[1] "ofn"        "-oTTHYM-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/THYM-TP/15092844/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/15111344/THYM-TP.mergedcluster.txt"

nPatients in clinical file=122, in cluster file=124, common to both=122
[1]  10 122
[1] "CN_CNMF"
[1] 3
 1  2  3 
64 30 27 
 1  2  3 
64 30 27 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
37 36 25 24 
 1  2  3  4 
37 36 25 24 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
27 24 37 
 1  2  3 
27 24 37 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
16 23 29 20 
 1  2  3  4 
16 23 29 20 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
44 31 29 14 
 1  2  3  4 
44 31 29 14 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
46 42 20 10 
 1  2  3  4 
46 42 20 10 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
57 61  1  2  1 
 1  2 
57 61 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
26 18 28  7 16 27 
 1  2  3  4  5  6 
26 18 28  7 16 27 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
17 59 46 
 1  2  3 
17 59 46 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
28 33 33 28 
 1  2  3  4 
28 33 33 28 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 122 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	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=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'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 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 122 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 63  1
  subtype2 26  4
  subtype3 24  1
subtype1 subtype2 subtype3 
      64       30       25 
subtype1 subtype2 subtype3 
       1        4        1 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL 
       56.65        59.15         9.96        34.52        89.23        56.75 
TCGA-4V-A9QM TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC 
       38.50        21.70        16.60        15.78        12.89        55.46 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        49.22 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         2.37 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       42.15       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ3 
       37.61         7.69        12.69        11.93        84.23        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92W TCGA-XU-A933 
      112.11        35.90        45.24       149.98       107.80        58.82 
TCGA-XU-AAXZ TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 
       50.53       107.44        13.32        22.78        12.79         0.13 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96B TCGA-ZB-A96C 
       18.58        16.57        12.46         0.66        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       42.81         0.23        37.48         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96V TCGA-ZC-AAAH TCGA-ZL-A9V6 
        7.17         8.52        16.34        68.91 

$subtype2
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QW 
       81.80        17.75        28.90        19.76        19.76        14.07 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC 
       39.45        19.50        11.57        10.36         1.64        97.41 
TCGA-XM-A8RD TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92R TCGA-XU-A92X TCGA-XU-A92Y 
       50.83        12.72        13.05        90.05        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        21.14       123.68        89.46 
TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       62.17        49.78         0.16         5.19        28.04        26.93 

$subtype3
TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QQ TCGA-4V-A9QX 
       90.61        15.35        13.48        88.83        45.07        11.24 
TCGA-4X-A9FB TCGA-5K-AAAP TCGA-5U-AB0F TCGA-X7-A8M0 TCGA-XM-A8R9 TCGA-XM-A8RF 
       23.57        34.65        15.09        14.50        48.92        26.20 
TCGA-XM-AAZ2 TCGA-XU-A92V TCGA-XU-A92Z TCGA-XU-AAY0 TCGA-YT-A95D TCGA-ZB-A962 
       32.25         4.08       120.43        49.38        18.67         0.20 
TCGA-ZB-A963 TCGA-ZB-A96A TCGA-ZB-A96G TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96R 
       30.74        10.68        32.35        31.50         0.30        35.34 
TCGA-ZC-AAAF 
       38.30 

subtype1 subtype2 subtype3 
    0.13     0.16     0.20 
subtype1 subtype2 subtype3 
  149.98   123.68   120.43 
subtype1 subtype2 subtype3 
  33.385   28.470   30.740 
[1] "0.1 - 150.0 (33.4)" "0.2 - 123.7 (28.5)" "0.2 - 120.4 (30.7)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 29 35
  subtype2 16 14
  subtype3 14 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   35
  subtype2   16   14
  subtype3   14   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       16       14
  MALE         35       14       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         4    53
  subtype2     4                         0    25
  subtype3     3                         2    22
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        4        3
  BLACK OR AFRICAN AMERICAN        4        0        2
  WHITE                           53       25       22
[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"
D1V5, binary
          cls
clus        0  1
  subtype1  2 53
  subtype2  4 22
  subtype3  3 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   53
  subtype2    4   22
  subtype3    3   23
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        4        3
  NOT HISPANIC OR LATINO       53       22       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 37  0
  subtype2 33  3
  subtype3 22  3
  subtype4 22  0
subtype1 subtype2 subtype3 subtype4 
      37       36       25       22 
subtype1 subtype2 subtype3 subtype4 
       0        3        3        0 
$subtype1
TCGA-3G-AB0O TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       56.65        15.35         9.96        34.52        89.23        88.83 
TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FB TCGA-4X-A9FC TCGA-X7-A8D6 
       45.07        21.70        15.78        23.57        55.46       138.90 
TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DG TCGA-X7-A8DI 
       10.68        65.49        49.22        36.62        22.85        23.18 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RH 
       83.28        30.08        37.61        50.83         7.69        11.93 
TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-A932 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       84.23       107.80        70.65       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-ZB-A96B TCGA-ZB-A96G TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96R 
       50.53        60.33        32.35         1.81        10.68        35.34 
TCGA-ZC-AAAH 
       16.34 

