[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/22507339/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.mergedcluster.txt"

nPatients in clinical file=124, in cluster file=124, common to both=124
[1]  10 124
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
36 27 19 31 10 
 1  2  3  4  5 
36 27 19 31 10 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7  8 
37 23 20 10 18  8  2  6 
 1  2  3  4  5  6  8 
37 23 20 10 18  8  6 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
31 25 34 
 1  2  3 
31 25 34 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
16 23 31 20 
 1  2  3  4 
16 23 31 20 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
46 30 30 14 
 1  2  3  4 
46 30 30 14 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
48 42 20 10 
 1  2  3  4 
48 42 20 10 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
57 61  5  1 
 1  2  3 
57 61  5 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
27 18 29  7 16 27 
 1  2  3  4  5  6 
27 18 29  7 16 27 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
28 51 44  1 
 1  2  3 
28 51 44 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
27 33 36 28 
 1  2  3  4 
27 33 36 28 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 124 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	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:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 124 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, 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 32  4
  subtype2 27  0
  subtype3 17  1
  subtype4 29  2
  subtype5  8  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      36       27       18       31       10 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        0        1        2        2 
$subtype1
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 
       23.57        50.83        13.05        68.58        81.80        25.48 
TCGA-4V-A9QI TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9F9 
       96.53        31.89        51.68        25.64        25.45        21.99 
TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8M3 TCGA-X7-A8M6 
       49.41        22.59        29.62        22.85         1.64       150.41 
TCGA-X7-A8M7 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-AAZ2 TCGA-XU-A92V TCGA-XU-A92X 
       64.83        52.54        48.92        32.25         4.08        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       82.65        52.90        70.65       123.68        89.46        62.17 
TCGA-ZB-A963 TCGA-ZB-A96F TCGA-ZB-A96O TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAH 
       48.72        57.90        34.52        59.31        26.93        16.34 

$subtype2
TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K 
       12.69        35.90        25.48        26.83        71.11        45.63 
TCGA-3G-AB0Q TCGA-3Q-A9WF TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4X-A9FA 
       59.15        15.35        93.67        62.73        41.19        12.89 
TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8M5 TCGA-XM-A8RF TCGA-XM-AAZ3 TCGA-XU-A92T 
       34.65        27.19        54.08        26.20        37.81        45.24 
TCGA-YT-A95D TCGA-YT-A95H TCGA-ZB-A964 TCGA-ZB-A96A TCGA-ZB-A96D TCGA-ZB-A96H 
       24.66        23.38        42.31        77.39        64.44        49.45 
TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZL-A9V6 
        0.46        22.19        68.91 

$subtype3
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-3S-A8YW TCGA-4V-A9QX TCGA-5G-A9ZZ TCGA-5U-AB0D 
       95.67        15.09        21.14        14.27        27.45        23.47 
TCGA-X7-A8DD TCGA-X7-A8M0 TCGA-XM-A8RC TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-A936 
       36.62        14.50        97.41       120.43        58.82        21.14 
TCGA-YT-A95G TCGA-ZB-A962 TCGA-ZB-A969 TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZT-A8OM 
       49.78        54.15        34.39        54.35        50.27        45.96 

$subtype4
TCGA-3S-AAYX TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9FC TCGA-X7-A8D6 
       18.77        26.73        20.61        20.71        68.12       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DI TCGA-X7-A8DJ 
       10.68         1.91        65.49        59.11        23.18         9.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RH 
       42.15       125.19        83.28        37.61        13.87        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92Y TCGA-XU-AAXZ 
       12.72        84.23       112.11        90.05       114.67        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E TCGA-ZB-A96B TCGA-ZB-A96G TCGA-ZB-A96P 
       49.38       107.44        35.18        72.69        52.80        24.76 
TCGA-ZC-AAA7 
       28.04 

$subtype5
TCGA-3T-AA9L TCGA-X7-A8DE TCGA-XH-A853 TCGA-XU-A92U TCGA-XU-A92W TCGA-ZB-A961 
       34.52        32.25        40.11       149.98       107.80         5.92 
TCGA-ZB-A966 TCGA-ZB-A96E TCGA-ZB-A96V TCGA-ZC-AAAF 
       12.46        59.80        30.64        38.30 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.64     0.46    14.27     1.91     5.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  150.41    93.67   120.43   138.90   149.98 
subtype1 subtype2 subtype3 subtype4 subtype5 
  49.165   37.810   41.290   42.150   36.410 
[1] "1.6 - 150.4 (49.2)"  "0.5 - 93.7 (37.8)"   "14.3 - 120.4 (41.3)"
[4] "1.9 - 138.9 (42.1)"  "5.9 - 150.0 (36.4)" 
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  9 27
  subtype2  5 22
  subtype3  7 12
  subtype4  4 27
  subtype5  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   27
  subtype2    5   22
  subtype3    7   12
  subtype4    4   27
  subtype5    2    8
                      clus
vv                     subtype1 subtype2 subtype3 subtype4 subtype5
  ANTERIOR MEDIASTINUM        9        5        7        4        2
  THYMUS                     27       22       12       27        8
[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"
D1V4, binary
          cls
clus        0  1
  subtype1 15 21
  subtype2 10 17
  subtype3 15  4
  subtype4 15 16
  subtype5  4  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   21
  subtype2   10   17
  subtype3   15    4
  subtype4   15   16
  subtype5    4    6
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       15       10       15       15        4
  MALE         21       17        4       16        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"
D1V5, binary
          cls
clus        0  1
  subtype1 17 19
  subtype2 21  6
  subtype3 12  7
  subtype4 25  6
  subtype5  6  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   19
  subtype2   21    6
  subtype3   12    7
  subtype4   25    6
  subtype5    6    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        17       21       12       25        6
  YES       19        6        7        6        4
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               2                4                5               17
  subtype2               9               14                0                2
  subtype3               3                4                1                3
  subtype4               1               13                8                6
  subtype5               2                3                1                2
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                7               1
  subtype2                2               0
  subtype3                1               7
  subtype4                2               1
  subtype5                0               2
D1V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4 subtype5
  THYMOMA; TYPE A         2        9        3        1        2
  THYMOMA; TYPE AB        4       14        4       13        3
  THYMOMA; TYPE B1        5        0        1        8        1
  THYMOMA; TYPE B2       17        2        3        6        2
  THYMOMA; TYPE B3        7        2        1        2        0
  THYMOMA; TYPE C         1        0        7        1        2
[1] 6 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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         1    30
  subtype2     1                         1    25
  subtype3     2                         0    17
  subtype4     5                         3    21
  subtype5     0                         1     9
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        1        2        5        0
  BLACK OR AFRICAN AMERICAN        1        1        0        3        1
  WHITE                           30       25       17       21        9
[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"
D1V8, binary
          cls
clus        0  1
  subtype1  3 30
  subtype2  1 21
  subtype3  3 15
  subtype4  2 27
  subtype5  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   30
  subtype2    1   21
  subtype3    3   15
  subtype4    2   27
  subtype5    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        3        2        0
  NOT HISPANIC OR LATINO       30       21       15       27        7
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 37  0
  subtype2 21  2
  subtype3 15  5
  subtype4  8  2
  subtype5 17  0
  subtype6  8  0
  subtype8  6  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
      37       23       20       10       17        8        6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
       0        2        5        2        0        0        0 
$subtype1
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-3G-AB0O TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       23.57        50.83        68.58        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FC 
       96.53        93.67        51.68        26.73        21.99        68.12 
TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DG 
      138.90        10.68        65.49        59.11        36.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8M4 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 
       23.18       125.19       150.41        64.83        83.28        40.11 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-AAXW 
       37.61        13.87        11.93        84.23       107.80       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAY1 TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96R 
       89.46        62.17       107.44        34.52        24.76        59.31 
TCGA-ZC-AAAH 
       16.34 

