[1] "ofn"        "-oTPCPG-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/PCPG-TP/22506925/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.mergedcluster.txt"

nPatients in clinical file=179, in cluster file=179, common to both=179
[1]  10 179
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
37 40 10 50 25 
 1  2  3  4  5 
37 40 10 50 25 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
45 84 50 
 1  2  3 
45 84 50 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
17 21 23 18 
 1  2  3  4 
17 21 23 18 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
33 18 28 
 1  2  3 
33 18 28 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
38 70 50 21 
 1  2  3  4 
38 70 50 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
39 71 48 21 
 1  2  3  4 
39 71 48 21 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
72 44 63 
 1  2  3 
72 44 63 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
77 59 18 25 
 1  2  3  4 
77 59 18 25 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5 
35 56 17 40 30 
 1  2  3  4  5 
35 56 17 40 30 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
21 47 31 16 26 18 19 
 1  2  3  4  5  6  7 
21 47 31 16 26 18 19 
[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] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "NUMBER_OF_LYMPH_NODES"               
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 179 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=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=164,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'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 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'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 179 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "GENDER"                      "RADIATION_THERAPY"          
[5] "KARNOFSKY_PERFORMANCE_SCORE" "HISTOLOGICAL_TYPE"          
[7] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=59, 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
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=4, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 34  3
  subtype2 40  0
  subtype3  9  1
  subtype4 48  2
  subtype5 25  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       40       10       50       25 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        0        1        2        0 
$subtype1
TCGA-QR-A70P TCGA-SR-A6MV TCGA-WB-A81Q TCGA-P7-A5NY TCGA-P8-A6RY TCGA-PR-A5PF 
      117.14       121.05        24.82        31.46         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70R 
       81.70        28.08         6.31        26.83         9.01        14.20 
TCGA-QR-A70X TCGA-QT-A5XK TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A686 TCGA-RW-A68D 
        6.02         6.94         8.09        86.89        19.30        72.79 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WT TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QK 
        2.89        20.09        42.77       114.77       109.25       111.25 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-W2-A7HA TCGA-W2-A7HE TCGA-WB-A80P 
       81.93       110.53        26.20         1.18        16.60       316.73 
TCGA-WB-A815 TCGA-WB-A81D TCGA-WB-A81H TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       53.59        35.84        63.98        45.83        62.04        12.99 
TCGA-WB-A81V 
       71.05 

$subtype2
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       58.88        30.51        32.15        44.52        41.88        13.87 
TCGA-S7-A7WU TCGA-WB-A817 TCGA-WB-A81E TCGA-P8-A5KC TCGA-QR-A6GS TCGA-QR-A6GY 
       30.51        43.07        48.53        29.03         1.25         1.05 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70G TCGA-QR-A70I 
        9.93        14.27        31.53         4.11         2.33        29.92 
TCGA-QR-A70N TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        1.41        12.39         1.81         0.79        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A7D0 TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW 
        0.92        50.63        11.57        35.51        27.91        23.21 
TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-W2-A7HH 
       17.95         9.73        49.61        37.35        13.32        25.61 
TCGA-WB-A81A TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A821 
       24.16        22.32        24.36        93.11 

$subtype3
TCGA-P8-A5KD TCGA-QR-A6GR TCGA-QR-A70C TCGA-QR-A70W TCGA-QT-A5XP TCGA-RW-A685 
        4.04        23.11       116.19        41.79         4.41         0.85 
TCGA-SP-A6QJ TCGA-W2-A7HC TCGA-WB-A80O TCGA-WB-A80Y 
       15.52        14.43        25.51        19.59 

$subtype4
TCGA-QR-A70D TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-WB-A814 
        0.23        26.96        18.94         3.12        19.86        74.04 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A6RX TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A702 
       10.16        20.19        17.75       137.59        19.04         1.28 
TCGA-QR-A70J TCGA-QT-A5XJ TCGA-QT-A5XN TCGA-QT-A5XO TCGA-RT-A6Y9 TCGA-RW-A67X 
       13.12        36.23        25.18         2.30       108.26         2.93 
TCGA-RW-A67Y TCGA-RW-A681 TCGA-RW-A689 TCGA-RW-A68C TCGA-S7-A7WL TCGA-S7-A7WM 
        7.10        37.51        27.22         6.28        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF 
       37.25        31.04        40.70        25.32        24.20        82.62 
TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-TT-A6YJ 
       79.46         0.10        51.22        68.61       106.75         4.34 
TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HD TCGA-W2-A7UY TCGA-WB-A80L 
       19.92        42.48        20.09        18.44        14.79        34.26 
TCGA-WB-A80N TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81S 
        4.73        29.16        42.35        33.90        57.11        23.77 
TCGA-WB-A81T TCGA-WB-A81W 
       25.51        78.21 