$subtype2
TCGA-3G-AB0Q TCGA-3G-AB19 TCGA-3S-A8YW TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4X-A9FA 
       59.15        90.61        13.48        56.75        38.50        12.89 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D8 TCGA-X7-A8M3 TCGA-X7-A8M5 
       34.65        11.57        27.19         1.91         1.64        54.08 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       26.20        12.69        32.25        37.81       112.11        35.90 
TCGA-XU-A92T TCGA-XU-A92V TCGA-XU-A92Z TCGA-XU-A933 TCGA-YT-A95D TCGA-ZB-A962 
       45.24         4.08       120.43        58.82        18.67         0.20 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96C TCGA-ZB-A96E 
       18.58        16.57        12.46         0.66        43.43         0.23 
TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZL-A9V6 
       37.48        31.50         0.30         8.52        28.04        68.91 

$subtype3
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD 
       81.80        17.75        28.90        19.76        19.76        39.45 
TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RC 
       19.50        10.36        14.50        52.54        48.92        97.41 
TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 TCGA-XU-A931 
       12.72        13.05        77.03       114.67        82.65        52.90 
TCGA-XU-A936 TCGA-XU-AAXV TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F TCGA-ZB-A96I 
       21.14       133.81        49.78         0.13         0.16         5.19 
TCGA-ZC-AAAA 
       26.93 

$subtype4
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-5U-AB0F TCGA-X7-A8DE TCGA-X7-A8DF 
       16.60        14.07        11.24        15.09        32.25        29.62 
TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-XU-A92R TCGA-XU-A92U TCGA-XU-AAY0 
        2.37        42.15       125.19        90.05       149.98        49.38 
TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A963 TCGA-ZB-A96A 
      107.44        13.32        22.78        12.79        30.74        10.68 
TCGA-ZB-A96D TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF 
       42.81         0.46         7.17        38.30 

subtype1 subtype2 subtype3 subtype4 
    1.81     0.20     0.13     0.46 
subtype1 subtype2 subtype3 subtype4 
  138.90   120.43   133.81   149.98 
subtype1 subtype2 subtype3 subtype4 
  37.610   27.615   26.930   26.200 
[1] "1.8 - 138.9 (37.6)" "0.2 - 120.4 (27.6)" "0.1 - 133.8 (26.9)"
[4] "0.5 - 150.0 (26.2)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 18 19
  subtype2 15 21
  subtype3 14 11
  subtype4 13 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   19
  subtype2   15   21
  subtype3   14   11
  subtype4   13   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18       15       14       13
  MALE         19       21       11       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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         5    30
  subtype2     5                         1    30
  subtype3     2                         0    22
  subtype4     4                         0    19
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        5        2        4
  BLACK OR AFRICAN AMERICAN        5        1        0        0
  WHITE                           30       30       22       19
[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"
D2V5, binary
          cls
clus        0  1
  subtype1  1 32
  subtype2  3 30
  subtype3  4 18
  subtype4  2 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    3   30
  subtype3    4   18
  subtype4    2   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        4        2
  NOT HISPANIC OR LATINO       32       30       18       18
[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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 24  3
  subtype2 23  1
  subtype3 35  1
subtype1 subtype2 subtype3 
      27       24       36 
subtype1 subtype2 subtype3 
       3        1        1 
$subtype1
TCGA-3G-AB0O TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QW TCGA-5G-A9ZZ TCGA-5U-AB0E 
       56.65        13.48        28.90        14.07        19.50        10.36 
TCGA-X7-A8M0 TCGA-X7-A8M3 TCGA-XM-A8R8 TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-A8RI 
       14.50         1.64        52.54        50.83        12.69        12.72 
TCGA-XM-AAZ1 TCGA-XU-A92Q TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 
       13.05        35.90        77.03       120.43        52.90        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A966 
       58.82        21.14        49.78         0.13        30.74        12.46 
TCGA-ZB-A96I TCGA-ZC-AAA7 TCGA-ZC-AAAA 
        5.19        28.04        26.93 