$subtype2
TCGA-3G-AB19 TCGA-XM-A8RG TCGA-XU-A92Q TCGA-ZB-A965 TCGA-ZB-A96C TCGA-3G-AB0Q 
       95.67        12.69        35.90        26.83        71.11        59.15 
TCGA-4V-A9QL TCGA-4X-A9FA TCGA-X7-A8D8 TCGA-X7-A8M1 TCGA-XM-A8RF TCGA-XM-AAZ2 
       62.73        12.89         1.91        42.15        26.20        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-XU-A92V TCGA-ZB-A962 TCGA-ZB-A964 
       37.81       112.11        45.24         4.08        54.15        42.31 
TCGA-ZB-A969 TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZL-A9V6 
       34.39        59.80        49.45        50.27        68.91 

$subtype3
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3G-AB14 TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS 
       13.05        81.80        25.48        31.89        25.64        25.45 
TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A92Y 
       49.41        22.59         1.64        97.41        77.03       114.67 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXV TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F 
       52.90        70.65       133.81        49.78         5.92        57.90 
TCGA-ZB-A96I TCGA-ZC-AAAA 
       54.35        26.93 

$subtype4
TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A933 
       21.14        27.45        23.47       120.43        82.65        58.82 
TCGA-XU-A936 TCGA-ZB-A966 TCGA-ZB-A96V TCGA-ZC-AAA7 
       21.14        12.46        30.64        28.04 

$subtype5
TCGA-YT-A95F TCGA-ZB-A96K TCGA-4V-A9QM TCGA-4V-A9QW TCGA-4V-A9QX TCGA-5K-AAAP 
       25.48        45.63        41.19        20.71        14.27        34.65 
TCGA-5V-A9RR TCGA-X7-A8DF TCGA-XU-A92R TCGA-XU-A92U TCGA-XU-AAY0 TCGA-YT-A95D 
       27.19        29.62        90.05       149.98        49.38        24.66 
TCGA-ZB-A96A TCGA-ZB-A96D TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF 
       77.39        64.44         0.46        22.19        38.30 

$subtype6
TCGA-4V-A9QU TCGA-X7-A8DE TCGA-X7-A8DJ TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A963 
       20.61        32.25         9.50        35.18        23.38        48.72 
TCGA-ZB-A96G TCGA-ZT-A8OM 
       52.80        45.96 

$subtype8
TCGA-X7-A8M0 TCGA-X7-A8M5 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RI TCGA-XU-AAXZ 
       14.50        54.08        52.54        48.92        12.72        50.53 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
   10.68     1.91     1.64    12.46     0.46     9.50    12.72 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
  150.41   112.11   133.81   120.43   149.98    52.80    54.08 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 
  51.680   42.310   49.595   27.745   34.650   33.715   49.725 
[1] "10.7 - 150.4 (51.7)" "1.9 - 112.1 (42.3)"  "1.6 - 133.8 (49.6)" 
[4] "12.5 - 120.4 (27.7)" "0.5 - 150.0 (34.6)"  "9.5 - 52.8 (33.7)"  
[7] "12.7 - 54.1 (49.7)" 
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  6 31
  subtype2  4 19
  subtype3  7 13
  subtype4  2  8
  subtype5  3 15
  subtype6  3  5
  subtype8  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   31
  subtype2    4   19
  subtype3    7   13
  subtype4    2    8
  subtype5    3   15
  subtype6    3    5
  subtype8    1    5
                      clus
vv                     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ANTERIOR MEDIASTINUM        6        4        7        2        3        3
  THYMUS                     31       19       13        8       15        5
                      clus
vv                     subtype8
  ANTERIOR MEDIASTINUM        1
  THYMUS                      5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus        0  1
  subtype1 19 18
  subtype2  9 14
  subtype3 10 10
  subtype4  5  5
  subtype5  9  9
  subtype6  3  5
  subtype8  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   18
  subtype2    9   14
  subtype3   10   10
  subtype4    5    5
  subtype5    9    9
  subtype6    3    5
  subtype8    4    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8
  FEMALE       19        9       10        5        9        3        4
  MALE         18       14       10        5        9        5        2
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 24 13
  subtype2 18  5
  subtype3  9 11
  subtype4  3  7
  subtype5 14  4
  subtype6  6  2
  subtype8  5  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   13
  subtype2   18    5
  subtype3    9   11
  subtype4    3    7
  subtype5   14    4
  subtype6    6    2
  subtype8    5    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8
  NO        24       18        9        3       14        6        5
  YES       13        5       11        7        4        2        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               0                7               13               15
  subtype2              13                8                0                0
  subtype3               1                2                1               10
  subtype4               0                0                0                0
  subtype5               1               15                0                2
  subtype6               1                5                0                2
  subtype8               1                0                0                2
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                2               0
  subtype2                1               1
  subtype3                6               0
  subtype4                1               9
  subtype5                0               0
  subtype6                0               0
  subtype8                2               1
D2V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  THYMOMA; TYPE A         0       13        1        0        1        1
  THYMOMA; TYPE AB        7        8        2        0       15        5
  THYMOMA; TYPE B1       13        0        1        0        0        0
  THYMOMA; TYPE B2       15        0       10        0        2        2
  THYMOMA; TYPE B3        2        1        6        1        0        0
  THYMOMA; TYPE C         0        1        0        9        0        0
                  clus
vv                 subtype8
  THYMOMA; TYPE A         1
  THYMOMA; TYPE AB        0
  THYMOMA; TYPE B1        0
  THYMOMA; TYPE B2        2
  THYMOMA; TYPE B3        2
  THYMOMA; TYPE C         1
[1] 6 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         5    30
  subtype2     4                         1    18
  subtype3     2                         0    18
  subtype4     2                         0     8
  subtype5     2                         0    16
  subtype6     0                         0     7
  subtype8     1                         0     4
D2V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        4        2        2        2
  BLACK OR AFRICAN AMERICAN        5        1        0        0        0
  WHITE                           30       18       18        8       16
                           clus
vv                          subtype6 subtype8
  ASIAN                            0        1
  BLACK OR AFRICAN AMERICAN        0        0
  WHITE                            7        4
[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"
D2V8, binary
          cls
clus        0  1
  subtype1  1 32
  subtype2  0 21
  subtype3  4 14
  subtype4  2  8
  subtype5  1 14
  subtype6  1  5
  subtype8  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    0   21
  subtype3    4   14
  subtype4    2    8
  subtype5    1   14
  subtype6    1    5
  subtype8    0    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        4        2        1        1
  NOT HISPANIC OR LATINO       32       21       14        8       14        5
                        clus
vv                       subtype8
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 26  4
  subtype2 23  2
  subtype3 32  2
subtype1 subtype2 subtype3 
      30       25       34 
subtype1 subtype2 subtype3 
       4        2        2 
$subtype1
TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q TCGA-3G-AB0O TCGA-4V-A9QN 
       50.83        12.69        13.05        35.90        68.58        31.89 
TCGA-4V-A9QW TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E TCGA-X7-A8DE TCGA-X7-A8M0 
       20.71        27.45        34.65        22.59        32.25        14.50 
TCGA-X7-A8M3 TCGA-XM-A8R8 TCGA-XM-A8RI TCGA-XM-AAZ3 TCGA-XU-A92U TCGA-XU-A92X 
        1.64        52.54        12.72        37.81       149.98        77.03 
TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-YT-A95G 
      120.43        52.90        70.65        58.82        21.14        49.78 
TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A966 TCGA-ZB-A96I TCGA-ZC-AAA7 TCGA-ZC-AAAA 
        5.92        48.72        12.46        54.35        28.04        26.93 

