81.57        86.93        62.79        19.79         0.56 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A161 
       28.67        23.93         1.74        21.99        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-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A174 
        2.63        33.63        10.65         3.95         3.65        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
        6.64        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-D1-A2G5 TCGA-DI-A1BY TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 
       41.42        36.62         6.67        16.04        16.80        49.15 
TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       51.52        24.89        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A549 TCGA-FI-A2F4 
       22.78        11.08         6.48        19.33        19.89        28.96 
TCGA-PG-A916 TCGA-QF-A5YS TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       11.24        18.84        12.92        23.64        18.28 

subtype1 subtype2 subtype3 
    0.07     0.13     0.39 
subtype1 subtype2 subtype3 
  191.84   185.79   116.25 
subtype1 subtype2 subtype3 
  20.035   27.140   24.890 
[1] "0.1 - 191.8 (20.0)" "0.1 - 185.8 (27.1)" "0.4 - 116.2 (24.9)"
D9V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      98
  subtype2                                     143
  subtype3                                     157
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            16                               104
  subtype2                             3                                 2
  subtype3                             2                                 2
D9V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       98      143      157
  MIXED SEROUS AND ENDOMETRIOID                 16        3        2
  SEROUS ENDOMETRIAL ADENOCARCINOMA            104        2        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"
D9V4, binary
          cls
clus         0   1
  subtype1  53 165
  subtype2  43 105
  subtype3  41 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53  165
  subtype2   43  105
  subtype3   41  120
     clus
vv    subtype1 subtype2 subtype3
  NO        53       43       41
  YES      165      105      120
[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        R0  R1  R2  RX
  subtype1 142  12  11  16
  subtype2 102   7   3   8
  subtype3 117   4   2  11
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142      102      117
  R1       12        7        4
  R2       11        3        2
  RX       16        8       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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     9                        49
  subtype2                                2     4                        28
  subtype3                                1     7                        25
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         6   134
  subtype2                                         2   105
  subtype3                                         1   125
D9V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        2        1
  ASIAN                                            9        4        7
  BLACK OR AFRICAN AMERICAN                       49       28       25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        6        2        1
  WHITE                                          134      105      125
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  10 151
  subtype2   2  98
  subtype3   2 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  151
  subtype2    2   98
  subtype3    2  120
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10        2        2
  NOT HISPANIC OR LATINO      151       98      120
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 187  26
  subtype2  53   3
  subtype3 132  10
  subtype4  87  27
subtype1 subtype2 subtype3 subtype4 
     213       56      142      114 
subtype1 subtype2 subtype3 subtype4 
      26        3       10       27 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       41.06        36.69       106.88        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       46.55        23.21        17.59        42.35        15.95         7.92 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.33         5.16         7.33        10.26         2.40        34.36 
TCGA-AJ-A3BG TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NE 
        0.76         1.64        14.66        22.49        20.81        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
       15.62        10.19        15.35        14.76        16.87        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
       20.78         0.13        83.67         5.95        23.31         8.22 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LM 
       20.91       125.42       117.99       110.37        63.16        27.12 
TCGA-AP-A0LO TCGA-AP-A0LT TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       33.40        49.22        71.67        60.36        55.89        31.30 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
       49.15         6.71        30.90        27.85        16.24        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
        0.56        13.58        35.34        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A0IZ TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN 
       27.39        43.82        76.83        72.56        67.50        25.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        61.18        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G6 
       17.75        31.13         0.23         0.20         0.20         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K4 
        1.18        18.35        56.91        32.55        28.64        17.88 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11P 
        8.71        88.34        75.72        45.90        43.96        36.82 
TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11X TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MW 
       32.09        16.73        19.59       191.84        50.89        14.70 
TCGA-B5-A1MX TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC 
       11.70        12.79        96.30        78.81        62.14        41.06 
TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MQ TCGA-BG-A0YV TCGA-BG-A18C 
       20.19        38.37        36.49        39.32        12.56        15.45 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TE 
        6.81        10.16        16.64        10.03         9.86         4.80 
TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0V8 
       67.99        30.74        67.20        85.84        81.57        49.55 
TCGA-BS-A0VI TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A101 TCGA-D1-A103 
       63.16         8.55         4.87        28.67         1.74        21.99 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16J 
        1.91         3.68        32.58        15.72        36.10        29.92 
TCGA-D1-A16N TCGA-D1-A16V TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17C TCGA-D1-A17H 
       31.07         3.95         6.64        18.02         0.99        28.01 
TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3DA 
       28.08        10.22        11.15        16.87         8.48         0.26 
TCGA-D1-A3JP TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1NO 
       16.93        10.92        27.16        16.31        39.29         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX 
       31.10        23.38        17.06         2.37        16.04         7.36 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        57.60        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GI 
       22.26        14.53         6.21        14.99         4.54        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       23.90        19.27        17.88        17.62        16.11        12.43 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        13.84        17.92        14.14        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        39.88         7.99        13.84         8.98 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-PG-A6IB TCGA-PG-A917 TCGA-QF-A5YS TCGA-QS-A744 
        2.43        23.74        15.45         6.97        18.84        14.83 
TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07         0.07         0.23 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       10.29        57.53        60.53        28.27        20.81        68.65 
TCGA-AJ-A3NC TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05T 
       36.99        31.73        83.97        82.52        25.08        19.82 
TCGA-AX-A05U TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A0IS TCGA-AX-A1C4 TCGA-AX-A3GB 
       29.69        46.45        45.99        35.01        13.28        14.47 
TCGA-B5-A0JU TCGA-B5-A0K0 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11F TCGA-B5-A11V 
       48.76        28.34        13.74        17.10       185.79        19.56 
TCGA-B5-A11Z TCGA-B5-A1MZ TCGA-BG-A0LW TCGA-BG-A0M3 TCGA-BG-A0MI TCGA-BG-A0MO 
       17.36        15.29        18.61        35.21        23.47        43.04 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VX TCGA-BG-A0W2 TCGA-BG-A186 
       30.81        20.28        24.39        34.29        56.58        13.78 
TCGA-BK-A13B TCGA-BS-A0T9 TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U8 TCGA-BS-A0UJ 
       31.76        46.95        77.95        61.87        97.41        82.39 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A102 
       72.72        59.51        63.58        66.48        16.83         4.44 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A17N TCGA-D1-A1O8 TCGA-DI-A1C3 TCGA-EY-A1GD 
       10.65         0.69         1.51         3.95        24.30        53.88 
TCGA-EY-A1GL TCGA-QF-A5YT 
       13.97        39.95 

$subtype3
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GQ 
       83.51        32.78       112.54       105.37        87.32        38.37 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A1OJ TCGA-A5-A1OK 
       19.59        24.62        29.06        11.97         9.60         8.02 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3OK 
        0.39        19.79        18.90         1.68        17.06        15.95 
TCGA-AJ-A5DV TCGA-AJ-A8CT TCGA-AP-A05O TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       22.32         2.70        12.20        61.64        80.78        63.06 
TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A06D TCGA-AX-A06J 
       35.54        10.42        68.35        72.03        12.26        30.02 
TCGA-AX-A06L TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A2H7 
       60.66        19.20        15.25        20.05        54.12        40.80 
TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0JS TCGA-B5-A0JT 
       30.74         0.56        43.82        20.52        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0KB TCGA-B5-A11G 
       40.67        44.71        30.51        25.91         4.11       113.36 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W 
       54.44        44.78        40.50        33.50        27.35        19.50 
TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH 
       18.41        16.57        14.40       116.25        33.11        14.27 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       19.33        20.94        28.27        10.72        41.52        48.56 
TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       63.45        43.30        21.17        15.42        26.66        16.34 
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-BS-A0TA TCGA-BS-A0TC 
       35.90        34.98        24.99        13.18        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 
       78.21        96.49        88.34        86.93        73.25        62.79 
TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A15W TCGA-D1-A161 TCGA-D1-A162 