$subtype2
TCGA-3G-AB0Q TCGA-3G-AB19 TCGA-4V-A9QL TCGA-4V-A9QX TCGA-5K-AAAP TCGA-5U-AB0F 
       59.15        90.61        56.75        11.24        34.65        15.09 
TCGA-5V-A9RR TCGA-X7-A8DE TCGA-X7-A8M5 TCGA-XM-A8RC TCGA-XM-A8RF TCGA-XM-AAZ2 
       27.19        32.25        54.08        97.41        26.20        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92R TCGA-XU-A92V TCGA-XU-AAY0 TCGA-YT-A95D TCGA-ZB-A962 
       37.81        90.05         4.08        49.38        18.67         0.20 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96C TCGA-ZB-A96Q TCGA-ZL-A9V6 
       18.58        16.57         0.66        43.43         7.17        68.91 

$subtype3
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-4V-A9QS TCGA-4X-A9F9 
       81.80        17.75        15.35         9.96        19.76        15.78 
TCGA-4X-A9FB TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DC 
       23.57        55.46       138.90        10.68        65.49        49.22 
TCGA-X7-A8DD TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 
       36.62        29.62        22.85        23.18         2.37        42.15 
TCGA-X7-A8M4 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-A92U 
      125.19        37.61         7.69        11.93        84.23       149.98 
TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B 
      107.44        13.32        22.78        12.79        10.68        60.33 
TCGA-ZB-A96D TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH 
       42.81        10.68        35.34         8.52        38.30        16.34 

subtype1 subtype2 subtype3 
    0.13     0.20     2.37 
subtype1 subtype2 subtype3 
  120.43    97.41   149.98 
subtype1 subtype2 subtype3 
  26.930   32.250   23.375 
[1] "0.1 - 120.4 (26.9)" "0.2 - 97.4 (32.2)"  "2.4 - 150.0 (23.4)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 12 15
  subtype2 14 10
  subtype3 17 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   15
  subtype2   14   10
  subtype3   17   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       14       17
  MALE         15       10       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         0    20
  subtype2     3                         1    20
  subtype3     2                         3    31
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        3        2
  BLACK OR AFRICAN AMERICAN        0        1        3
  WHITE                           20       20       31
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1  4 20
  subtype2  2 20
  subtype3  2 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   20
  subtype2    2   20
  subtype3    2   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO       20       20       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 16  0
  subtype2 21  1
  subtype3 28  1
  subtype4 17  3
subtype1 subtype2 subtype3 subtype4 
      16       22       29       20 
subtype1 subtype2 subtype3 subtype4 
       0        1        1        3 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QW TCGA-4V-A9QX TCGA-5U-AB0F 
       56.65        17.75        15.35        14.07        11.24        15.09 
TCGA-X7-A8DD TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E 
       36.62        97.41         7.69        49.38       107.44        13.32 
TCGA-ZB-A963 TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZC-AAAH 
       30.74         7.17        38.30        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-3G-AB19 TCGA-4V-A9QL TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8DE 
       59.15        90.61        56.75        34.65        27.19        32.25 
TCGA-X7-A8M0 TCGA-X7-A8M5 TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       14.50        54.08        26.20        12.69        32.25        37.81 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92V TCGA-YT-A95D TCGA-ZB-A962 TCGA-ZB-A964 
       35.90        90.05         4.08        18.67         0.20        18.58 
TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96C TCGA-ZL-A9V6 
       16.57         0.66        43.43        68.91 

$subtype3
TCGA-3G-AB0T TCGA-3S-AAYX TCGA-4V-A9QS TCGA-4X-A9F9 TCGA-4X-A9FB TCGA-4X-A9FC 
       81.80         9.96        19.76        15.78        23.57        55.46 
TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DF TCGA-X7-A8DG 
      138.90        10.68        65.49        49.22        29.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-XM-A8RB TCGA-XM-A8RD 
       23.18         2.37        42.15       125.19        37.61        50.83 
TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-A92U TCGA-XU-A932 TCGA-YT-A95F TCGA-YT-A95H 
       11.93        84.23       149.98        70.65        22.78        12.79 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96P TCGA-ZB-A96R 
       10.68        60.33        42.81        10.68        35.34 