$subtype5
TCGA-QR-A6H1 TCGA-RW-A68A TCGA-RW-A68B TCGA-W2-A7HF TCGA-QR-A6GO TCGA-QR-A6H0 
       14.17        25.05        23.90        17.69        35.01         9.21 
TCGA-QR-A6H6 TCGA-QR-A7IP TCGA-QT-A5XM TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A684 
       15.58        17.95         0.72        19.86        47.64         1.05 
TCGA-RW-A688 TCGA-SP-A6QI TCGA-SQ-A6I4 TCGA-SR-A6MY TCGA-W2-A7H7 TCGA-WB-A80K 
        1.22       110.04         1.41        24.66        17.16        41.26 
TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A81G TCGA-WB-A81K TCGA-WB-A81R 
        4.47       127.56        41.23        38.76        40.04         1.61 
TCGA-WB-A822 
      103.17 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.18     0.79     0.85     0.10     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 
  316.73    93.11   116.19   137.59   127.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
  31.460   24.260   17.555   25.415   19.860 
[1] "1.2 - 316.7 (31.5)" "0.8 - 93.1 (24.3)"  "0.8 - 116.2 (17.6)"
[4] "0.1 - 137.6 (25.4)" "0.7 - 127.6 (19.9)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 33  4
  subtype2 28 12
  subtype3 10  0
  subtype4 42  8
  subtype5 21  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    4
  subtype2   28   12
  subtype3   10    0
  subtype4   42    8
  subtype5   21    4
                    clus
vv                   subtype1 subtype2 subtype3 subtype4 subtype5
  ADRENAL GLAND            33       28       10       42       21
  EXTRA-ADRENAL SITE        4       12        0        8        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"
D1V4, binary
          cls
clus        0  1
  subtype1 21 16
  subtype2 21 19
  subtype3  8  2
  subtype4 28 22
  subtype5 10 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   16
  subtype2   21   19
  subtype3    8    2
  subtype4   28   22
  subtype5   10   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       21       21        8       28       10
  MALE         16       19        2       22       15
[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 33  4
  subtype2 40  0
  subtype3 10  0
  subtype4 49  0
  subtype5 23  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    4
  subtype2   40    0
  subtype3   10    0
  subtype4   49    0
  subtype5   23    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        33       40       10       49       23
  YES        4        0        0        0        1
[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"
D1V6, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       14        1       20        7 
 [1] "subtype4" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype1" "subtype4" "subtype4" "subtype4" "subtype2"
[19] "subtype4" "subtype4" "subtype1" "subtype2" "subtype2" "subtype4"
[25] "subtype2" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
[31] "subtype5" "subtype1" "subtype4" "subtype1" "subtype5" "subtype1"
[37] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype5"
[43] "subtype4" "subtype5" "subtype1" "subtype4" "subtype1" "subtype4"
[49] "subtype5" "subtype1" "subtype2" "subtype2" "subtype5" "subtype1"
[55] "subtype1" "subtype4" "subtype4" "subtype2" "subtype5"
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             3                                             1
  subtype2             5                                             7
  subtype3             0                                             0
  subtype4             6                                             1
  subtype5             2                                             2
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               33
  subtype2               28
  subtype3               10
  subtype4               43
  subtype5               21
D1V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        3        5        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        1        7        0
  PHEOCHROMOCYTOMA                                    33       28       10
                                               clus
vv                                              subtype4 subtype5
  PARAGANGLIOMA                                        6        2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        1        2
  PHEOCHROMOCYTOMA                                    43       21
[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, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        2        2        7        2 
 [1] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype1"
 [7] "subtype1" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                         2
  subtype2                                0     1                         8
  subtype3                                0     0                         2
  subtype4                                0     2                         6
  subtype5                                0     0                         1
          vv
clus       WHITE
  subtype1    31
  subtype2    31
  subtype3     8
  subtype4    41
  subtype5    23
D1V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   2        1        0        2        0
  BLACK OR AFRICAN AMERICAN               2        8        2        6        1
  WHITE                                  31       31        8       41       23
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus        0  1
  subtype1  0 29
  subtype2  0 33
  subtype3  0  8
  subtype4  1 41
  subtype5  1 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   29
  subtype2    0   33
  subtype3    0    8
  subtype4    1   41
  subtype5    1   17
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        0        1        1
  NOT HISPANIC OR LATINO       29       33        8       41       17
[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 42  3
  subtype2 81  3
  subtype3 50  0
subtype1 subtype2 subtype3 
      45       84       50 
subtype1 subtype2 subtype3 
       3        3        0 
$subtype1
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        32.15        10.42         0.23       117.14 
TCGA-QR-A70T TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-SR-A6MV TCGA-SR-A6MX 
        8.78        44.52        13.87        30.51       121.05         3.12 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-P7-A5NX TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GT 
       48.53        24.82        26.89        17.75         5.88       137.59 
TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A70A TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70Q 
       14.27        15.58        69.67         2.33        29.92         4.60 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RM-A68T 
       12.39        17.95        36.23         1.81        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A68D TCGA-SP-A6QD 
        0.92       108.26        47.64        37.51        72.79       109.25 
TCGA-SP-A6QG TCGA-SR-A6N0 TCGA-W2-A7H7 TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A81G 
       79.46        49.61        17.16       316.73       127.56        38.76 
TCGA-WB-A81I TCGA-WB-A81P TCGA-WB-A822 
       22.32        12.99       103.17 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68G TCGA-W2-A7HB 
       14.17         3.65        25.05        23.90        41.88        19.86 
TCGA-W2-A7HF TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG 
       17.69        10.16        31.46         4.04        17.95        81.70 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GW TCGA-QR-A6GY TCGA-QR-A6H2 
       35.01        23.11         1.25        16.14         1.05         9.93 
TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70M 
       87.48         1.28        13.08        26.83         9.01        33.99 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XN 
       14.20        48.43         0.07        41.79         6.94        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
        2.30         4.41         0.79        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       19.86         7.10         0.85        19.30         1.22        27.22 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
        2.89        20.09        31.59        36.56        37.25        40.70 
TCGA-S7-A7WT TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI 
       42.77        25.32        24.20       114.77        82.62       110.04 
TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MY 
       15.52         1.41         0.10        51.22        81.93        24.66 
TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80L 
        4.34        19.92         1.18        14.43        18.44        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
        4.47         4.73        25.51        29.16        19.59        53.59 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81K 
       42.35        33.90        35.84        57.11        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       45.83         1.61        23.77        25.51        71.05        78.21 

$subtype3
TCGA-QR-A6ZZ TCGA-QR-A703 TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SP-A6QH TCGA-SR-A6MR 
        1.58        38.37        26.96        18.94        72.43        79.20 
TCGA-WB-A814 TCGA-WB-A817 TCGA-XG-A823 TCGA-P8-A5KC TCGA-PR-A5PH TCGA-QR-A6GX 
       74.04        43.07        20.19        29.03        28.08        19.04 
TCGA-QR-A6H0 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70C TCGA-QR-A70E 
        9.21        31.53         4.11         1.15       116.19         6.31 
TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70X TCGA-QT-A5XM TCGA-RW-A67X TCGA-RW-A684 
       13.12         1.41         6.02         0.72         2.93         1.05 
TCGA-RW-A68C TCGA-RW-A7D0 TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WV TCGA-S7-A7WW 
        6.28        11.57        35.51        31.04        27.91        23.21 
TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QK TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MU 
       17.95         9.73       111.25        68.61       106.75       110.53 
TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HE 
       26.20        37.35        13.32        42.48        20.09        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A816 TCGA-WB-A81A TCGA-WB-A81H 
       25.61        14.79        41.26        41.23        24.16        63.98 
TCGA-WB-A81N TCGA-WB-A821 
       62.04        93.11 

subtype1 subtype2 subtype3 
    0.23     0.07     0.72 
subtype1 subtype2 subtype3 
  316.73   114.77   116.19 
subtype1 subtype2 subtype3 
  30.510   23.835   25.905 
[1] "0.2 - 316.7 (30.5)" "0.1 - 114.8 (23.8)" "0.7 - 116.2 (25.9)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 24 21
  subtype2 82  2
  subtype3 41  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   21
  subtype2   82    2
  subtype3   41    9
                    clus
vv                   subtype1 subtype2 subtype3
  ADRENAL GLAND            24       82       41
  EXTRA-ADRENAL SITE       21        2        9
[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"
D2V4, binary
          cls
clus        0  1
  subtype1 22 23
  subtype2 45 39
  subtype3 34 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   23
  subtype2   45   39
  subtype3   34   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       45       34
  MALE         23       39       16
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 40  5
  subtype2 82  0
  subtype3 50  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    5
  subtype2   82    0
  subtype3   50    0
     clus
vv    subtype1 subtype2 subtype3
  NO        40       82       50
  YES        5        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1            12                                             8
  subtype2             2                                             0
  subtype3             4                                             5
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               25
  subtype2               82
  subtype3               41
D2V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                       12        2        4
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        8        0        5
  PHEOCHROMOCYTOMA                                    25       82       41
[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"
D2V8, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         7
  subtype2                                1     2                         5
  subtype3                                0     3                         8
          vv
clus       WHITE
  subtype1    36
  subtype2    73
  subtype3    39
D2V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1        2        3
  BLACK OR AFRICAN AMERICAN               7        5        8
  WHITE                                  36       73       39
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
          cls
clus        0  1
  subtype1  1 35
  subtype2  2 61
  subtype3  2 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   35
  subtype2    2   61
  subtype3    2   42
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        2
  NOT HISPANIC OR LATINO       35       61       42
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 17  0
  subtype2 20  1
  subtype3 23  0
  subtype4 17  1
subtype1 subtype2 subtype3 subtype4 
      17       21       23       18 
subtype1 subtype2 subtype3 subtype4 
       0        1        0        1 
$subtype1
TCGA-QR-A6GZ TCGA-RW-A68B TCGA-RW-A68G TCGA-S7-A7WU TCGA-P7-A5NX TCGA-QR-A70W 
       30.51        23.90        41.88        30.51        26.89        41.79 
TCGA-QT-A5XK TCGA-QT-A69Q TCGA-RW-A685 TCGA-RW-A68D TCGA-RX-A8JQ TCGA-SR-A6MQ 
        6.94         0.79         0.85        72.79        20.09        68.61 
TCGA-TT-A6YN TCGA-W2-A7HC TCGA-WB-A818 TCGA-WB-A81P TCGA-WB-A81W 
       19.92        14.43        42.35        12.99        78.21 