       19.79         0.56        23.93        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-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B 
       33.63         3.65        19.53        30.15         1.58         7.00 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17L TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       30.44         1.28        26.37         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       22.92         1.41        18.25        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A2G5 TCGA-DF-A2KV TCGA-DI-A1BY TCGA-E6-A2P9 TCGA-EC-A24G 
        1.05        41.42        89.33        36.62         6.67        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       49.15        51.52        24.89        24.36        27.16        23.34 
TCGA-EY-A1GK TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A549 TCGA-FI-A2F4 
       22.78        11.08         6.48        19.33        19.89        28.96 
TCGA-PG-A916 TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       11.24        12.92        23.64        18.28 

$subtype4
TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GR TCGA-A5-A0R6 
      149.56        46.95        37.02        17.85        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP 
       11.44        36.33        91.04        46.32        28.64        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM 
        1.18        14.43        29.39        34.16         1.12        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI 
       21.21        16.87        48.79         3.39        36.36        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06F TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       46.78        21.90        51.09        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CP 
       65.88        16.96        13.55        20.28        12.43        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO 
       11.08         4.77        30.12        19.36         2.96        64.93 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        1.38         0.30         0.30         0.39        80.38        27.29 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD 
       17.85        11.01       102.31        11.87        29.65        34.13 
TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZP 
       34.95        34.98        22.06        10.22        24.13        29.95 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S 
       22.55        39.48        29.88        27.42        11.51        18.67 
TCGA-D1-A16Y TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G0 TCGA-D1-A2G7 
       17.49        14.73        13.22         0.72         3.52        44.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.27         4.11        35.38        12.39       110.10        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KW 
       27.32        10.92        37.71        51.42        26.96        16.34 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 
        6.90        18.84        15.09        15.81        12.59        10.19 
TCGA-EY-A2ON TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       20.05        11.38        41.06        39.95        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.07        28.93        25.02        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74         7.76        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       18.21        23.24        23.97        12.92         7.00         4.44 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.69     0.39     0.30 
subtype1 subtype2 subtype3 subtype4 
  191.84   185.79   116.25   149.56 
subtype1 subtype2 subtype3 subtype4 
   20.65    31.27    24.49    21.98 
[1] "0.1 - 191.8 (20.6)" "0.7 - 185.8 (31.3)" "0.4 - 116.2 (24.5)"
[4] "0.3 - 149.6 (22.0)"
D10V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                     185
  subtype2                                      56
  subtype3                                     139
  subtype4                                      18
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            10                                19
  subtype2                             0                                 0
  subtype3                             1                                 2
  subtype4                            10                                87
D10V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3 subtype4
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA      185       56      139       18
  MIXED SEROUS AND ENDOMETRIOID                 10        0        1       10
  SEROUS ENDOMETRIAL ADENOCARCINOMA             19        0        2       87
[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"
D10V4, binary
          cls
clus         0   1
  subtype1  64 150
  subtype2  12  44
  subtype3  37 105
  subtype4  24  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64  150
  subtype2   12   44
  subtype3   37  105
  subtype4   24   91
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        64       12       37       24
  YES      150       44      105       91
[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        R0  R1  R2  RX
  subtype1 148  10   6  11
  subtype2  36   4   1   4
  subtype3 101   3   2  11
  subtype4  76   6   7   9
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      148       36      101       76
  R1       10        4        3        6
  R2        6        1        2        7
  RX       11        4       11        9
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                        38
  subtype2                                1     3                         8
  subtype3                                0     6                        22
  subtype4                                1     3                        34
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         4   146
  subtype2                                         2    40