$subtype4
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8R8 
       13.48        28.90        19.50        10.36         1.64        52.54 
TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A933 
       12.72        13.05        77.03       120.43        52.90        58.82 
TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A966 TCGA-ZB-A96I TCGA-ZB-A96V 
       21.14        49.78         0.13        12.46         5.19         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

subtype1 subtype2 subtype3 subtype4 
    7.17     0.20     2.37     0.13 
subtype1 subtype2 subtype3 subtype4 
  107.44    90.61   149.98   120.43 
subtype1 subtype2 subtype3 subtype4 
  17.045   32.250   35.340   20.320 
[1] "7.2 - 107.4 (17.0)" "0.2 - 90.6 (32.2)"  "2.4 - 150.0 (35.3)"
[4] "0.1 - 120.4 (20.3)"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  7  9
  subtype2 13 10
  subtype3 13 16
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2   13   10
  subtype3   13   16
  subtype4   10   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       13       13       10
  MALE          9       10       16       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    13
  subtype2     3                         1    19
  subtype3     2                         2    24
  subtype4     4                         0    15
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        3        2        4
  BLACK OR AFRICAN AMERICAN        1        1        2        0
  WHITE                           13       19       24       15
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  1 20
  subtype3  2 24
  subtype4  4 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    1   20
  subtype3    2   24
  subtype4    4   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        2        4
  NOT HISPANIC OR LATINO       13       20       24       13
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 41  3
  subtype2 30  0
  subtype3 27  1
  subtype4 12  2
subtype1 subtype2 subtype3 subtype4 
      44       30       28       14 
subtype1 subtype2 subtype3 subtype4 
       3        0        1        2 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       56.65        81.80        17.75        15.35         9.96        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4X-A9F9 
       89.23        88.83        19.76        19.76        21.70        15.78 
TCGA-4X-A9FB TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DG 
       23.57        39.45        10.36        10.68        65.49        22.85 
TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI TCGA-XM-A8RL 
        1.64        37.61        97.41        50.83        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 TCGA-XU-A931 
       13.05       107.80        77.03       114.67        82.65        52.90 
TCGA-XU-A932 TCGA-XU-AAXV TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-YT-A95G 
       70.65       133.81       123.68        89.46        62.17        49.78 
TCGA-ZB-A961 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96R 
        0.13         0.16         5.19         1.81        10.68        35.34 
TCGA-ZC-AAAA TCGA-ZC-AAAH 
       26.93        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FA 
       59.15        56.75        16.60        14.07        11.24        12.89 
TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8DD 
       55.46        34.65        15.09        27.19       138.90        36.62 
TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DJ TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XH-A853 
       32.25        29.62         2.37       125.19        83.28        30.08 
TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XU-A92O TCGA-XU-A92U TCGA-XU-AAY0 TCGA-XU-AAY1 
        7.69        11.93       112.11       149.98        49.38       107.44 
TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96G TCGA-ZC-AAAF 
       13.32        12.79        10.68        60.33        32.35        38.30 

$subtype3
TCGA-3G-AB19 TCGA-4V-A9QM TCGA-X7-A8D8 TCGA-X7-A8M1 TCGA-XM-A8RF TCGA-XM-A8RG 
       90.61        38.50         1.91        42.15        26.20        12.69 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92Q TCGA-XU-A92T TCGA-XU-A92V TCGA-XU-A92Z 
       32.25        37.81        35.90        45.24         4.08       120.43 
TCGA-YT-A95D TCGA-YT-A95F TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       18.67        22.78         0.20        30.74        18.58        16.57 
TCGA-ZB-A969 TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96K 
        0.66        43.43        42.81         0.23        37.48        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZL-A9V6 
        0.30         0.46         7.17        68.91 

$subtype4
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8M0 TCGA-X7-A8M5 
       13.48        28.90        19.50        11.57        14.50        54.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXZ TCGA-ZB-A966 
       52.54        48.92        58.82        21.14        50.53        12.46 
TCGA-ZB-A96V TCGA-ZC-AAA7 
        8.52        28.04 