$subtype2
TCGA-RW-A68A TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SP-A6QH TCGA-SR-A6MX TCGA-WB-A814 
       25.05        26.96        18.94        72.43         3.12        74.04 
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-QR-A6GT TCGA-QT-A5XL TCGA-RM-A68W TCGA-RW-A67X 
       29.03        17.75       137.59         1.81         0.92         2.93 
TCGA-RW-A68C TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-SR-A6MY TCGA-SR-A6MZ 
        6.28        27.91        25.32        17.95        24.66        26.20 
TCGA-WB-A815 TCGA-WB-A81S TCGA-WB-A81T 
       53.59        23.77        25.51 

$subtype3
TCGA-W2-A7HF TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QT-A5XM TCGA-QT-A5XN 
       17.69         4.04        81.70        35.01         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A688 
        2.30         4.41        13.08        50.63         8.09         1.22 
TCGA-RW-A689 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WP TCGA-S7-A7WR 
       27.22        31.59        36.56        37.25        31.04        40.70 
TCGA-S7-A7X2 TCGA-SP-A6QJ TCGA-WB-A80Q TCGA-WB-A819 TCGA-WB-A81V 
       24.20        15.52       127.56        33.90        71.05 

$subtype4
TCGA-QR-A6GU TCGA-RW-A68F TCGA-WB-A817 TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH 
       58.88        44.52        43.07         5.88        17.95        28.08 
TCGA-QR-A6H2 TCGA-QT-A5XJ TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RW-A67V TCGA-RW-A680 
        9.93        36.23        77.98       108.26        86.89        47.64 
TCGA-RW-A681 TCGA-RW-A8AZ TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-WB-A81G TCGA-WB-A81M 
       37.51         2.89        23.21         9.73        38.76        45.83 

subtype1 subtype2 subtype3 subtype4 
    0.79     0.92     0.72     2.89 
subtype1 subtype2 subtype3 subtype4 
   78.21   137.59   127.56   108.26 
subtype1 subtype2 subtype3 subtype4 
  26.890   25.050   27.220   38.135 
[1] "0.8 - 78.2 (26.9)"  "0.9 - 137.6 (25.1)" "0.7 - 127.6 (27.2)"
[4] "2.9 - 108.3 (38.1)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 15  2
  subtype2 15  6
  subtype3 22  1
  subtype4 15  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    2
  subtype2   15    6
  subtype3   22    1
  subtype4   15    3
                    clus
vv                   subtype1 subtype2 subtype3 subtype4
  ADRENAL GLAND            15       15       22       15
  EXTRA-ADRENAL SITE        2        6        1        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus        0  1
  subtype1  8  9
  subtype2 11 10
  subtype3 13 10
  subtype4  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    9
  subtype2   11   10
  subtype3   13   10
  subtype4    8   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       11       13        8
  MALE          9       10       10       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"
D3V5, binary
          cls
clus        0
  subtype1 17
  subtype2 21
  subtype3 23
  subtype4 18
[1] "NOT AVAILABLE: table only has an event [0]"
D3V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             2                                             0
  subtype2             2                                             3
  subtype3             0                                             1
  subtype4             1                                             2
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               15
  subtype2               16
  subtype3               22
  subtype4               15
D3V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        2        2        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0        3        1
  PHEOCHROMOCYTOMA                                    15       16       22
                                               clus
vv                                              subtype4
  PARAGANGLIOMA                                        1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        2
  PHEOCHROMOCYTOMA                                    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"
D3V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        1        3        4 
[1] "subtype3" "subtype4" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    13
  subtype2     1                         1    19
  subtype3     0                         4    19
  subtype4     1                         3    14
D3V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        1
  BLACK OR AFRICAN AMERICAN        1        1        4        3
  WHITE                           13       19       19       14
[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"
D3V10, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2  0 16
  subtype3  0 20
  subtype4  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2    0   16
  subtype3    0   20
  subtype4    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        0        0
  NOT HISPANIC OR LATINO       11       16       20       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(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 31  2
  subtype2 18  0
  subtype3 28  0
subtype1 subtype2 subtype3 
      33       18       28 
subtype1 subtype2 subtype3 
       2        0        0 
$subtype1
TCGA-QR-A6GU TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WU TCGA-SP-A6QH TCGA-SR-A6MX 
       58.88        44.52        41.88        30.51        72.43         3.12 
TCGA-WB-A814 TCGA-WB-A817 TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF 
       74.04        43.07        26.89        29.03         5.88        17.95 
TCGA-PR-A5PH TCGA-QR-A6GT TCGA-QT-A5XJ TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
       28.08       137.59        36.23        77.98         0.92       108.26 
TCGA-RW-A67V TCGA-RW-A680 TCGA-RW-A68C TCGA-RW-A8AZ TCGA-S7-A7WW TCGA-S7-A7WX 
       86.89        47.64         6.28         2.89        23.21        25.32 
TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SR-A6MY TCGA-WB-A80Q TCGA-WB-A815 TCGA-WB-A81G 
       17.95         9.73        24.66       127.56        53.59        38.76 
TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S 
       45.83        12.99        23.77 

$subtype2
TCGA-QR-A6GZ TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A70W TCGA-QT-A5XK TCGA-RW-A685 
       30.51         4.04        81.70        41.79         6.94         0.85 
TCGA-RW-A688 TCGA-RX-A8JQ TCGA-S7-A7WR TCGA-S7-A7X2 TCGA-SR-A6MQ TCGA-SR-A6MZ 
        1.22        20.09        40.70        24.20        68.61        26.20 
TCGA-TT-A6YN TCGA-W2-A7HC TCGA-WB-A818 TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       19.92        14.43        42.35        25.51        71.05        78.21 

$subtype3
TCGA-RW-A68A TCGA-RW-A68B TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-W2-A7HF TCGA-P8-A6RX 
       25.05        23.90        26.96        18.94        17.69        17.75 
TCGA-QR-A6GO TCGA-QR-A6H2 TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       35.01         9.93         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67X 
        4.41         0.79        13.08        50.63         8.09         2.93 
TCGA-RW-A681 TCGA-RW-A689 TCGA-RW-A68D TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       37.51        27.22        72.79        31.59        36.56        37.25 
TCGA-S7-A7WP TCGA-S7-A7WV TCGA-SP-A6QJ TCGA-WB-A819 
       31.04        27.91        15.52        33.90 