$subtype2
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-3G-AB0Q TCGA-3S-A8YW 
       95.67        15.09        26.83        71.11        59.15        21.14 
TCGA-4V-A9QL TCGA-4V-A9QX TCGA-5V-A9RR TCGA-X7-A8M5 TCGA-XM-A8RC TCGA-XM-A8RF 
       62.73        14.27        27.19        54.08        97.41        26.20 
TCGA-XM-AAZ2 TCGA-XU-A92R TCGA-XU-A92V TCGA-XU-AAY0 TCGA-YT-A95D TCGA-YT-A95H 
       32.25        90.05         4.08        49.38        24.66        23.38 
TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96D TCGA-ZB-A96Q TCGA-ZC-AAAF 
       54.15        42.31        34.39        64.44        22.19        38.30 
TCGA-ZL-A9V6 
       68.91 

$subtype3
TCGA-4X-A9FB TCGA-YT-A95F TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX 
       23.57        25.48        81.80        25.48        15.35        18.77 
TCGA-4V-A9QS TCGA-4X-A9F9 TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB 
       25.45        21.99        68.12       138.90        10.68        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       59.11        36.62        29.62        22.85        23.18         9.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-XM-A8RB TCGA-XM-A8RE 
       42.15       125.19       150.41        64.83        37.61        13.87 
TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-AAY1 TCGA-YT-A95E TCGA-ZB-A96A TCGA-ZB-A96B 
       11.93        84.23       107.44        35.18        77.39        72.69 
TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAH 
       24.76        59.31        30.64        16.34 

subtype1 subtype2 subtype3 
    1.64     4.08     9.50 
subtype1 subtype2 subtype3 
  149.98    97.41   150.41 
subtype1 subtype2 subtype3 
   33.45    38.30    32.91 
[1] "1.6 - 150.0 (33.5)" "4.1 - 97.4 (38.3)"  "9.5 - 150.4 (32.9)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  6 25
  subtype2  8 17
  subtype3  8 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   25
  subtype2    8   17
  subtype3    8   26
                      clus
vv                     subtype1 subtype2 subtype3
  ANTERIOR MEDIASTINUM        6        8        8
  THYMUS                     25       17       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus        0  1
  subtype1 14 17
  subtype2 15 10
  subtype3 14 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   17
  subtype2   15   10
  subtype3   14   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       15       14
  MALE         17       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"
D3V5, binary
          cls
clus        0  1
  subtype1 19 12
  subtype2 17  8
  subtype3 26  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   12
  subtype2   17    8
  subtype3   26    8
     clus
vv    subtype1 subtype2 subtype3
  NO        19       17       26
  YES       12        8        8
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               4                5                1               10
  subtype2               7               14                0                1
  subtype3               0                9               11               13
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                4               7
  subtype2                1               2
  subtype3                0               1
D3V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  THYMOMA; TYPE A         4        7        0
  THYMOMA; TYPE AB        5       14        9
  THYMOMA; TYPE B1        1        0       11
  THYMOMA; TYPE B2       10        1       13
  THYMOMA; TYPE B3        4        1        0
  THYMOMA; TYPE C         7        2        1
[1] 6 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    24
  subtype2     3                         1    21
  subtype3     2                         3    28
D3V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        3        2
  BLACK OR AFRICAN AMERICAN        0        1        3
  WHITE                           24       21       28
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2  2 20
  subtype3  2 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2    2   20
  subtype3    2   29
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO       23       20       29
[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 15  1
  subtype2 20  2
  subtype3 30  1
  subtype4 16  4
subtype1 subtype2 subtype3 subtype4 
      16       22       31       20 
subtype1 subtype2 subtype3 subtype4 
       1        2        1        4 
$subtype1
TCGA-5U-AB0F TCGA-3G-AB0O TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QW TCGA-4V-A9QX 
       15.09        68.58        25.48        15.35        20.71        14.27 
TCGA-X7-A8DD TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E 
       36.62        97.41        13.87        49.38       107.44        35.18 
TCGA-ZB-A963 TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZC-AAAH 
       48.72        22.19        38.30        16.34 

$subtype2
TCGA-3G-AB19 TCGA-XM-A8RG TCGA-XU-A92Q TCGA-ZB-A965 TCGA-ZB-A96C TCGA-3G-AB0Q 
       95.67        12.69        35.90        26.83        71.11        59.15 
TCGA-4V-A9QL TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8DE TCGA-X7-A8M0 TCGA-X7-A8M5 
       62.73        34.65        27.19        32.25        14.50        54.08 
TCGA-XM-A8RF TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92R TCGA-XU-A92V TCGA-YT-A95D 
       26.20        32.25        37.81        90.05         4.08        24.66 
TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZL-A9V6 
       54.15        42.31        34.39        68.91 