  subtype3                                         2   110
  subtype4                                         1    68
D10V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE                 2        1        0        1
  ASIAN                                            8        3        6        3
  BLACK OR AFRICAN AMERICAN                       38        8       22       34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        4        2        2        1
  WHITE                                          146       40      110       68
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1   7 148
  subtype2   1  36
  subtype3   3 103
  subtype4   3  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  148
  subtype2    1   36
  subtype3    3  103
  subtype4    3   82
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7        1        3        3
  NOT HISPANIC OR LATINO      148       36      103       82
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 136  27
  subtype2  78  14
  subtype3 123  11
subtype1 subtype2 subtype3 
     163       92      134 
subtype1 subtype2 subtype3 
      27       14       11 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0GB TCGA-A5-A1OF TCGA-A5-A1OG 
       41.06        36.69       106.88        32.78         7.92        11.44 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
        1.18        14.43        29.39        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC 
        0.76         1.68        14.66        22.26        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CW 
       20.65        10.19        14.76        16.87        12.82         0.13 
TCGA-AP-A0LF TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A064 TCGA-AX-A1CI 
        3.39        16.24        21.90         0.56        34.98        72.56 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A3FS 
       34.32        46.49        19.36        26.33        17.75         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G6 
        0.20         0.56         0.20        20.52         1.38         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0K8 TCGA-B5-A11H 
        1.18        18.35         0.39        56.91        17.85        88.34 
TCGA-B5-A11J TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A3FA TCGA-B5-A3FB 
       54.44       191.84       102.31        14.70        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        33.11        14.27        29.65        34.13        34.95 
TCGA-BG-A0YV TCGA-BG-A221 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       12.56         1.81        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-D1-A15V 
        6.81        10.22        31.76        16.64        10.03        39.48 
TCGA-D1-A15X TCGA-D1-A167 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A1NU 
       29.88        15.72        11.51        18.67        17.49        13.22 
TCGA-D1-A2G0 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY 
        3.52         0.26         4.27         4.11        89.33        10.92 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
       35.38         9.37        12.39       110.10        48.36        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A2CH TCGA-EO-A3AU 
       10.92        37.71        61.55        46.26        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       35.15        17.19        26.96        22.26        16.34        14.53 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR 
        6.21        14.99         4.54        23.90        19.27        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       15.09        15.81        10.19        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
       31.04        27.35        13.84        11.38        17.92        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A6IB 
        2.43        23.74        13.28         9.47        26.10        15.45 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A917 TCGA-QF-A5YS TCGA-SJ-A6ZI TCGA-SL-A6J9 
       12.92         7.00         6.97        18.84        14.07         0.07 
TCGA-SL-A6JA 
        0.23 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0GG TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A1OK 
       10.29        87.32        60.53        36.82        36.33         8.02 
TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3EJ TCGA-AJ-A3EL 
        7.33        10.26         0.39         2.40         1.64        22.49 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3QS TCGA-AJ-A6NU 
       21.21        15.62        15.35        15.95        16.87        20.78 
TCGA-AJ-A8CT TCGA-AP-A059 TCGA-AP-A05O TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AP-A1E0 
        2.70         8.22        12.20        27.12        46.78        30.90 
TCGA-AP-A1E3 TCGA-AX-A06H TCGA-AX-A0IZ TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CN 
       27.85        27.39        43.82        13.55        12.43        25.12 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3GB 
       30.74         2.96        31.13        64.93         0.30        14.47 
TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       45.90        40.50        16.73        50.89        11.87        12.79 
TCGA-B5-A5OC TCGA-BG-A0MA TCGA-BG-A18A TCGA-BK-A26L TCGA-BK-A6W4 TCGA-BS-A0V7 
       41.06        10.72        14.01        24.13         9.86        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A168 TCGA-D1-A17C 
       49.55        63.16         8.55         4.87        36.10         0.99 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3JP 
        0.72        16.87         3.95         8.48        44.88        16.93 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A2P8 
       27.16        16.31        39.29        24.30        31.10         2.37 
TCGA-EO-A22R TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       61.74        66.90        57.60        51.52        51.42        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3L0 TCGA-EY-A1GD TCGA-EY-A1GM TCGA-EY-A1GP 