subtype1 subtype2 subtype3 
    0.92     0.85     0.72 
subtype1 subtype2 subtype3 
  137.59    81.70    72.79 
subtype1 subtype2 subtype3 
  30.510   25.855   24.475 
[1] "0.9 - 137.6 (30.5)" "0.8 - 81.7 (25.9)"  "0.7 - 72.8 (24.5)" 
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 25  8
  subtype2 16  2
  subtype3 26  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    8
  subtype2   16    2
  subtype3   26    2
                    clus
vv                   subtype1 subtype2 subtype3
  ADRENAL GLAND            25       16       26
  EXTRA-ADRENAL SITE        8        2        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus        0  1
  subtype1 20 13
  subtype2 10  8
  subtype3 10 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   13
  subtype2   10    8
  subtype3   10   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       10       10
  MALE         13        8       18
[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"
D4V5, binary
          cls
clus        0
  subtype1 33
  subtype2 18
  subtype3 28
[1] "NOT AVAILABLE: table only has an event [0]"
D4V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             2                                             5
  subtype2             2                                             0
  subtype3             1                                             1
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               26
  subtype2               16
  subtype3               26
D4V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        2        2        1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        5        0        1
  PHEOCHROMOCYTOMA                                    26       16       26
[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"
D4V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       6        2        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    28
  subtype2     1                         1    16
  subtype3     2                         4    21
D4V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        4        1        4
  WHITE                           28       16       21
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus        0  1
  subtype1  1 24
  subtype2  0 15
  subtype3  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   24
  subtype2    0   15
  subtype3    0   19
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       24       15       19
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 36  2
  subtype2 68  2
  subtype3 48  2
  subtype4 21  0
subtype1 subtype2 subtype3 subtype4 
      38       70       50       21 
subtype1 subtype2 subtype3 subtype4 
       2        2        2        0 
$subtype1
TCGA-QR-A6GU TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68F 
       58.88        10.42         0.23       117.14         8.78        44.52 
TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-SR-A6MX TCGA-W2-A7HF TCGA-WB-A81E TCGA-P7-A5NX 
       13.87        30.51         3.12        17.69        48.53        26.89 
TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A707 TCGA-QR-A70E 
       19.04         9.21        14.27        15.58        13.08         6.31 
TCGA-QR-A70I TCGA-QR-A70Q TCGA-QR-A70V TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-RM-A68T 
       29.92         4.60         0.07        17.95        36.23        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A688 TCGA-RW-A68D 
        0.92       108.26         7.10        47.64         1.22        72.79 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-W2-A7H7 TCGA-W2-A7HH 
      109.25        79.46       106.75         4.34        17.16        25.61 
TCGA-WB-A80P TCGA-WB-A81G 
      316.73        38.76 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-RW-A68B TCGA-W2-A7HB TCGA-WB-A81Q 
       14.17         3.65        25.05        23.90        19.86        24.82 
TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS 
       10.16        31.46         4.04        81.70        35.01         1.25 
TCGA-QR-A6GW TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70M 
       16.14        87.48         1.28        26.83         9.01        33.99 
TCGA-QR-A70U TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP 
       48.43        41.79         6.94         0.72        25.18         4.41 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A689 
       50.63         8.09        19.86        37.51         1.05        27.22 
TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
       11.57        20.09        31.59        36.56        37.25        40.70 
TCGA-S7-A7WT TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI 
       42.77        25.32        24.20       114.77        82.62       110.04 
TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MY 
       15.52         1.41         0.10        51.22        68.61        24.66 
TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80M 
       19.92        20.09         1.18        14.43        18.44         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
        4.73        25.51        29.16        42.35        33.90        35.84 
TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       57.11        24.36        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       23.77        25.51        71.05        78.21 

$subtype3
TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-S7-A7WQ TCGA-S7-A7X1 
       30.51         1.58        32.15        38.37        26.96        18.94 
TCGA-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-WB-A814 TCGA-P8-A5KC TCGA-P8-A6RX 
       72.43        79.20       121.05        74.04        29.03        17.75 
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H2 
        5.88        17.95        28.08       137.59         1.05         9.93 
TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70J 
       31.53         4.11         1.15        69.67       116.19        13.12 
TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 
        1.41        14.20        12.39         1.81         0.79        13.08 
TCGA-RW-A67V TCGA-RW-A67X TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A8AZ TCGA-S7-A7WP 
       86.89         2.93        19.30         6.28         2.89        31.04 
TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SR-A6MS TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7UY 
       17.95         9.73        81.93        37.35        42.48        14.79 
TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81I 
       34.26       127.56        19.59        53.59        24.16        22.32 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

$subtype4
TCGA-RW-A68G TCGA-WB-A817 TCGA-XG-A823 TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X 
       41.88        43.07        20.19        23.11         2.33         6.02 
TCGA-QT-A5XO TCGA-RW-A685 TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK 
        2.30         0.85        35.51        27.91        23.21       111.25 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80K 
      110.53        26.20        49.61        13.32        16.60        41.26 
TCGA-WB-A816 TCGA-WB-A81H TCGA-WB-A81K 
       41.23        63.98        40.04 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.79     0.85 
subtype1 subtype2 subtype3 subtype4 
  316.73   114.77   137.59   111.25 
subtype1 subtype2 subtype3 subtype4 
  18.495   24.935   23.240   27.910 
[1] "0.1 - 316.7 (18.5)" "0.1 - 114.8 (24.9)" "0.8 - 137.6 (23.2)"
[4] "0.8 - 111.2 (27.9)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 19 19
  subtype2 67  3
  subtype3 40 10
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   19
  subtype2   67    3
  subtype3   40   10
  subtype4   21    0
                    clus
vv                   subtype1 subtype2 subtype3 subtype4
  ADRENAL GLAND            19       67       40       21
  EXTRA-ADRENAL SITE       19        3       10        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 35 35
  subtype3 27 23
  subtype4 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   35   35
  subtype3   27   23
  subtype4   14    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       35       27       14
  MALE         13       35       23        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"
D5V5, binary
          cls
clus        0  1
  subtype1 36  2
  subtype2 67  1
  subtype3 48  2
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    2
  subtype2   67    1
  subtype3   48    2
  subtype4   21    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        36       67       48       21
  YES        2        1        2        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1            11                                             8
  subtype2             3                                             0
  subtype3             4                                             5
  subtype4             0                                             0
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               19
  subtype2               67
  subtype3               41
  subtype4               21
D5V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                       11        3        4
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        8        0        5
  PHEOCHROMOCYTOMA                                    19       67       41
                                               clus
vv                                              subtype4
  PARAGANGLIOMA                                        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0
  PHEOCHROMOCYTOMA                                    21
[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, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       6        5        9        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         7
  subtype2                                1     2                         3
  subtype3                                0     2                         6
  subtype4                                0     1                         4
          vv
clus       WHITE
  subtype1    27
  subtype2    63
  subtype3    42
  subtype4    16
D5V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        2        2        1
  BLACK OR AFRICAN AMERICAN               7        3        6        4
  WHITE                                  27       63       42       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus        0  1
  subtype1  2 26
  subtype2  1 56
  subtype3  0 40
  subtype4  2 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   26
  subtype2    1   56
  subtype3    0   40
  subtype4    2   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        0        2
  NOT HISPANIC OR LATINO       26       56       40       16
[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 37  2
  subtype2 69  2
  subtype3 46  2
  subtype4 21  0
subtype1 subtype2 subtype3 subtype4 
      39       71       48       21 
subtype1 subtype2 subtype3 subtype4 
       2        2        2        0 
$subtype1
TCGA-QR-A700 TCGA-QR-A70T TCGA-S7-A7WU TCGA-SR-A6MR TCGA-WB-A81E TCGA-P7-A5NX 
       32.15         8.78        30.51        79.20        48.53        26.89 
TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A6H2 
       29.03         5.88        17.95        28.08         1.05         9.93 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70R 
        1.15        69.67       116.19         6.31        26.83        14.20 
TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A686 
       36.23         0.79       108.26        86.89        37.51        19.30 
TCGA-RW-A68D TCGA-RW-A8AZ TCGA-S7-A7WT TCGA-SA-A6C2 TCGA-SR-A6MS TCGA-SR-A6MT 
       72.79         2.89        42.77         9.73        81.93       106.75 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 
       25.61        41.26         4.47       127.56        19.59        53.59 
TCGA-WB-A81A TCGA-WB-A81I TCGA-WB-A81M 
       24.16        22.32        45.83 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-RW-A68B TCGA-W2-A7HB TCGA-W2-A7HF 
       14.17         3.65        25.05        23.90        19.86        17.69 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO 
       24.82        10.16        31.46         4.04        81.70        35.01 
TCGA-QR-A6GS TCGA-QR-A6GW TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70K 
        1.25        16.14        87.48         1.28        13.08         9.01 
TCGA-QR-A70M TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XM 
       33.99        48.43         0.07        41.79         6.94         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W 
       25.18         2.30         4.41        50.63         8.09        19.86 
TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A7D0 TCGA-RX-A8JQ 
        7.10         1.05         1.22        27.22        11.57        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 
       31.59        36.56        37.25        40.70        25.32        24.20 
TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MP 
      114.77        82.62       110.04        15.52         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA 
       68.61        24.66         4.34        19.92        20.09         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A818 
       14.43        18.44         4.73        25.51        29.16        42.35 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P 
       33.90        35.84        57.11        24.36        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
        1.61        23.77        25.51        71.05        78.21 