$subtype3
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-YT-A95F TCGA-3G-AB0T TCGA-3S-AAYX TCGA-4V-A9QS 
       23.57        50.83        25.48        81.80        18.77        25.45 
TCGA-4X-A9F9 TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DC 
       21.99        68.12       138.90        10.68        65.49        59.11 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 
       29.62        22.85        23.18         9.50        42.15       125.19 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-XM-A8RB TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-A92U 
      150.41        64.83        37.61        11.93        84.23       149.98 
TCGA-XU-A932 TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96P 
       70.65        23.38        77.39        72.69        64.44        24.76 
TCGA-ZB-A96R 
       59.31 

$subtype4
TCGA-XM-AAZ1 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-X7-A8M3 
       13.05        21.14        31.89        27.45        22.59         1.64 
TCGA-XM-A8R8 TCGA-XM-A8RI TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A933 
       52.54        12.72        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         5.92        12.46        54.35        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

subtype1 subtype2 subtype3 subtype4 
   13.87     4.08     9.50     1.64 
subtype1 subtype2 subtype3 subtype4 
  107.44    95.67   150.41   120.43 
subtype1 subtype2 subtype3 subtype4 
  30.330   35.275   50.830   27.745 
[1] "13.9 - 107.4 (30.3)" "4.1 - 95.7 (35.3)"   "9.5 - 150.4 (50.8)" 
[4] "1.6 - 120.4 (27.7)" 
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  5 11
  subtype2  5 18
  subtype3  7 24
  subtype4  5 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   11
  subtype2    5   18
  subtype3    7   24
  subtype4    5   15
                      clus
vv                     subtype1 subtype2 subtype3 subtype4
  ANTERIOR MEDIASTINUM        5        5        7        5
  THYMUS                     11       18       24       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"
D4V4, binary
          cls
clus        0  1
  subtype1  7  9
  subtype2 13 10
  subtype3 13 18
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2   13   10
  subtype3   13   18
  subtype4   10   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       13       13       10
  MALE          9       10       18       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"
D4V5, binary
          cls
clus        0  1
  subtype1 13  3
  subtype2 19  4
  subtype3 21 10
  subtype4  9 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    3
  subtype2   19    4
  subtype3   21   10
  subtype4    9   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        13       19       21        9
  YES        3        4       10       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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               0                9                2                5
  subtype2              10                9                0                2
  subtype3               0                9               10               12
  subtype4               1                1                0                5
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                0               0
  subtype2                1               1
  subtype3                0               0
  subtype4                4               9
D4V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  THYMOMA; TYPE A         0       10        0        1
  THYMOMA; TYPE AB        9        9        9        1
  THYMOMA; TYPE B1        2        0       10        0
  THYMOMA; TYPE B2        5        2       12        5
  THYMOMA; TYPE B3        0        1        0        4
  THYMOMA; TYPE C         0        1        0        9
[1] 6 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    26
  subtype4     4                         0    15
D4V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        3        2        4
  BLACK OR AFRICAN AMERICAN        1        1        2        0
  WHITE                           13       19       26       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"
D4V8, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  1 20
  subtype3  2 26
  subtype4  4 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    1   20
  subtype3    2   26
  subtype4    4   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        2        4
  NOT HISPANIC OR LATINO       13       20       26       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  5
  subtype2 30  0
  subtype3 27  2
  subtype4 12  2
subtype1 subtype2 subtype3 subtype4 
      46       30       29       14 
subtype1 subtype2 subtype3 subtype4 
       5        0        2        2 
$subtype1
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 
       23.57        50.83        13.05        68.58        81.80        25.48 
TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QR 
       15.35        18.77        34.52        96.53        93.67        25.64 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8D7 
       25.45        26.73        21.99        49.41        22.59        10.68 
TCGA-X7-A8DB TCGA-X7-A8DG TCGA-X7-A8M3 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-XM-A8RB 
       65.49        22.85         1.64       150.41        64.83        37.61 
TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       97.41        12.72        84.23       107.80        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXV TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65       133.81       123.68        89.46 
TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96O 
       62.17        49.78         5.92        57.90        54.35        34.52 
TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAH 
       24.76        59.31        26.93        16.34 

$subtype2
TCGA-5U-AB0F TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       15.09        59.15        62.73        20.61        20.71        14.27 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8DD 
       12.89        68.12        34.65        27.19       138.90        36.62 
TCGA-X7-A8DF TCGA-X7-A8DJ TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE 
       29.62         9.50       125.19        83.28        40.11        13.87 
TCGA-XM-A8RH TCGA-XU-A92O TCGA-XU-A92U TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E 
       11.93       112.11       149.98        49.38       107.44        35.18 
TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96G TCGA-ZC-AAAF TCGA-ZT-A8OM 
       23.38        77.39        72.69        52.80        38.30        45.96 

$subtype3
TCGA-3G-AB19 TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C 
       95.67        12.69        35.90        25.48        26.83        71.11 
TCGA-ZB-A96K TCGA-4V-A9QM TCGA-X7-A8D8 TCGA-X7-A8DE TCGA-X7-A8M1 TCGA-XM-A8RF 
       45.63        41.19         1.91        32.25        42.15        26.20 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92T TCGA-XU-A92V TCGA-XU-A92Z TCGA-YT-A95D 
       32.25        37.81        45.24         4.08       120.43        24.66 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96D TCGA-ZB-A96E 
       54.15        48.72        42.31        34.39        64.44        59.80 
TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZL-A9V6 
       49.45        50.27         0.46        22.19        68.91 