       27.16        17.88        24.89        53.88         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A210 TCGA-EY-A2OQ TCGA-FI-A2F8 TCGA-FI-A2F9 
       17.88        16.11        12.59        29.10        25.02        29.23 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QF-A5YT TCGA-QS-A5YR TCGA-QS-A744 
       18.21        23.24        23.97        39.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZJ 
        4.44        18.28 

$subtype3
TCGA-A5-A0GQ TCGA-A5-A1OJ TCGA-AJ-A2QL TCGA-AJ-A3BI TCGA-AJ-A3I9 TCGA-AJ-A5DV 
       38.37         9.60        19.79        18.90        17.06        22.32 
TCGA-AP-A0LS TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       63.06        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A5FX TCGA-AX-A06L TCGA-AX-A1C4 
       49.15         6.71        10.42        36.13        60.66        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ 
       19.20        15.25        20.28        20.05        76.83        54.12 
TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0JU 
       67.50        36.39        11.08        43.82        43.13        48.76 
TCGA-B5-A0JX TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11P 
       44.71         4.11       113.36        44.78        43.96        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A121 
       32.09        33.50        27.35        19.50        17.36        16.57 
TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-BG-A0MH TCGA-BG-A0MK 
       14.40        11.70        15.29       116.25        63.45        43.30 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18B 
       26.66        16.34        34.29        13.78        14.73        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BK-A0CA TCGA-BK-A139 TCGA-BK-A13C TCGA-BK-A56F 
       15.45         9.57        34.98        10.16        24.99        13.18 
TCGA-BS-A0T9 TCGA-BS-A0UA TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-D1-A0ZN TCGA-D1-A0ZO 
       46.95        88.34        59.51        62.79        16.83        19.79 
TCGA-D1-A102 TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 
        4.44        30.08         3.68        29.33        37.64        32.58 
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-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.95         3.65        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       14.73         1.58         7.00        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
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-D1-A2G5 TCGA-DI-A1BY TCGA-E6-A1LX 
        2.07        15.06         1.05        41.42        36.62        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
       17.06         6.67        16.04         7.36        16.80        49.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-FI-A2F4 
       12.43        11.08        19.33        14.40        18.87        28.96 
TCGA-PG-A916 TCGA-QS-A5YQ 
       11.24        12.92 

subtype1 subtype2 subtype3 
    0.07     0.30     0.66 
subtype1 subtype2 subtype3 
  191.84    87.32   116.25 
subtype1 subtype2 subtype3 
  17.750   20.995   20.165 
[1] "0.1 - 191.8 (17.8)" "0.3 - 87.3 (21.0)"  "0.7 - 116.2 (20.2)"
D11V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      89
  subtype2                                      63
  subtype3                                     126
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                             8                                68
  subtype2                             8                                21
  subtype3                             3                                 5
D11V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       89       63      126
  MIXED SEROUS AND ENDOMETRIOID                  8        8        3
  SEROUS ENDOMETRIAL ADENOCARCINOMA             68       21        5
[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"
D11V4, binary
          cls
clus         0   1
  subtype1  26 139
  subtype2  20  72
  subtype3  42  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26  139
  subtype2   20   72
  subtype3   42   92
     clus
vv    subtype1 subtype2 subtype3
  NO        26       20       42
  YES      139       72       92
[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        R0  R1  R2  RX
  subtype1 102   7   8  11
  subtype2  70   4   1   6
  subtype3  89   6   4  12
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      102       70       89
  R1        7        4        6
  R2        8        1        4
  RX       11        6       12
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        44
  subtype2                                1     4                        24
  subtype3                                0     2                        20
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   102
  subtype2                                         4    54
  subtype3                                         1   109
D11V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        0
  ASIAN                                            1        4        2
  BLACK OR AFRICAN AMERICAN                       44       24       20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        4        1
  WHITE                                          102       54      109
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus         0   1
  subtype1   8 115
  subtype2   1  64
  subtype3   2 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  115
  subtype2    1   64
  subtype3    2  101
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        1        2
  NOT HISPANIC OR LATINO      115       64      101
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 116  22
  subtype2 104  10
  subtype3 117  20
subtype1 subtype2 subtype3 
     138      114      137 
subtype1 subtype2 subtype3 
      22       10       20 
$subtype1
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A2K2 