$subtype3
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A70D 
       58.88        30.51         1.58        38.37        10.42         0.23 
TCGA-QR-A70P TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SP-A6QH 
      117.14        44.52        13.87        26.96        18.94        72.43 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-WB-A814 TCGA-P8-A6RX TCGA-QR-A6GT TCGA-QR-A6GX 
      121.05         3.12        74.04        17.75       137.59        19.04 
TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A70I 
        9.21        14.27        31.53        15.58         4.11        29.92 
TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70Q TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XL 
       13.12         1.41         4.60        12.39        17.95         1.81 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A68C 
       13.08        77.98         0.92         2.93        47.64         6.28 
TCGA-S7-A7WP TCGA-S7-A7X0 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-TT-A6YK TCGA-TT-A6YP 
       31.04        17.95       109.25        79.46        37.35        42.48 
TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80P TCGA-WB-A81G TCGA-WB-A821 TCGA-WB-A822 
       17.16        14.79       316.73        38.76        93.11       103.17 

$subtype4
TCGA-RW-A68G TCGA-WB-A817 TCGA-XG-A823 TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X 
       41.88        43.07        20.19        23.11         2.33         6.02 
TCGA-RW-A685 TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SQ-A6I4 
        0.85        35.51        27.91        23.21       111.25         1.41 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80L 
      110.53        26.20        49.61        13.32        16.60        34.26 
TCGA-WB-A816 TCGA-WB-A81H TCGA-WB-A81K 
       41.23        63.98        40.04 

subtype1 subtype2 subtype3 subtype4 
    0.79     0.07     0.23     0.85 
subtype1 subtype2 subtype3 subtype4 
  127.56   114.77   316.73   111.25 
subtype1 subtype2 subtype3 subtype4 
   28.08    23.90    18.99    27.91 
[1] "0.8 - 127.6 (28.1)" "0.1 - 114.8 (23.9)" "0.2 - 316.7 (19.0)"
[4] "0.8 - 111.2 (27.9)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 34  5
  subtype2 68  3
  subtype3 24 24
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    5
  subtype2   68    3
  subtype3   24   24
  subtype4   21    0
                    clus
vv                   subtype1 subtype2 subtype3 subtype4
  ADRENAL GLAND            34       68       24       21
  EXTRA-ADRENAL SITE        5        3       24        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 23 16
  subtype2 41 30
  subtype3 23 25
  subtype4 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   16
  subtype2   41   30
  subtype3   23   25
  subtype4   14    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23       41       23       14
  MALE         16       30       25        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"
D6V5, binary
          cls
clus        0  1
  subtype1 39  0
  subtype2 69  1
  subtype3 44  4
  subtype4 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   69    1
  subtype3   44    4
  subtype4   20    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        39       69       44       20
  YES        0        1        4        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             3                                             2
  subtype2             3                                             0
  subtype3            12                                            11
  subtype4             0                                             0
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               34
  subtype2               68
  subtype3               25
  subtype4               21
D6V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        3        3       12
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        2        0       11
  PHEOCHROMOCYTOMA                                    34       68       25
                                               clus
vv                                              subtype4
  PARAGANGLIOMA                                        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0
  PHEOCHROMOCYTOMA                                    21
[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, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       9        5        6        1 
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1"
[19] "subtype1" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         4
  subtype2                                1     2                         5
  subtype3                                0     1                         8
  subtype4                                0     1                         3
          vv
clus       WHITE
  subtype1    33
  subtype2    60
  subtype3    38
  subtype4    17
D6V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   2        2        1        1
  BLACK OR AFRICAN AMERICAN               4        5        8        3
  WHITE                                  33       60       38       17
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
          cls
clus        0  1
  subtype1  1 29
  subtype2  2 55
  subtype3  0 38
  subtype4  2 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   29
  subtype2    2   55
  subtype3    0   38
  subtype4    2   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       29       55       38       16
[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 67  5
  subtype2 43  1
  subtype3 63  0
subtype1 subtype2 subtype3 
      72       44       63 
subtype1 subtype2 subtype3 
       5        1        0 
$subtype1
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-QR-A705 
       58.88        30.51         1.58        32.15        38.37        10.42 
TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
        0.23       117.14        44.52        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-WB-A814 
       18.94        72.43        79.20       121.05         3.12        74.04 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-P7-A5NX TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GX 
       48.53        24.82        26.89        17.75        17.95        19.04 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A708 
        9.21         9.93        31.53        15.58         4.11         1.15 
TCGA-QR-A70A TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70Q 
       69.67         6.31        29.92        13.12         1.41         4.60 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RM-A68W 
       12.39        17.95        36.23         1.81        13.08         0.92 
TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A68C TCGA-RW-A68D 
      108.26         2.93        47.64        37.51         6.28        72.79 
TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QD TCGA-SQ-A6I4 
        2.89        31.04        17.95         9.73       109.25         1.41 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       51.22       106.75        37.35        42.48        17.16         1.18 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       25.61        14.79        41.26       316.73       127.56        19.59 
TCGA-WB-A81A TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81P TCGA-WB-A821 TCGA-WB-A822 
       24.16        38.76        22.32        12.99        93.11       103.17 

$subtype2
TCGA-RW-A68G TCGA-WB-A817 TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       41.88        43.07        10.16        20.19        31.46        29.03 
TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6H3 
        5.88        28.08        23.11         1.25       137.59        14.27 
TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70R TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
      116.19         2.33        14.20         0.72         2.30         4.41 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RW-A67V TCGA-RW-A685 TCGA-RW-A686 TCGA-RX-A8JQ 
        0.79        77.98        86.89         0.85        19.30        20.09 
TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-SP-A6QG TCGA-SP-A6QK 
       35.51        27.91        23.21        25.32        79.46       111.25 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE 
       81.93       110.53        26.20        49.61        13.32        16.60 
TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A81H TCGA-WB-A81K 
       34.26        25.51        53.59        41.23        63.98        40.04 
TCGA-WB-A81S TCGA-WB-A81T 
       23.77        25.51 

$subtype3
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-QR-A70T TCGA-RW-A68A TCGA-RW-A68B TCGA-W2-A7HB 
       14.17         3.65         8.78        25.05        23.90        19.86 
TCGA-W2-A7HF TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GW TCGA-QR-A6GY 
       17.69         4.04        81.70        35.01        16.14         1.05 
TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70M 
       87.48         1.28        13.08        26.83         9.01        33.99 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XK TCGA-QT-A5XN 
       48.43         0.07        41.79         6.02         6.94        25.18 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A688 
       50.63         8.09        19.86         7.10         1.05         1.22 
TCGA-RW-A689 TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
       27.22        11.57        31.59        36.56        37.25        40.70 
TCGA-S7-A7WT TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       42.77        24.20       114.77        82.62       110.04        15.52 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H5 
        0.10        68.61        24.66         4.34        19.92        20.09 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80V TCGA-WB-A818 
       14.43        18.44         4.47         4.73        29.16        42.35 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N 
       33.90        35.84        57.11        24.36        45.83        62.04 
TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A81W 
        1.61        71.05        78.21 