$subtype4
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8M0 TCGA-X7-A8M5 
       21.14        31.89        27.45        23.47        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 
       30.64        28.04 

subtype1 subtype2 subtype3 subtype4 
    1.64     9.50     0.46    12.46 
subtype1 subtype2 subtype3 subtype4 
  150.41   149.98   120.43    58.82 
subtype1 subtype2 subtype3 subtype4 
  50.305   39.205   41.190   29.340 
[1] "1.6 - 150.4 (50.3)" "9.5 - 150.0 (39.2)" "0.5 - 120.4 (41.2)"
[4] "12.5 - 58.8 (29.3)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 12 34
  subtype2  6 24
  subtype3  6 24
  subtype4  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   34
  subtype2    6   24
  subtype3    6   24
  subtype4    3   11
                      clus
vv                     subtype1 subtype2 subtype3 subtype4
  ANTERIOR MEDIASTINUM       12        6        6        3
  THYMUS                     34       24       24       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"
D5V4, binary
          cls
clus        0  1
  subtype1 20 26
  subtype2 13 17
  subtype3 14 16
  subtype4 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   26
  subtype2   13   17
  subtype3   14   16
  subtype4   10    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       13       14       10
  MALE         26       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"
D5V5, binary
          cls
clus        0  1
  subtype1 24 22
  subtype2 25  5
  subtype3 22  8
  subtype4  7  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   22
  subtype2   25    5
  subtype3   22    8
  subtype4    7    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        24       25       22        7
  YES       22        5        8        7
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               1                3               12               23
  subtype2               5               16                3                6
  subtype3              10               16                0                1
  subtype4               1                0                0                1
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                7               0
  subtype2                0               0
  subtype3                1               2
  subtype4                3               9
D5V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  THYMOMA; TYPE A         1        5       10        1
  THYMOMA; TYPE AB        3       16       16        0
  THYMOMA; TYPE B1       12        3        0        0
  THYMOMA; TYPE B2       23        6        1        1
  THYMOMA; TYPE B3        7        0        1        3
  THYMOMA; TYPE C         0        0        2        9
[1] 6 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     3                         2    24
  subtype3     4                         1    25
  subtype4     2                         0    12
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        3        4        2
  BLACK OR AFRICAN AMERICAN        3        2        1        0
  WHITE                           39       24       25       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"
D5V8, binary
          cls
clus        0  1
  subtype1  4 35
  subtype2  3 24
  subtype3  0 26
  subtype4  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   35
  subtype2    3   24
  subtype3    0   26
  subtype4    3   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        3        0        3
  NOT HISPANIC OR LATINO       35       24       26       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  5
  subtype2 40  1
  subtype3 19  1
  subtype4  8  2
subtype1 subtype2 subtype3 subtype4 
      48       41       20       10 
subtype1 subtype2 subtype3 subtype4 
       5        1        1        2 
$subtype1
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 
       23.57        50.83        13.05        68.58        81.80        25.48 
TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QN 
       15.35        18.77        34.52        96.53        93.67        31.89 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FD TCGA-5U-AB0E 
       25.64        25.45        26.73        21.99        49.41        22.59 
TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DG TCGA-X7-A8M3 TCGA-X7-A8M6 TCGA-X7-A8M7 
       10.68        65.49        22.85         1.64       150.41        64.83 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-A92X 
       37.61        97.41        12.72        84.23       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXV TCGA-XU-AAXW 
      114.67        82.65        52.90        70.65       133.81       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F 
       89.46        62.17        50.53        49.78         5.92        57.90 
TCGA-ZB-A96I TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAH 
       54.35        34.52        24.76        59.31        26.93        16.34 

$subtype2
TCGA-5U-AB0F TCGA-YT-A95F TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0Q TCGA-4V-A9QL 
       15.09        25.48        71.11        45.63        59.15        62.73 
TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FA TCGA-4X-A9FC 
       41.19        20.61        20.71        14.27        12.89        68.12 
TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D8 TCGA-X7-A8DD TCGA-X7-A8DF 
       34.65        27.19       138.90         1.91        36.62        29.62 
TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE 
        9.50        42.15       125.19        83.28        40.11        13.87 
TCGA-XM-A8RH TCGA-XM-AAZ2 TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-AAY0 TCGA-XU-AAY1 
       11.93        32.25       149.98         4.08        49.38       107.44 
TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       24.66        35.18        23.38        77.39        72.69        64.44 
TCGA-ZB-A96G TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZT-A8OM 
       52.80         0.46        22.19        38.30        45.96 

$subtype3
TCGA-3G-AB19 TCGA-XM-A8RG TCGA-XU-A92Q TCGA-ZB-A965 TCGA-X7-A8DE TCGA-X7-A8M0 
       95.67        12.69        35.90        26.83        32.25        14.50 
TCGA-X7-A8M5 TCGA-XM-A8R9 TCGA-XM-A8RF TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T 
       54.08        48.92        26.20        37.81       112.11        45.24 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96E TCGA-ZB-A96H 
       54.15        48.72        42.31        34.39        59.80        49.45 
TCGA-ZB-A96L TCGA-ZL-A9V6 
       50.27        68.91 

$subtype4
TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XM-A8R8 TCGA-XU-A92Z TCGA-XU-A933 
       21.14        27.45        23.47        52.54       120.43        58.82 
TCGA-XU-A936 TCGA-ZB-A966 TCGA-ZB-A96V TCGA-ZC-AAA7 
       21.14        12.46        30.64        28.04 

subtype1 subtype2 subtype3 subtype4 
    1.64     0.46    12.69    12.46 
subtype1 subtype2 subtype3 subtype4 
  150.41   149.98   112.11   120.43 
subtype1 subtype2 subtype3 subtype4 
  50.155   36.620   46.980   27.745 
[1] "1.6 - 150.4 (50.2)"  "0.5 - 150.0 (36.6)"  "12.7 - 112.1 (47.0)"
[4] "12.5 - 120.4 (27.7)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 12 36
  subtype2  9 33
  subtype3  4 16
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   36
  subtype2    9   33
  subtype3    4   16
  subtype4    2    8
                      clus
vv                     subtype1 subtype2 subtype3 subtype4
  ANTERIOR MEDIASTINUM       12        9        4        2
  THYMUS                     36       33       16        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"
D6V4, binary
          cls
clus        0  1
  subtype1 21 27
  subtype2 20 22
  subtype3 10 10
  subtype4  6  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   27
  subtype2   20   22
  subtype3   10   10
  subtype4    6    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       21       20       10        6
  MALE         27       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"
D6V5, binary
          cls
clus        0  1
  subtype1 24 24
  subtype2 35  7
  subtype3 15  5
  subtype4  4  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   24
  subtype2   35    7
  subtype3   15    5
  subtype4    4    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        24       35       15        4
  YES       24        7        5        6
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               1                3               12               23
  subtype2               5               28                3                6
  subtype3              11                4                0                2
  subtype4               0                0                0                0
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                9               0
  subtype2                0               0
  subtype3                2               1
  subtype4                0              10
D6V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  THYMOMA; TYPE A         1        5       11        0
  THYMOMA; TYPE AB        3       28        4        0
  THYMOMA; TYPE B1       12        3        0        0
  THYMOMA; TYPE B2       23        6        2        0
  THYMOMA; TYPE B3        9        0        2        0
  THYMOMA; TYPE C         0        0        1       10
[1] 6 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    41
  subtype2     4                         3    34
  subtype3     2                         0    18
  subtype4     3                         0     7
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        4        2        3
  BLACK OR AFRICAN AMERICAN        3        3        0        0
  WHITE                           41       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"
D6V8, binary
          cls
clus        0  1
  subtype1  5 36
  subtype2  3 34
  subtype3  0 18
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   36
  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       36       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 51  6
  subtype2 59  1
  subtype3  3  2
subtype1 subtype2 subtype3 
      57       60        5 
subtype1 subtype2 subtype3 
       6        1        2 
$subtype1
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0O 
       95.67        23.57        15.09        50.83        13.05        68.58 
TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       25.48        15.35        21.14        18.77        34.52        96.53 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FD 
       31.89        51.68        25.64        26.73        21.99        49.41 
TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DG 
       27.45        23.47        22.59        10.68        65.49        22.85 
TCGA-X7-A8M3 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
        1.64       150.41        64.83        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       97.41        12.72        84.23       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXV TCGA-XU-AAXW 
      120.43        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         5.92        48.72 
TCGA-ZB-A966 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96O TCGA-ZB-A96R TCGA-ZB-A96V 
       12.46        57.90        54.35        34.52        59.31        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAH 
       28.04        26.93        16.34 