subtype1 subtype2 subtype3 subtype4 
    0.13     2.37     0.20     8.52 
subtype1 subtype2 subtype3 subtype4 
  133.81   149.98   120.43    58.82 
subtype1 subtype2 subtype3 subtype4 
   34.93    32.30    28.47    24.59 
[1] "0.1 - 133.8 (34.9)" "2.4 - 150.0 (32.3)" "0.2 - 120.4 (28.5)"
[4] "8.5 - 58.8 (24.6)" 
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 20 24
  subtype2 14 17
  subtype3 13 16
  subtype4 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   24
  subtype2   14   17
  subtype3   13   16
  subtype4   10    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       14       13       10
  MALE         24       17       16        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    37
  subtype2     3                         2    25
  subtype3     4                         1    24
  subtype4     2                         0    12
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        3        4        2
  BLACK OR AFRICAN AMERICAN        3        2        1        0
  WHITE                           37       25       24       12
[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"
D5V5, binary
          cls
clus        0  1
  subtype1  4 33
  subtype2  3 25
  subtype3  0 25
  subtype4  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   33
  subtype2    3   25
  subtype3    0   25
  subtype4    3   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        3        0        3
  NOT HISPANIC OR LATINO       33       25       25       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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 43  3
  subtype2 39  1
  subtype3 20  0
  subtype4  8  2
subtype1 subtype2 subtype3 subtype4 
      46       40       20       10 
subtype1 subtype2 subtype3 subtype4 
       3        1        0        2 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       56.65        81.80        17.75        15.35         9.96        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       89.23        88.83        28.90        19.76        19.76        21.70 
TCGA-4X-A9F9 TCGA-4X-A9FB TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8D7 TCGA-X7-A8DB 
       15.78        23.57        39.45        10.36        10.68        65.49 
TCGA-X7-A8DG TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI 
       22.85         1.64        37.61        97.41        50.83        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 
       84.23        13.05       107.80        77.03       114.67        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXV TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        70.65       133.81       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96O 
       50.53        49.78         0.13         0.16         5.19         1.81 
TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAH 
       10.68        35.34        26.93        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       59.15        56.75        38.50        16.60        14.07        11.24 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       12.89        55.46        34.65        15.09        27.19       138.90 
TCGA-X7-A8D8 TCGA-X7-A8DD TCGA-X7-A8DF TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 
        1.91        36.62        29.62         2.37        42.15       125.19 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-AAZ2 TCGA-XU-A92U 
       83.28        30.08         7.69        11.93        32.25       149.98 
TCGA-XU-A92V TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95F 
        4.08        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96G 
       12.79        10.68        60.33        43.43        42.81        32.35 
TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF 
       31.50         0.46         7.17        38.30 

$subtype3
TCGA-3G-AB19 TCGA-X7-A8DE TCGA-X7-A8M0 TCGA-X7-A8M5 TCGA-XM-A8R9 TCGA-XM-A8RF 
       90.61        32.25        14.50        54.08        48.92        26.20 
TCGA-XM-A8RG TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-ZB-A962 
       12.69        37.81       112.11        35.90        45.24         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96E TCGA-ZB-A96H 
       30.74        18.58        16.57         0.66         0.23        37.48 
TCGA-ZB-A96L TCGA-ZL-A9V6 
        0.30        68.91 

$subtype4
TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XM-A8R8 TCGA-XU-A92Z TCGA-XU-A933 
       13.48        19.50        11.57        52.54       120.43        58.82 
TCGA-XU-A936 TCGA-ZB-A966 TCGA-ZB-A96V TCGA-ZC-AAA7 
       21.14        12.46         8.52        28.04 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.46     0.20     8.52 
subtype1 subtype2 subtype3 subtype4 
  133.81   149.98   112.11   120.43 
subtype1 subtype2 subtype3 subtype4 
  34.930   30.790   31.495   20.320 
[1] "0.1 - 133.8 (34.9)" "0.5 - 150.0 (30.8)" "0.2 - 112.1 (31.5)"
[4] "8.5 - 120.4 (20.3)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 21 25
  subtype2 20 22
  subtype3 10 10
  subtype4  6  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   25
  subtype2   20   22
  subtype3   10   10
  subtype4    6    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       21       20       10        6
  MALE         25       22       10        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    39
  subtype2     4                         3    34
  subtype3     2                         0    18
  subtype4     3                         0     7
D6V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        4        2        3
  BLACK OR AFRICAN AMERICAN        3        3        0        0
  WHITE                           39       34       18        7
[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"
D6V5, binary
          cls
clus        0  1
  subtype1  5 34
  subtype2  3 34
  subtype3  0 18
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   34
  subtype2    3   34
  subtype3    0   18
  subtype4    2    8
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        3        0        2
  NOT HISPANIC OR LATINO       34       34       18        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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 53  4
  subtype2 58  1
subtype1 subtype2 
      57       59 
subtype1 subtype2 
       4        1 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       56.65        81.80        17.75        15.35        13.48         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       34.52        89.23        28.90        45.07        19.76        19.76 
TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FB TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D 
       21.70        15.78        23.57        39.45        19.50        11.57 
TCGA-5U-AB0E TCGA-5U-AB0F TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DG TCGA-X7-A8M3 
       10.36        15.09        10.68        65.49        22.85         1.64 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI 
       52.54        48.92        37.61        97.41        50.83        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
       84.23        13.05       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXV TCGA-XU-AAXW 
       82.65        70.65        58.82        21.14       133.81       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A963 
       89.46        62.17        50.53        49.78         0.13        30.74 
TCGA-ZB-A966 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96O TCGA-ZB-A96R TCGA-ZB-A96V 
       12.46         0.16         5.19         1.81        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAH 
       28.04        26.93        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW 
       59.15        88.83        56.75        38.50        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 
       11.24        12.89        55.46        34.65        27.19       138.90 
TCGA-X7-A8D8 TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DI 
        1.91        49.22        36.62        32.25        29.62        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
        2.37        14.50        42.15       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-AAZ2 
       30.08         7.69        26.20        12.69        11.93        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        90.05        45.24       149.98 
TCGA-XU-A92V TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95F 
        4.08        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96A 
       12.79         0.20        18.58        16.57         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96K 
       60.33        43.43        42.81         0.23        37.48        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZL-A9V6 
        0.30         0.46         7.17        38.30        68.91 