subtype1 subtype2 subtype3 
    0.23     0.72     0.07 
subtype1 subtype2 subtype3 
  316.73   137.59   114.77 
subtype1 subtype2 subtype3 
  24.490   25.855   24.200 
[1] "0.2 - 316.7 (24.5)" "0.7 - 137.6 (25.9)" "0.1 - 114.8 (24.2)"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 48 24
  subtype2 39  5
  subtype3 60  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   24
  subtype2   39    5
  subtype3   60    3
                    clus
vv                   subtype1 subtype2 subtype3
  ADRENAL GLAND            48       39       60
  EXTRA-ADRENAL SITE       24        5        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"
D7V4, binary
          cls
clus        0  1
  subtype1 40 32
  subtype2 25 19
  subtype3 36 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   32
  subtype2   25   19
  subtype3   36   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       25       36
  MALE         32       19       27
[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 66  5
  subtype2 44  0
  subtype3 62  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    5
  subtype2   44    0
  subtype3   62    0
     clus
vv    subtype1 subtype2 subtype3
  NO        66       44       62
  YES        5        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1            11                                            13
  subtype2             4                                             0
  subtype3             3                                             0
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               48
  subtype2               40
  subtype3               60
D7V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                       11        4        3
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA       13        0        0
  PHEOCHROMOCYTOMA                                    48       40       60
[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, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         9
  subtype2                                0     1                         6
  subtype3                                0     2                         5
          vv
clus       WHITE
  subtype1    58
  subtype2    37
  subtype3    53
D7V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   3        1        2
  BLACK OR AFRICAN AMERICAN               9        6        5
  WHITE                                  58       37       53
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
          cls
clus        0  1
  subtype1  1 57
  subtype2  2 32
  subtype3  2 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   57
  subtype2    2   32
  subtype3    2   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        2
  NOT HISPANIC OR LATINO       57       32       49
[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 73  4
  subtype2 57  2
  subtype3 18  0
  subtype4 25  0
subtype1 subtype2 subtype3 subtype4 
      77       59       18       25 
subtype1 subtype2 subtype3 subtype4 
       4        2        0        0 
$subtype1
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-QR-A705 
       58.88        30.51         1.58        32.15        38.37        10.42 
TCGA-QR-A70D TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ 
        0.23       117.14         8.78        44.52        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX 
       30.51        18.94        72.43        79.20       121.05         3.12 
TCGA-WB-A814 TCGA-WB-A81E TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY 
       74.04        48.53        26.89        29.03        17.75         5.88 
TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H4 
       17.95       137.59        19.04         9.21         9.93        87.48 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70A 
       31.53        15.58         1.28         4.11         1.15        69.67 
TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70Q 
      116.19         6.31        13.12         9.01         1.41         4.60 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RM-A68W 
       12.39        17.95        36.23         1.81        13.08         0.92 
TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A68C 
      108.26         2.93        47.64        37.51        19.30         6.28 
TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WP TCGA-S7-A7X0 TCGA-SA-A6C2 
       72.79         2.89        20.09        31.04        17.95         9.73 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SQ-A6I4 TCGA-SR-A6MT TCGA-TT-A6YK TCGA-TT-A6YP 
      109.25        79.46         1.41       106.75        37.35        42.48 
TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       17.16        14.79        41.26       316.73       127.56        19.59 
TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81P TCGA-WB-A821 TCGA-WB-A822 
       38.76        22.32        12.99        93.11       103.17 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-RW-A68B TCGA-W2-A7HF TCGA-WB-A81Q 
       14.17         3.65        25.05        23.90        17.69        24.82 
TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS 
       10.16        31.46         4.04        81.70        35.01         1.25 
TCGA-QR-A6GW TCGA-QR-A70I TCGA-QR-A70M TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W 
       16.14        29.92        33.99        48.43         0.07        41.79 
TCGA-QT-A5XK TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67Y 
        6.94        25.18        50.63         8.09        19.86         7.10 
TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.05         1.22        11.57        31.59        36.56        37.25 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       25.32        24.20       114.77        82.62       110.04        15.52 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN 
        0.10        51.22        68.61        24.66         4.34        19.92 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HH TCGA-WB-A80O 
       20.09         1.18        14.43        18.44        25.61        25.51 
TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J 
       29.16        42.35        33.90        35.84        57.11        24.36 
TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W 
       62.04         1.61        23.77        71.05        78.21 

$subtype3
TCGA-RW-A68G TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A70H TCGA-QR-A70R TCGA-QT-A5XM 
       41.88        28.08         1.05        26.83        14.20         0.72 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RW-A67V TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MS 
        4.41         0.79        86.89        40.70        42.77        81.93 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M 
       34.26         4.47        53.59        24.16        40.04        45.83 

$subtype4
TCGA-W2-A7HB TCGA-WB-A817 TCGA-XG-A823 TCGA-QR-A6GR TCGA-QR-A6H3 TCGA-QR-A707 
       19.86        43.07        20.19        23.11        14.27        13.08 
TCGA-QR-A70G TCGA-QR-A70X TCGA-QT-A5XO TCGA-RM-A68T TCGA-RW-A685 TCGA-RW-A689 
        2.33         6.02         2.30        77.98         0.85        27.22 
TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SR-A6MU TCGA-SR-A6MZ 
       35.51        27.91        23.21       111.25       110.53        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80N TCGA-WB-A816 TCGA-WB-A81H 
       49.61        13.32        16.60         4.73        41.23        63.98 
TCGA-WB-A81T 
       25.51 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.07     0.72     0.85 
subtype1 subtype2 subtype3 subtype4 
  316.73   114.77    86.89   111.25 
subtype1 subtype2 subtype3 subtype4 
   20.09    24.82    31.17    23.21 
[1] "0.2 - 316.7 (20.1)" "0.1 - 114.8 (24.8)" "0.7 - 86.9 (31.2)" 
[4] "0.8 - 111.2 (23.2)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 50 27
  subtype2 56  3
  subtype3 18  0
  subtype4 23  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   27
  subtype2   56    3
  subtype3   18    0
  subtype4   23    2
                    clus
vv                   subtype1 subtype2 subtype3 subtype4
  ADRENAL GLAND            50       56       18       23
  EXTRA-ADRENAL SITE       27        3        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus        0  1
  subtype1 42 35
  subtype2 35 24
  subtype3  9  9
  subtype4 15 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   35
  subtype2   35   24
  subtype3    9    9
  subtype4   15   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       35        9       15
  MALE         35       24        9       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"
D8V5, binary
          cls
clus        0  1
  subtype1 72  4
  subtype2 57  1
  subtype3 18  0
  subtype4 25  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    4
  subtype2   57    1
  subtype3   18    0
  subtype4   25    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        72       57       18       25
  YES        4        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1            13                                            13
  subtype2             3                                             0
  subtype3             0                                             0
  subtype4             2                                             0
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               51
  subtype2               56
  subtype3               18
  subtype4               23
D8V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                       13        3        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA       13        0        0
  PHEOCHROMOCYTOMA                                    51       56       18
                                               clus
vv                                              subtype4
  PARAGANGLIOMA                                        2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0
  PHEOCHROMOCYTOMA                                    23
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      14        3        3        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        10
  subtype2                                1     2                         4
  subtype3                                0     0                         1
  subtype4                                0     1                         5
          vv
clus       WHITE
  subtype1    63
  subtype2    49
  subtype3    17
  subtype4    19
D8V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   3        2        0        1
  BLACK OR AFRICAN AMERICAN              10        4        1        5
  WHITE                                  63       49       17       19
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus        0  1
  subtype1  1 61
  subtype2  2 45
  subtype3  0 12
  subtype4  2 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   61
  subtype2    2   45
  subtype3    0   12
  subtype4    2   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       61       45       12       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 35  0
  subtype2 54  2
  subtype3 16  1
  subtype4 38  2
  subtype5 29  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      35       56       17       40       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        2        1        2        1 
$subtype1
TCGA-QR-A70D TCGA-QR-A70T TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WU TCGA-P7-A5NX 
        0.23         8.78        44.52        41.88        30.51        26.89 
TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A70H TCGA-QR-A70R 
        5.88        28.08        19.04         1.05        26.83        14.20 
TCGA-QT-A5XJ TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RT-A6YA 
       36.23         0.72         4.41         0.79       108.26        50.63 
TCGA-RW-A67V TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 TCGA-S7-A7WR TCGA-S7-A7WT 
       86.89        47.64        37.51        19.30        40.70        42.77 
TCGA-SA-A6C2 TCGA-SR-A6MS TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q 
        9.73        81.93        41.26        34.26         4.47       127.56 
TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P 
       53.59        24.16        40.04        45.83        12.99 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A81Q 
       14.17         3.65        25.05        19.86        17.69        24.82 
TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GW 
       10.16        31.46         4.04        81.70        35.01        16.14 
TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70U TCGA-QR-A70V 
        1.28        13.08         9.01        33.99        48.43         0.07 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-RT-A6YC 
       41.79         6.02         6.94        25.18         2.30         8.09 
TCGA-RW-A67W TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RX-A8JQ TCGA-S7-A7WL 
       19.86         0.85         1.22        27.22        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       36.56        37.25       114.77        82.62       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I6 TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN 
      111.25         0.10       110.53        26.20         4.34        19.92 
TCGA-W2-A7H5 TCGA-W2-A7HD TCGA-WB-A80N TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 
       20.09        18.44         4.73        29.16        42.35        33.90 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81T 
       35.84        57.11        24.36        62.04         1.61        25.51 
TCGA-WB-A81V TCGA-WB-A81W 
       71.05        78.21 