$subtype2
TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K 
       12.69        35.90        25.48        26.83        71.11        45.63 
TCGA-3G-AB0Q TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW 
       59.15        93.67        62.73        41.19        20.61        20.71 
TCGA-4V-A9QX TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 
       14.27        12.89        68.12        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        59.11        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 
        9.50        14.50        42.15       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       40.11        13.87        26.20        11.93        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-AAY0 
      112.11        90.05        45.24       149.98         4.08        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A964 
      107.44        24.66        35.18        23.38        54.15        42.31 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96H 
       34.39        77.39        72.69        64.44        59.80        49.45 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       50.27         0.46        22.19        38.30        68.91        45.96 

$subtype3
TCGA-3G-AB0T TCGA-4V-A9QS TCGA-XU-A930 TCGA-XU-A931 TCGA-ZB-A96G 
       81.80        25.45        82.65        52.90        52.80 

subtype1 subtype2 subtype3 
    1.64     0.46    25.45 
subtype1 subtype2 subtype3 
  150.41   149.98    82.65 
subtype1 subtype2 subtype3 
  48.720   39.205   52.900 
[1] "1.6 - 150.4 (48.7)" "0.5 - 150.0 (39.2)" "25.4 - 82.7 (52.9)"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 15 42
  subtype2 11 50
  subtype3  1  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   42
  subtype2   11   50
  subtype3    1    4
                      clus
vv                     subtype1 subtype2 subtype3
  ANTERIOR MEDIASTINUM       15       11        1
  THYMUS                     42       50        4
[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"
D7V4, binary
          cls
clus        0  1
  subtype1 29 28
  subtype2 29 32
  subtype3  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   28
  subtype2   29   32
  subtype3    2    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       29        2
  MALE         28       32        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 29 28
  subtype2 51 10
  subtype3  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   28
  subtype2   51   10
  subtype3    0    5
     clus
vv    subtype1 subtype2 subtype3
  NO        29       51        0
  YES       28       10        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               3                5               10               22
  subtype2              14               32                3                8
  subtype3               0                1                1                1
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                7              10
  subtype2                3               1
  subtype3                2               0
D7V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  THYMOMA; TYPE A         3       14        0
  THYMOMA; TYPE AB        5       32        1
  THYMOMA; TYPE B1       10        3        1
  THYMOMA; TYPE B2       22        8        1
  THYMOMA; TYPE B3        7        3        2
  THYMOMA; TYPE C        10        1        0
[1] 6 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                         3    47
  subtype2     7                         3    50
  subtype3     0                         0     5
D7V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        7        0
  BLACK OR AFRICAN AMERICAN        3        3        0
  WHITE                           47       50        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"
D7V8, binary
          cls
clus        0  1
  subtype1  8 43
  subtype2  2 52
  subtype3  0  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   43
  subtype2    2   52
  subtype3    0    4
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        2        0
  NOT HISPANIC OR LATINO       43       52        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 24  3
  subtype2 16  1
  subtype3 26  3
  subtype4  5  2
  subtype5 16  0
  subtype6 27  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      27       17       29        7       16       27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        1        3        2        0        0 
$subtype1
TCGA-4X-A9FB TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QI 
       23.57        68.58        81.80        25.48        15.35        96.53 
TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-X7-A8DG TCGA-X7-A8M7 TCGA-XM-A8RC 
       31.89        25.64        25.45        22.85        64.83        97.41 
TCGA-XM-A8RI TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
       12.72       107.80        77.03       120.43        82.65        52.90 
TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A963 TCGA-ZB-A96F 
      123.68        89.46        62.17        49.78        48.72        57.90 
TCGA-ZB-A96G TCGA-ZB-A96O TCGA-ZC-AAAH 
       52.80        34.52        16.34 

$subtype2
TCGA-YT-A95F TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QM 
       25.48        71.11        45.63        59.15        62.73        41.19 
TCGA-4X-A9FA TCGA-5K-AAAP TCGA-X7-A8D8 TCGA-X7-A8M1 TCGA-XM-AAZ2 TCGA-XU-A92U 
       12.89        34.65         1.91        42.15        32.25       149.98 
TCGA-XU-A92V TCGA-YT-A95D TCGA-ZB-A96D TCGA-ZB-A96M TCGA-ZB-A96Q 
        4.08        24.66        64.44         0.46        22.19 

$subtype3
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3S-AAYX TCGA-3T-AA9L 
       95.67        15.09        50.83        13.05        18.77        34.52 
TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E 
       51.68        26.73        21.99        49.41        27.45        22.59 
TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8M3 TCGA-X7-A8M6 TCGA-XM-A8R9 TCGA-XM-A8RB 
       10.68        65.49         1.64       150.41        48.92        37.61 
TCGA-XM-A8RL TCGA-XU-A92Y TCGA-XU-A932 TCGA-XU-A936 TCGA-XU-AAXV TCGA-XU-AAXZ 
       84.23       114.67        70.65        21.14       133.81        50.53 
TCGA-ZB-A961 TCGA-ZB-A96I TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAA 
        5.92        54.35        24.76        59.31        26.93 

$subtype4
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XM-A8R8 TCGA-XU-A933 TCGA-ZB-A966 TCGA-ZB-A96V 
       21.14        23.47        52.54        58.82        12.46        30.64 
TCGA-ZC-AAA7 
       28.04 

$subtype5
TCGA-XM-A8RG TCGA-XU-A92Q TCGA-ZB-A965 TCGA-4V-A9QJ TCGA-X7-A8M0 TCGA-X7-A8M5 
       12.69        35.90        26.83        93.67        14.50        54.08 
TCGA-XM-A8RF TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-ZB-A962 TCGA-ZB-A964 
       26.20        37.81       112.11        45.24        54.15        42.31 
TCGA-ZB-A969 TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZL-A9V6 
       34.39        49.45        50.27        68.91 