subtype1 subtype2 
    0.13     0.20 
subtype1 subtype2 
  133.81   149.98 
subtype1 subtype2 
    28.9     31.5 
[1] "0.1 - 133.8 (28.9)" "0.2 - 150.0 (31.5)"
[1] "hr=" "3.6"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 29 28
  subtype2 29 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   28
  subtype2   29   32
        clus
vv       subtype1 subtype2
  FEMALE       29       29
  MALE         28       32
[1] 2 2
[1] FALSE
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         3    47
  subtype2     7                         3    50
D7V4, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            6        7
  BLACK OR AFRICAN AMERICAN        3        3
  WHITE                           47       50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1  8 43
  subtype2  2 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   43
  subtype2    2   52
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            8        2
  NOT HISPANIC OR LATINO       43       52
[1] 2 2
[1] FALSE

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 24  2
  subtype2 16  1
  subtype3 27  1
  subtype4  5  2
  subtype5 16  0
  subtype6 26  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      26       17       28        7       16       26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        1        1        2        0        0 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QI TCGA-4V-A9QN 
       56.65        81.80        17.75        15.35        89.23        28.90 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FB TCGA-X7-A8DG TCGA-XM-A8RC TCGA-XM-A8RI 
       19.76        19.76        23.57        22.85        97.41        12.72 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-AAXW 
      107.80        77.03       120.43        82.65        52.90       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A963 TCGA-ZB-A96F TCGA-ZB-A96G 
       89.46        62.17        49.78        30.74         0.16        32.35 
TCGA-ZB-A96O TCGA-ZC-AAAH 
        1.81        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4X-A9FA TCGA-5K-AAAP TCGA-X7-A8D8 
       59.15        56.75        38.50        12.89        34.65         1.91 
TCGA-X7-A8M1 TCGA-XM-AAZ2 TCGA-XU-A92U TCGA-XU-A92V TCGA-YT-A95D TCGA-YT-A95F 
       42.15        32.25       149.98         4.08        18.67        22.78 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96Q 
       43.43        42.81        31.50         0.46         7.17 

$subtype3
TCGA-3G-AB19 TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4X-A9F9 
       90.61         9.96        34.52        45.07        21.70        15.78 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-5U-AB0F TCGA-X7-A8D7 TCGA-X7-A8DB 
       39.45        19.50        10.36        15.09        10.68        65.49 
TCGA-X7-A8M3 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RL TCGA-XM-AAZ1 
        1.64        48.92        37.61        50.83        84.23        13.05 
TCGA-XU-A92Y TCGA-XU-A932 TCGA-XU-A936 TCGA-XU-AAXV TCGA-XU-AAXZ TCGA-ZB-A961 
      114.67        70.65        21.14       133.81        50.53         0.13 
TCGA-ZB-A96I TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAA 
        5.19        10.68        35.34        26.93 

$subtype4
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XM-A8R8 TCGA-XU-A933 TCGA-ZB-A966 TCGA-ZB-A96V 
       13.48        11.57        52.54        58.82        12.46         8.52 
TCGA-ZC-AAA7 
       28.04 

$subtype5
TCGA-4V-A9QJ TCGA-X7-A8M0 TCGA-X7-A8M5 TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-AAZ3 
       88.83        14.50        54.08        26.20        12.69        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 
      112.11        35.90        45.24         0.20        18.58        16.57 
TCGA-ZB-A969 TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZL-A9V6 
        0.66        37.48         0.30        68.91 