$subtype3
TCGA-RW-A68B TCGA-P8-A5KC TCGA-PR-A5PF TCGA-QR-A6GS TCGA-QR-A6H4 TCGA-QR-A70C 
       23.90        29.03        17.95         1.25        87.48       116.19 
TCGA-QR-A70J TCGA-QT-A7U0 TCGA-RW-A684 TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WX 
       13.12        13.08         1.05        11.57         2.89        25.32 
TCGA-S7-A7X2 TCGA-SR-A6MQ TCGA-W2-A7HA TCGA-W2-A7HC TCGA-WB-A80O 
       24.20        68.61         1.18        14.43        25.51 

$subtype4
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-QR-A705 
       58.88        30.51         1.58        32.15        38.37        10.42 
TCGA-QR-A70P TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SR-A6MR TCGA-SR-A6MV 
      117.14        13.87        26.96        18.94        79.20       121.05 
TCGA-WB-A814 TCGA-WB-A81E TCGA-P8-A6RX TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A706 
       74.04        48.53        17.75         9.93        31.53         4.11 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70N TCGA-QR-A70Q 
        1.15        69.67         6.31        29.92         1.41         4.60 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XL TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A68D 
       12.39        17.95         1.81         2.93         7.10        72.79 
TCGA-S7-A7WP TCGA-SP-A6QD TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MY TCGA-TT-A6YP 
       31.04       109.25        51.22       106.75        24.66        42.48 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80Y TCGA-WB-A821 
       25.61        14.79        19.59        93.11 

$subtype5
TCGA-SP-A6QH TCGA-SR-A6MX TCGA-WB-A817 TCGA-XG-A823 TCGA-QR-A6GR TCGA-QR-A6GT 
       72.43         3.12        43.07        20.19        23.11       137.59 
TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A70G TCGA-RM-A68T TCGA-RM-A68W 
        9.21        14.27        15.58         2.33        77.98         0.92 
TCGA-RW-A68C TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-SP-A6QG 
        6.28        35.51        27.91        23.21        17.95        79.46 
TCGA-SQ-A6I4 TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-W2-A7H7 TCGA-W2-A7HE 
        1.41        49.61        37.35        13.32        17.16        16.60 
TCGA-WB-A80P TCGA-WB-A816 TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81S TCGA-WB-A822 
      316.73        41.23        38.76        63.98        23.77       103.17 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.07     1.05     1.15     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  127.56   114.77   116.19   121.05   316.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  30.510   24.590   17.950   26.285   23.490 
[1] "0.2 - 127.6 (30.5)" "0.1 - 114.8 (24.6)" "1.1 - 116.2 (17.9)"
[4] "1.1 - 121.0 (26.3)" "0.9 - 316.7 (23.5)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 31  4
  subtype2 54  2
  subtype3 15  2
  subtype4 27 13
  subtype5 19 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    4
  subtype2   54    2
  subtype3   15    2
  subtype4   27   13
  subtype5   19   11
                    clus
vv                   subtype1 subtype2 subtype3 subtype4 subtype5
  ADRENAL GLAND            31       54       15       27       19
  EXTRA-ADRENAL SITE        4        2        2       13       11
[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"
D9V4, binary
          cls
clus        0  1
  subtype1 22 13
  subtype2 30 26
  subtype3 11  6
  subtype4 24 16
  subtype5 14 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   13
  subtype2   30   26
  subtype3   11    6
  subtype4   24   16
  subtype5   14   16
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       30       11       24       14
  MALE         13       26        6       16       16
[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"
D9V5, binary
          cls
clus        0  1
  subtype1 35  0
  subtype2 54  1
  subtype3 17  0
  subtype4 38  2
  subtype5 27  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    0
  subtype2   54    1
  subtype3   17    0
  subtype4   38    2
  subtype5   27    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        35       54       17       38       27
  YES        0        1        0        2        2
[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"
D9V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             2                                             2
  subtype2             2                                             0
  subtype3             1                                             1
  subtype4             8                                             5
  subtype5             5                                             5
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               31
  subtype2               54
  subtype3               15
  subtype4               27
  subtype5               20
D9V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        2        2        1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        2        0        1
  PHEOCHROMOCYTOMA                                    31       54       15
                                               clus
vv                                              subtype4 subtype5
  PARAGANGLIOMA                                        8        5
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        5        5
  PHEOCHROMOCYTOMA                                    27       20
[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"
D9V8, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       9        4        1        5        2 
 [1] "subtype4" "subtype1" "subtype4" "subtype1" "subtype4" "subtype4"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         6
  subtype2                                0     2                         5
  subtype3                                1     1                         1
  subtype4                                0     2                         5
  subtype5                                0     1                         3
          vv
clus       WHITE
  subtype1    29
  subtype2    47
  subtype3    13
  subtype4    32
  subtype5    26
D9V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        2        1        2        1
  BLACK OR AFRICAN AMERICAN               6        5        1        5        3
  WHITE                                  29       47       13       32       26
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus        0  1
  subtype1  1 24
  subtype2  2 45
  subtype3  0 12
  subtype4  0 31
  subtype5  2 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   24
  subtype2    2   45
  subtype3    0   12
  subtype4    0   31
  subtype5    2   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        2        0        0        2
  NOT HISPANIC OR LATINO       24       45       12       31       25
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 20  1
  subtype2 45  2
  subtype3 28  3
  subtype4 16  0
  subtype5 26  0
  subtype6 18  0
  subtype7 19  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      21       47       31       16       26       18       19 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       1        2        3        0        0        0        0 
$subtype1
TCGA-QR-A70T TCGA-RW-A68F TCGA-S7-A7WU TCGA-WB-A81E TCGA-P7-A5NX TCGA-P8-A6RY 
        8.78        44.52        30.51        48.53        26.89         5.88 
TCGA-QR-A6GX TCGA-QR-A6H2 TCGA-QR-A702 TCGA-QR-A70A TCGA-QR-A70E TCGA-QR-A7IP 
       19.04         9.93         1.28        69.67         6.31        17.95 
TCGA-RT-A6Y9 TCGA-RW-A681 TCGA-RW-A688 TCGA-RW-A68D TCGA-SA-A6C2 TCGA-SR-A6MT 
      108.26        37.51         1.22        72.79         9.73       106.75 
TCGA-W2-A7HH TCGA-WB-A80Y TCGA-WB-A81P 
       25.61        19.59        12.99 