$subtype6
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FC TCGA-5V-A9RR TCGA-X7-A8D6 
       20.61        20.71        14.27        68.12        27.19       138.90 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ 
       59.11        36.62        32.25        29.62        23.18         9.50 
TCGA-X7-A8M4 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XU-A92R 
      125.19        83.28        40.11        13.87        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        35.18        23.38        77.39        72.69 
TCGA-ZB-A96E TCGA-ZC-AAAF TCGA-ZT-A8OM 
       59.80        38.30        45.96 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   12.72     0.46     1.64    12.46    12.69     9.50 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  123.68   149.98   150.41    58.82   112.11   138.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  52.900   34.650   37.610   28.040   43.775   38.300 
[1] "12.7 - 123.7 (52.9)" "0.5 - 150.0 (34.6)"  "1.6 - 150.4 (37.6)" 
[4] "12.5 - 58.8 (28.0)"  "12.7 - 112.1 (43.8)" "9.5 - 138.9 (38.3)" 
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2  3 15
  subtype3 11 18
  subtype4  1  6
  subtype5  3 13
  subtype6  5 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2    3   15
  subtype3   11   18
  subtype4    1    6
  subtype5    3   13
  subtype6    5   22
                      clus
vv                     subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ANTERIOR MEDIASTINUM        4        3       11        1        3        5
  THYMUS                     23       15       18        6       13       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"
D8V4, binary
          cls
clus        0  1
  subtype1  8 19
  subtype2  8 10
  subtype3 19 10
  subtype4  4  3
  subtype5  7  9
  subtype6 14 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   19
  subtype2    8   10
  subtype3   19   10
  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         19       10       10        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"
D8V5, binary
          cls
clus        0  1
  subtype1 12 15
  subtype2 14  4
  subtype3 15 14
  subtype4  3  4
  subtype5 12  4
  subtype6 25  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   15
  subtype2   14    4
  subtype3   15   14
  subtype4    3    4
  subtype5   12    4
  subtype6   25    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        12       14       15        3       12       25
  YES       15        4       14        4        4        2
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               0                4                3               15
  subtype2               4               13                0                1
  subtype3               3                2                9                8
  subtype4               0                0                0                0
  subtype5               8                3                0                1
  subtype6               2               16                3                6
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                4               1
  subtype2                0               0
  subtype3                5               2
  subtype4                0               7
  subtype5                3               1
  subtype6                0               0
D8V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  THYMOMA; TYPE A         0        4        3        0        8        2
  THYMOMA; TYPE AB        4       13        2        0        3       16
  THYMOMA; TYPE B1        3        0        9        0        0        3
  THYMOMA; TYPE B2       15        1        8        0        1        6
  THYMOMA; TYPE B3        4        0        5        0        3        0
  THYMOMA; TYPE C         1        0        2        7        1        0
[1] 6 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    22
  subtype2     2                         1    15
  subtype3     1                         2    26
  subtype4     2                         0     5
  subtype5     2                         0    14
  subtype6     3                         2    21
D8V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        1        2        2
  BLACK OR AFRICAN AMERICAN        1        1        2        0        0
  WHITE                           22       15       26        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"
D8V8, binary
          cls
clus        0  1
  subtype1  1 20
  subtype2  1 14
  subtype3  5 23
  subtype4  2  5
  subtype5  0 14
  subtype6  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   20
  subtype2    1   14
  subtype3    5   23
  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       20       14       23        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 28  0
  subtype2 49  1
  subtype3 36  8
subtype1 subtype2 subtype3 
      28       50       44 
subtype1 subtype2 subtype3 
       0        1        8 
$subtype1
TCGA-4X-A9FB TCGA-3G-AB0O TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       23.57        68.58        15.35        18.77        34.52        96.53 
TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8D7 
       51.68        26.73        21.99        68.12       138.90        10.68 
TCGA-X7-A8DB TCGA-X7-A8DD TCGA-X7-A8DG TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XM-A8RB 
       65.49        36.62        22.85        64.83        83.28        37.61 
TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XU-A92W TCGA-XU-AAY1 TCGA-ZB-A96B 
       13.87        11.93        84.23       107.80       107.44        72.69 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZC-AAAH 
       34.52        24.76        59.31        16.34 

$subtype2
TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K 
       12.69        35.90        25.48        26.83        71.11        45.63 
TCGA-3G-AB0Q TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       59.15        62.73        41.19        20.61        20.71        14.27 
TCGA-4X-A9FA TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D8 TCGA-X7-A8DC TCGA-X7-A8DE 
       12.89        34.65        27.19         1.91        59.11        32.25 
TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 
       29.62        23.18         9.50        42.15       125.19        54.08 
TCGA-XH-A853 TCGA-XM-A8RF TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       40.11        26.20        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-AAY0 TCGA-YT-A95D TCGA-YT-A95E 
       45.24       149.98         4.08        49.38        24.66        35.18 
TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96D 
       23.38        54.15        42.31        34.39        77.39        64.44 
TCGA-ZB-A96E TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF 
       59.80        49.45        50.27         0.46        22.19        38.30 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

$subtype3
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3G-AB14 
       95.67        15.09        50.83        13.05        81.80        25.48 
TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5G-A9ZZ 
       21.14        93.67        31.89        25.64        49.41        27.45 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-X7-A8M3 TCGA-X7-A8M6 TCGA-XM-A8R8 
       23.47        22.59        14.50         1.64       150.41        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
       48.92        97.41        12.72        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXV 
       82.65        52.90        70.65        58.82        21.14       133.81 
TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-YT-A95G TCGA-ZB-A961 
      123.68        89.46        62.17        50.53        49.78         5.92 
TCGA-ZB-A963 TCGA-ZB-A966 TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96I TCGA-ZB-A96V 
       48.72        12.46        57.90        52.80        54.35        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