       41.06        36.69       106.88         7.92        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QM 
       46.32        28.64         5.33        14.96         1.18        29.39 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3OL 
       34.16         1.12         0.76         1.64        10.19        14.76 
TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A059 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AP-A1DO 
       16.87         0.13         8.22         3.39        63.06        31.30 
TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A1C5 TCGA-AX-A1CA 
        6.71        10.42        21.90         0.56        19.20        20.28 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       20.05        76.83        67.50        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A3FT 
       71.24        61.18        46.49        26.33        17.75         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GI TCGA-B5-A0JU TCGA-B5-A0K8 
        1.38         0.26         1.18         0.39        48.76        17.85 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MR TCGA-B5-A1MS 
      113.36        88.34        36.82        32.09       191.84       102.31 
TCGA-B5-A1MW TCGA-B5-A3FA TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0YV 
       14.70        96.30        29.65        34.13        34.95        12.56 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         1.81         9.57        23.70        20.12        11.31 
TCGA-BK-A139 TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A167 TCGA-D1-A16I 
       10.16        39.48        29.88         3.68        15.72        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A179 
       31.07        18.67         3.95        17.49        30.15        14.73 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G0 TCGA-D1-A3DA 
       28.08        26.37        13.22         0.72         3.52         0.26 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LZ TCGA-E6-A8L9 
        4.11        35.38         9.37        12.39        48.36        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22U TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 
       10.92        37.71        46.26        19.40        35.15        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ 
       16.34        14.53         6.21        14.99         4.54        23.90 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 
       17.62        15.09        12.43        15.81        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       11.38        17.92        40.01        41.06        39.95        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01         9.07        28.93        28.96        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76        14.04         2.43        23.74         9.47        26.10 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A917 TCGA-QF-A5YS TCGA-SL-A6J9 TCGA-SL-A6JA 
       12.92         7.00         6.97        18.84         0.07         0.23 

$subtype2
TCGA-5S-A9Q8 TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-AJ-A2QK 
       10.29        87.32        38.37         9.60         8.02         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       19.79        34.36        18.90         1.68        17.06        36.99 
TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A8CT TCGA-AP-A05O TCGA-AP-A1DP TCGA-AP-A5FX 
       15.95        22.32         2.70        12.20        35.54        36.13 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A1C4 TCGA-AX-A1C9 TCGA-AX-A1CJ TCGA-AX-A2H7 
       27.39        60.66        13.28        15.25        54.12        40.80 
TCGA-AX-A2HJ TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GB TCGA-B5-A0JT 
       30.74         0.56        43.82        20.52        14.47        43.13 
TCGA-B5-A0JX TCGA-B5-A0KB TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11R 
       44.71         4.11        54.44        44.78        40.50        33.50 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MZ 
       27.35        19.50        17.36        16.57        14.40        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3FH TCGA-BG-A0MA TCGA-BG-A0MH 
      116.25        78.81        33.11        14.27        10.72        63.45 
TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A186 TCGA-BG-A187 
       43.30        26.66        16.34        34.29        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       14.01        15.45        34.98        31.76        24.99        13.18 
TCGA-BS-A0UA TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A102 
       88.34        62.79        63.58        19.79         8.55         4.44 
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-A16R 
       37.51        36.79         2.63        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A175 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
        3.65         6.64         1.58         7.00        30.44         1.28 
TCGA-D1-A17N TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX 
        1.51        24.30         2.33        22.92         1.41        18.25 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A2G5 TCGA-DF-A2KV 
       18.02         2.07        15.06         1.05        41.42        89.33 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 
       36.62        24.30         6.67        16.04        16.80        49.15 
TCGA-EO-A22Y TCGA-EO-A3L0 TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GK 
       51.52        24.89        24.36        27.16        23.34        22.78 
TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-PG-A916 TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZJ 
       11.08        19.33        11.24        12.92        23.64        18.28 

$subtype3
TCGA-A5-A0GB TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K7 TCGA-A5-A3LO 