$subtype2
TCGA-QR-A6H1 TCGA-QR-A70O TCGA-RW-A68A TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A81Q 
       14.17         3.65        25.05        19.86        17.69        24.82 
TCGA-WB-A820 TCGA-P7-A5NY TCGA-QR-A6GO TCGA-QR-A6GW TCGA-QR-A707 TCGA-QR-A70M 
       10.16        31.46        35.01        16.14        13.08        33.99 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XN TCGA-RT-A6YA 
       48.43         0.07        41.79         6.94        25.18        50.63 
TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A689 TCGA-RX-A8JQ TCGA-S7-A7WL 
        8.09        19.86         7.10        27.22        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 
       36.56        37.25        82.62       110.04        15.52         1.41 
TCGA-SQ-A6I6 TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HD TCGA-WB-A80N 
        0.10         4.34        19.92        20.09        18.44         4.73 
TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J 
       29.16        42.35        33.90        35.84        57.11        24.36 
TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W 
       62.04         1.61        23.77        71.05        78.21 

$subtype3
TCGA-QR-A6GU TCGA-QR-A700 TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A7CZ 
       58.88        32.15        10.42         0.23       117.14        13.87 
TCGA-SR-A6MR TCGA-SR-A6MX TCGA-P8-A5KC TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6H0 
       79.20         3.12        29.03        17.95       137.59         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A708 TCGA-QR-A70C TCGA-QR-A70Q TCGA-QT-A5XJ 
       14.27        15.58         1.15       116.19         4.60        36.23 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RW-A680 TCGA-RW-A686 TCGA-RW-A8AZ TCGA-SP-A6QD 
       77.98         0.92        47.64        19.30         2.89       109.25 
TCGA-SP-A6QG TCGA-W2-A7H7 TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A81G 
       79.46        17.16        41.26       316.73       127.56        38.76 
TCGA-WB-A822 
      103.17 

$subtype4
TCGA-RW-A68B TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GS TCGA-QR-A6H4 TCGA-QR-A70K 
       23.90         4.04        81.70         1.25        87.48         9.01 
TCGA-RW-A684 TCGA-RW-A7D0 TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SR-A6MQ 
        1.05        11.57        25.32        24.20       114.77        68.61 
TCGA-SR-A6MY TCGA-W2-A7HA TCGA-W2-A7HC TCGA-WB-A80O 
       24.66         1.18        14.43        25.51 

$subtype5
TCGA-QR-A6GZ TCGA-QR-A6ZZ TCGA-QR-A703 TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SP-A6QH 
       30.51         1.58        38.37        26.96        18.94        72.43 
TCGA-SR-A6MV TCGA-WB-A814 TCGA-P8-A6RX TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70I 
      121.05        74.04        17.75        31.53         4.11        29.92 
TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RW-A67X 
       13.12         1.41        12.39         1.81        13.08         2.93 
TCGA-RW-A68C TCGA-S7-A7WP TCGA-S7-A7X0 TCGA-SR-A6MP TCGA-TT-A6YK TCGA-TT-A6YP 
        6.28        31.04        17.95        51.22        37.35        42.48 
TCGA-W2-A7UY TCGA-WB-A821 
       14.79        93.11 

$subtype6
TCGA-RW-A68G TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A70H TCGA-QR-A70R TCGA-QT-A5XM 
       41.88        28.08         1.05        26.83        14.20         0.72 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RW-A67V TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MS 
        4.41         0.79        86.89        40.70        42.77        81.93 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M 
       34.26         4.47        53.59        24.16        40.04        45.83 

$subtype7
TCGA-WB-A817 TCGA-XG-A823 TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X TCGA-QT-A5XO 
       43.07        20.19        23.11         2.33         6.02         2.30 
TCGA-RW-A685 TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SR-A6MU 
        0.85        35.51        27.91        23.21       111.25       110.53 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A816 TCGA-WB-A81H 
       26.20        49.61        13.32        16.60        41.23        63.98 
TCGA-WB-A81T 
       25.51 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1.22     0.07     0.23     1.05     1.41     0.72     0.85 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  108.26   110.04   316.73   114.77   121.05    86.89   111.25 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   19.59    24.36    32.15    24.05    22.95    31.17    25.51 
[1] "1.2 - 108.3 (19.6)" "0.1 - 110.0 (24.4)" "0.2 - 316.7 (32.1)"
[4] "1.1 - 114.8 (24.0)" "1.4 - 121.0 (23.0)" "0.7 - 86.9 (31.2)" 
[7] "0.8 - 111.2 (25.5)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1 15  6
  subtype2 46  1
  subtype3 15 16
  subtype4 15  1
  subtype5 18  8
  subtype6 18  0
  subtype7 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    6
  subtype2   46    1
  subtype3   15   16
  subtype4   15    1
  subtype5   18    8
  subtype6   18    0
  subtype7   19    0
                    clus
vv                   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ADRENAL GLAND            15       46       15       15       18       18
  EXTRA-ADRENAL SITE        6        1       16        1        8        0
                    clus
vv                   subtype7
  ADRENAL GLAND            19
  EXTRA-ADRENAL SITE        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 23 24
  subtype3 13 18
  subtype4 11  5
  subtype5 14 12
  subtype6  9  9
  subtype7 14  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   23   24
  subtype3   13   18
  subtype4   11    5
  subtype5   14   12
  subtype6    9    9
  subtype7   14    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       17       23       13       11       14        9       14
  MALE          4       24       18        5       12        9        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"
D10V5, binary
          cls
clus        0  1
  subtype1 21  0
  subtype2 44  1
  subtype3 28  3
  subtype4 16  0
  subtype5 25  1
  subtype6 18  0
  subtype7 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    0
  subtype2   44    1
  subtype3   28    3
  subtype4   16    0
  subtype5   25    1
  subtype6   18    0
  subtype7   19    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        21       44       28       16       25       18       19
  YES        0        1        3        0        1        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, continuous
          vv
clus       PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  subtype1             4                                             2
  subtype2             1                                             0
  subtype3             8                                             7
  subtype4             1                                             0
  subtype5             4                                             4
  subtype6             0                                             0
  subtype7             0                                             0
          vv
clus       PHEOCHROMOCYTOMA
  subtype1               15
  subtype2               46
  subtype3               16
  subtype4               15
  subtype5               18
  subtype6               18
  subtype7               19
D10V7, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  PARAGANGLIOMA                                        4        1        8
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        2        0        7
  PHEOCHROMOCYTOMA                                    15       46       16
                                               clus
vv                                              subtype4 subtype5 subtype6
  PARAGANGLIOMA                                        1        4        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0        4        0
  PHEOCHROMOCYTOMA                                    15       18       18
                                               clus
vv                                              subtype7
  PARAGANGLIOMA                                        0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA        0
  PHEOCHROMOCYTOMA                                    19
[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"
D10V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
[4] "subtype5"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       3        2        9        1        2        3        1 
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype6"
 [7] "subtype1" "subtype3" "subtype6" "subtype6" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype1"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         3
  subtype2                                0     1                         3
  subtype3                                0     0                         4
  subtype4                                1     1                         0
  subtype5                                0     1                         5
  subtype6                                0     0                         1
  subtype7                                0     1                         4
          vv
clus       WHITE
  subtype1    16
  subtype2    41
  subtype3    26
  subtype4    13
  subtype5    20
  subtype6    17
  subtype7    14
D10V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   2        1        0        1        1
  BLACK OR AFRICAN AMERICAN               3        3        4        0        5
  WHITE                                  16       41       26       13       20
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               1        4
  WHITE                                  17       14
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus        0  1
  subtype1  1 15
  subtype2  2 37
  subtype3  0 24
  subtype4  0 12
  subtype5  0 22
  subtype6  0 12
  subtype7  2 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   15
  subtype2    2   37
  subtype3    0   24
  subtype4    0   12
  subtype5    0   22
  subtype6    0   12
  subtype7    2   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        0        0        0        0
  NOT HISPANIC OR LATINO       15       37       24       12       22       12
                        clus
vv                       subtype7
  HISPANIC OR LATINO            2
  NOT HISPANIC OR LATINO       15
[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"