subtype1 subtype2 subtype3 
   10.68     0.46     1.64 
subtype1 subtype2 subtype3 
  138.90   149.98   150.41 
subtype1 subtype2 subtype3 
  37.115   38.055   50.155 
[1] "10.7 - 138.9 (37.1)" "0.5 - 150.0 (38.1)"  "1.6 - 150.4 (50.2)" 
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1  5 23
  subtype2 11 40
  subtype3 11 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   23
  subtype2   11   40
  subtype3   11   33
                      clus
vv                     subtype1 subtype2 subtype3
  ANTERIOR MEDIASTINUM        5       11       11
  THYMUS                     23       40       33
[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"
D9V4, binary
          cls
clus        0  1
  subtype1 15 13
  subtype2 22 29
  subtype3 22 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   13
  subtype2   22   29
  subtype3   22   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       22       22
  MALE         13       29       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"
D9V5, binary
          cls
clus        0  1
  subtype1 20  8
  subtype2 42  9
  subtype3 19 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    8
  subtype2   42    9
  subtype3   19   25
     clus
vv    subtype1 subtype2 subtype3
  NO        20       42       19
  YES        8        9       25
[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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               0                4               14                9
  subtype2              14               29                0                5
  subtype3               3                5                1               16
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                1               0
  subtype2                2               1
  subtype3                9              10
D9V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  THYMOMA; TYPE A         0       14        3
  THYMOMA; TYPE AB        4       29        5
  THYMOMA; TYPE B1       14        0        1
  THYMOMA; TYPE B2        9        5       16
  THYMOMA; TYPE B3        1        2        9
  THYMOMA; TYPE C         0        1       10
[1] 6 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                         4    23
  subtype2     6                         2    42
  subtype3     6                         0    37
D9V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        6        6
  BLACK OR AFRICAN AMERICAN        4        2        0
  WHITE                           23       42       37
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1  1 24
  subtype2  2 42
  subtype3  7 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   24
  subtype2    2   42
  subtype3    7   33
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        7
  NOT HISPANIC OR LATINO       24       42       33
[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 24  3
  subtype2 31  1
  subtype3 31  5
  subtype4 28  0
subtype1 subtype2 subtype3 subtype4 
      27       32       36       28 
subtype1 subtype2 subtype3 subtype4 
       3        1        5        0 
$subtype1
TCGA-4X-A9FB TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-4V-A9QI 
       23.57        68.58        81.80        25.48        15.35        96.53 
TCGA-4V-A9QN TCGA-4V-A9QS TCGA-X7-A8DG TCGA-X7-A8M7 TCGA-XM-A8R8 TCGA-XM-A8RC 
       31.89        25.45        22.85        64.83        52.54        97.41 
TCGA-XM-A8RI TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
       12.72       107.80        77.03       120.43        82.65        52.90 
TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-YT-A95G TCGA-ZB-A963 TCGA-ZB-A96F 
      123.68        89.46        62.17        49.78        48.72        57.90 
TCGA-ZB-A96G TCGA-ZB-A96O TCGA-ZC-AAAH 
       52.80        34.52        16.34 

$subtype2
TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K 
       12.69        35.90        25.48        26.83        71.11        45.63 
TCGA-3G-AB0Q TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4X-A9FA TCGA-5K-AAAP 
       59.15        93.67        62.73        41.19        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-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-XU-A92V TCGA-YT-A95D 
       32.25        37.81       112.11        45.24         4.08        24.66 
TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M 
       54.15        42.31        34.39        49.45        50.27         0.46 
TCGA-ZB-A96Q TCGA-ZL-A9V6 
       22.19        68.91 

$subtype3
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3S-A8YW TCGA-3S-AAYX 
       95.67        15.09        50.83        13.05        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FD 
       34.52        51.68        25.64        26.73        21.99        49.41 
TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8M3 
       27.45        23.47        22.59        10.68        65.49         1.64 
TCGA-X7-A8M6 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RL TCGA-XU-A92Y TCGA-XU-A932 
      150.41        48.92        37.61        84.23       114.67        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXV TCGA-XU-AAXZ TCGA-ZB-A961 TCGA-ZB-A966 
       58.82        21.14       133.81        50.53         5.92        12.46 
TCGA-ZB-A96I TCGA-ZB-A96P TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       54.35        24.76        59.31        30.64        28.04        26.93 

$subtype4
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9FC TCGA-X7-A8D6 TCGA-X7-A8DC 
       20.61        20.71        14.27        68.12       138.90        59.11 
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         9.50       125.19 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XU-A92R TCGA-XU-A92U 
       83.28        40.11        13.87        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        35.18        23.38        77.39        72.69 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZC-AAAF TCGA-ZT-A8OM 
       64.44        59.80        38.30        45.96 

subtype1 subtype2 subtype3 subtype4 
   12.72     0.46     1.64     9.50 
subtype1 subtype2 subtype3 subtype4 
  123.68   112.11   150.41   149.98 
subtype1 subtype2 subtype3 subtype4 
  52.900   36.855   29.340   43.035 
[1] "12.7 - 123.7 (52.9)" "0.5 - 112.1 (36.9)"  "1.6 - 150.4 (29.3)" 
[4] "9.5 - 150.0 (43.0)" 
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2  6 27
  subtype3 12 24
  subtype4  5 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2    6   27
  subtype3   12   24
  subtype4    5   23
                      clus
vv                     subtype1 subtype2 subtype3 subtype4
  ANTERIOR MEDIASTINUM        4        6       12        5
  THYMUS                     23       27       24       23
[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"
D10V4, binary
          cls
clus        0  1
  subtype1  8 19
  subtype2 14 19
  subtype3 23 13
  subtype4 15 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   19
  subtype2   14   19
  subtype3   23   13
  subtype4   15   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       14       23       15
  MALE         19       19       13       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"
D10V5, binary
          cls
clus        0  1
  subtype1 13 14
  subtype2 27  6
  subtype3 17 19
  subtype4 24  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   14
  subtype2   27    6
  subtype3   17   19
  subtype4   24    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        13       27       17       24
  YES       14        6       19        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       THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2
  subtype1               0                4                3               15
  subtype2              12               16                0                1
  subtype3               3                2                9                8
  subtype4               2               16                3                7
          vv
clus       THYMOMA; TYPE B3 THYMOMA; TYPE C
  subtype1                3               2
  subtype2                3               1
  subtype3                6               8
  subtype4                0               0
D10V6, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  THYMOMA; TYPE A         0       12        3        2
  THYMOMA; TYPE AB        4       16        2       16
  THYMOMA; TYPE B1        3        0        9        3
  THYMOMA; TYPE B2       15        1        8        7
  THYMOMA; TYPE B3        3        3        6        0
  THYMOMA; TYPE C         2        1        8        0
[1] 6 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    21
  subtype2     4                         1    28
  subtype3     2                         2    32
  subtype4     3                         2    22
D10V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        4        2        3
  BLACK OR AFRICAN AMERICAN        1        1        2        2
  WHITE                           21       28       32       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"
D10V8, binary
          cls
clus        0  1
  subtype1  1 20
  subtype2  1 28
  subtype3  7 28
  subtype4  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   20
  subtype2    1   28
  subtype3    7   28
  subtype4    1   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        7        1
  NOT HISPANIC OR LATINO       20       28       28       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"