$subtype6
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FC TCGA-5V-A9RR TCGA-X7-A8D6 
       16.60        14.07        11.24        55.46        27.19       138.90 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ 
       49.22        36.62        32.25        29.62        23.18         2.37 
TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XU-A92R 
      125.19        83.28        30.08         7.69        11.93        90.05 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B 
       49.38       107.44        13.32        12.79        10.68        60.33 
TCGA-ZB-A96E TCGA-ZC-AAAF 
        0.23        38.30 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.16     0.46     0.13     8.52     0.20     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  123.68   149.98   133.81    58.82   112.11   138.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  41.065   32.250   30.725   13.480   31.050   29.850 
[1] "0.2 - 123.7 (41.1)" "0.5 - 150.0 (32.2)" "0.1 - 133.8 (30.7)"
[4] "8.5 - 58.8 (13.5)"  "0.2 - 112.1 (31.0)" "0.2 - 138.9 (29.9)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  8 18
  subtype2  8 10
  subtype3 19  9
  subtype4  4  3
  subtype5  7  9
  subtype6 14 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   18
  subtype2    8   10
  subtype3   19    9
  subtype4    4    3
  subtype5    7    9
  subtype6   14   13
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        8        8       19        4        7       14
  MALE         18       10        9        3        9       13
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    21
  subtype2     2                         1    15
  subtype3     1                         2    25
  subtype4     2                         0     5
  subtype5     2                         0    14
  subtype6     3                         2    21
D8V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        1        2        2
  BLACK OR AFRICAN AMERICAN        1        1        2        0        0
  WHITE                           21       15       25        5       14
                           clus
vv                          subtype6
  ASIAN                            3
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           21
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1  1 19
  subtype2  1 14
  subtype3  5 22
  subtype4  2  5
  subtype5  0 14
  subtype6  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   19
  subtype2    1   14
  subtype3    5   22
  subtype4    2    5
  subtype5    0   14
  subtype6    1   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        5        2        0        1
  NOT HISPANIC OR LATINO       19       14       22        5       14       24
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 17  0
  subtype2 56  1
  subtype3 41  5
subtype1 subtype2 subtype3 
      17       57       46 
subtype1 subtype2 subtype3 
       0        1        5 
$subtype1
TCGA-3G-AB0O TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QJ TCGA-4V-A9QQ TCGA-4V-A9QT 
       56.65         9.96        34.52        88.83        45.07        21.70 
TCGA-4X-A9F9 TCGA-4X-A9FB TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-XM-A8RB TCGA-XM-A8RL 
       15.78        23.57        10.68        65.49        37.61        84.23 
TCGA-XU-A92W TCGA-XU-A932 TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAH 
      107.80        70.65        10.68        35.34        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       59.15        56.75        38.50        16.60        14.07        11.24 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D8 
       12.89        55.46        34.65        27.19       138.90         1.91 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ 
       49.22        36.62        32.25        29.62        23.18         2.37 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE 
       42.15       125.19        54.08        83.28        30.08         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       26.20        12.69        11.93        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-AAY0 
       35.90        90.05        45.24       149.98         4.08        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A962 
      107.44        18.67        13.32        22.78        12.79         0.20 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       18.58        16.57         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       42.81         0.23        37.48        31.50         0.30         0.46 
TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZL-A9V6 
        7.17        38.30        68.91 

$subtype3
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-4V-A9QI 
       81.80        17.75        90.61        15.35        13.48        89.23 
TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D 
       28.90        19.76        19.76        39.45        19.50        11.57 
TCGA-5U-AB0E TCGA-5U-AB0F TCGA-X7-A8DG TCGA-X7-A8M0 TCGA-X7-A8M3 TCGA-XM-A8R8 
       10.36        15.09        22.85        14.50         1.64        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X 
       48.92        97.41        50.83        12.72        13.05        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A933 TCGA-XU-A936 
      114.67       120.43        82.65        52.90        58.82        21.14 
TCGA-XU-AAXV TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-YT-A95G 
      133.81       123.68        89.46        62.17        50.53        49.78 
TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A966 TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96I 
        0.13        30.74        12.46         0.16        32.35         5.19 
TCGA-ZB-A96O TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
        1.81         8.52        28.04        26.93 