       32.78        60.53        36.82        36.33         5.16         7.33 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QN TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       14.43        10.26         2.40        14.66        22.49        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3QS 
       20.81        20.65        21.21        15.62        15.35        16.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AP-A0LM TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       12.82        20.78        27.12        71.67        60.36        55.89 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A064 
       46.78        49.15        30.90        27.85        16.24        34.98 
TCGA-AX-A0IZ TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP 
       43.82        13.55        12.43        72.56        25.12        36.39 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       81.37        34.32        19.36         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G9 TCGA-B5-A0JR TCGA-B5-A11L 
        0.23         0.20         0.30        18.35        56.91        45.90 
TCGA-B5-A11N TCGA-B5-A11U TCGA-B5-A1MU TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1N2 
       43.96        16.73        50.89        11.70        11.87        12.79 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A2AD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       62.14        41.06        20.02         6.81        10.22        24.13 
TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0V4 TCGA-BS-A0V8 
       16.64        10.03         9.86        46.95        59.51        49.55 
TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZS TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16G 
       63.16        16.83         4.87        32.58        36.10        27.42 
TCGA-D1-A16J TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A17M 
       29.92        19.53        18.02         0.99        28.01        10.22 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.78        11.15        16.87         3.95         8.48        44.88 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.27        16.93        10.92        27.16        16.31        39.29 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1QX 
       31.10       110.10        23.38        17.06         2.37         7.36 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS 
       61.74        61.55        66.90        57.60        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EY-A1GD 
       26.43        17.19        27.16        17.88        22.26        53.88 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A54A TCGA-EY-A5W2 
       16.11        12.59        29.10        13.84        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F8 
        5.88        39.88         7.99        13.84         8.98        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       29.23        41.06        13.28        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-QF-A5YT TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       23.97        39.95        14.83         4.44        14.07 

subtype1 subtype2 subtype3 
    0.07     0.39     0.20 
subtype1 subtype2 subtype3 
  191.84   116.25   110.10 
subtype1 subtype2 subtype3 
  17.800   20.155   20.020 
[1] "0.1 - 191.8 (17.8)" "0.4 - 116.2 (20.2)" "0.2 - 110.1 (20.0)"
D12V2, continuous
          vv
clus       ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  subtype1                                      70
  subtype2                                     110
  subtype3                                      98
          vv
clus       MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  subtype1                            11                                59
  subtype2                             2                                 2
  subtype3                             6                                33
D12V3, multiclass
                                         clus
vv                                        subtype1 subtype2 subtype3
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA       70      110       98
  MIXED SEROUS AND ENDOMETRIOID                 11        2        6
  SEROUS ENDOMETRIAL ADENOCARCINOMA             59        2       33
[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"
D12V4, binary
          cls
clus         0   1
  subtype1  27 113
  subtype2  24  90
  subtype3  37 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27  113
  subtype2   24   90
  subtype3   37  100
     clus
vv    subtype1 subtype2 subtype3
  NO        27       24       37
  YES      113       90      100
[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       R0 R1 R2 RX
  subtype1 90  7  8  9
  subtype2 72  4  1 13
  subtype3 99  6  4  7
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       90       72       99
  R1        7        4        6
  R2        8        1        4
  RX        9       13        7
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        33
  subtype2                                1     3                        23
  subtype3                                0     3                        32
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    96
  subtype2                                         1    83
  subtype3                                         4    86
D12V6, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        0
  ASIAN                                            1        3        3
  BLACK OR AFRICAN AMERICAN                       33       23       32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        4
  WHITE                                           96       83       86
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus         0   1
  subtype1   6 106
  subtype2   2  84
  subtype3   3  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  106
  subtype2    2   84
  subtype3    3   90
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        3
  NOT HISPANIC OR LATINO      106       84       90
[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"