subtype1 subtype2 subtype3 
    9.96     0.20     0.13 
subtype1 subtype2 subtype3 
  107.80   149.98   133.81 
subtype1 subtype2 subtype3 
   35.34    31.50    28.47 
[1] "10.0 - 107.8 (35.3)" "0.2 - 150.0 (31.5)"  "0.1 - 133.8 (28.5)" 
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1  8  9
  subtype2 28 31
  subtype3 24 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    9
  subtype2   28   31
  subtype3   24   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       28       24
  MALE          9       31       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    14
  subtype2     7                         3    48
  subtype3     5                         1    39
D9V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        7        5
  BLACK OR AFRICAN AMERICAN        2        3        1
  WHITE                           14       48       39
[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"
D9V5, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  2 50
  subtype3  7 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    2   50
  subtype3    7   35
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        7
  NOT HISPANIC OR LATINO       13       50       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 26  2
  subtype2 31  1
  subtype3 30  3
  subtype4 27  0
subtype1 subtype2 subtype3 subtype4 
      28       32       33       27 
subtype1 subtype2 subtype3 subtype4 
       2        1        3        0 
$subtype1
TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QI TCGA-4V-A9QN 
       56.65        81.80        17.75        15.35        89.23        28.90 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FB TCGA-5U-AB0E TCGA-X7-A8DG TCGA-XM-A8R8 
       19.76        19.76        23.57        10.36        22.85        52.54 
TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 
       97.41        12.72       107.80        77.03       120.43        82.65 
TCGA-XU-A931 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A963 
       52.90       123.68        89.46        62.17        49.78        30.74 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96O TCGA-ZC-AAAH 
        0.16        32.35         1.81        16.34 

$subtype2
TCGA-3G-AB0Q TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4X-A9FA TCGA-5K-AAAP 
       59.15        88.83        56.75        38.50        12.89        34.65 
TCGA-5V-A9RR TCGA-X7-A8D8 TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M5 TCGA-XM-A8RF 
       27.19         1.91        14.50        42.15        54.08        26.20 
TCGA-XM-A8RG TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T 
       12.69        32.25        37.81       112.11        35.90        45.24 
TCGA-XU-A92V TCGA-YT-A95D TCGA-YT-A95F TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 
        4.08        18.67        22.78         0.20        18.58        16.57 
TCGA-ZB-A969 TCGA-ZB-A96C TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
        0.66        43.43        37.48        31.50         0.30         0.46 
TCGA-ZB-A96Q TCGA-ZL-A9V6 
        7.17        68.91 

$subtype3
TCGA-3G-AB19 TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QQ TCGA-4V-A9QT 
       90.61        13.48         9.96        34.52        45.07        21.70 
TCGA-4X-A9F9 TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0F TCGA-X7-A8D7 
       15.78        39.45        19.50        11.57        15.09        10.68 
TCGA-X7-A8DB TCGA-X7-A8M3 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RL 
       65.49         1.64        48.92        37.61        50.83        84.23 
TCGA-XM-AAZ1 TCGA-XU-A92Y TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXV 
       13.05       114.67        70.65        58.82        21.14       133.81 
TCGA-XU-AAXZ TCGA-ZB-A961 TCGA-ZB-A966 TCGA-ZB-A96I TCGA-ZB-A96P TCGA-ZB-A96R 
       50.53         0.13        12.46         5.19        10.68        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
        8.52        28.04        26.93 

$subtype4
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8DC 
       16.60        14.07        11.24        55.46       138.90        49.22 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M4 
       36.62        32.25        29.62        23.18         2.37       125.19 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XU-A92R TCGA-XU-A92U 
       83.28        30.08         7.69        11.93        90.05       149.98 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B 
       49.38       107.44        13.32        12.79        10.68        60.33 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZC-AAAF 
       42.81         0.23        38.30 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.20     0.13     0.23 
subtype1 subtype2 subtype3 subtype4 
  123.68   112.11   133.81   149.98 
subtype1 subtype2 subtype3 subtype4 
  41.065   29.345   26.930   32.250 
[1] "0.2 - 123.7 (41.1)" "0.2 - 112.1 (29.3)" "0.1 - 133.8 (26.9)"
[4] "0.2 - 150.0 (32.2)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1  9 19
  subtype2 14 19
  subtype3 22 11
  subtype4 15 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   19
  subtype2   14   19
  subtype3   22   11
  subtype4   15   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       14       22       15
  MALE         19       19       11       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         1    22
  subtype2     4                         1    28
  subtype3     2                         2    29
  subtype4     3                         2    22
D10V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        4        2        3
  BLACK OR AFRICAN AMERICAN        1        1        2        2
  WHITE                           22       28       29       22
[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"
D10V5, binary
          cls
clus        0  1
  subtype1  2 20
  subtype2  1 28
  subtype3  6 26
  subtype4  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   20
  subtype2    1   28
  subtype3    6   26
  subtype4    1   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        6        1
  NOT HISPANIC OR LATINO       20       28       26       24
[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"
