[1] "ofn"       "-oTACC-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/ACC-TP/22489368/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/22541000/ACC-TP.mergedcluster.txt"

nPatients in clinical file=92, in cluster file=92, common to both=92
[1] 10 92
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5  6  7 
19 18 13 18 11  6  5 
 1  2  3  4  5  6  7 
19 18 13 18 11  6  5 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
16 14  8 18  9 13  2 
 1  2  3  4  5  6 
16 14  8 18  9 13 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
10 11 11 14 
 1  2  3  4 
10 11 11 14 
[1] "RPPA_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 8 
8 7 7 3 4 4 7 6 
1 2 3 4 5 6 7 8 
8 7 7 3 4 4 7 6 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
24 15 17 23 
 1  2  3  4 
24 15 17 23 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
23 24  7 25 
 1  2  3  4 
23 24  7 25 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
31 24 25 
 1  2  3 
31 24 25 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
17 27 12 20  4 
 1  2  3  4  5 
17 27 12 20  4 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
16 19 17 26 
 1  2  3  4 
16 19 17 26 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
 7 24 11 14 11 11 
 1  2  3  4  5  6 
 7 24 11 14 11 11 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 92 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=33,	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=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'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] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 92 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "GENDER"                "RADIATION_THERAPY"    
 [7] "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=50, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 9 49 11 21 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 9 49 11 21 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 9 49 11 21 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 9 49 11 21 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=7, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 11  8
  subtype2 17  1
  subtype3  8  5
  subtype4  6 12
  subtype5  6  5
  subtype6  6  0
  subtype7  3  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      19       18       13       18       11        6        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       8        1        5       12        5        0        2 
$subtype1
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 
       33.83        12.59        44.55        55.13        88.87        19.04 
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5K6 TCGA-OR-A5KB 
       18.12        39.25        12.59         9.50        49.08        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LL 
       88.01        95.18       127.50       152.15        21.76        53.03 
TCGA-PK-A5H9 
       20.25 

$subtype2
TCGA-OR-A5L5 TCGA-OR-A5J3 TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K1 
       43.30        68.75       121.25        29.82        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 
      113.92        35.57        68.25        58.55        31.79        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       28.64        23.64        14.63        61.05        28.04        24.85 

$subtype3
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JX 
       13.91        12.00        66.25        17.79        16.11        31.23 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LS 
       24.62        46.49        83.80        12.85        29.10        36.03 
TCGA-OU-A5PI 
       38.50 

$subtype4
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JV 
       16.11        44.45        49.22        18.48        15.25        66.51 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5LC 
       18.15        32.68        16.37        44.84        60.89         5.23 
TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-P6-A5OH 
       39.35        52.24        14.33        36.33        79.07         0.00 

$subtype5
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       91.30        42.51        30.31        57.53        69.21        67.59 
TCGA-OR-A5JW TCGA-OR-A5K9 TCGA-OR-A5KZ TCGA-PK-A5HA TCGA-PK-A5HC 
       72.39        11.31         4.11        39.48        22.32 

$subtype6
TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JQ TCGA-OR-A5LN TCGA-OR-A5LT 
       99.88        69.37        76.64        36.26        77.00        18.05 

$subtype7
TCGA-OR-A5LB TCGA-OR-A5KU TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM 
       39.58       153.63        78.41        90.08        61.08 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    9.50    14.63    12.00     0.00     4.11    18.05    39.58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  152.15   121.25    83.80    79.07    91.30    99.88   153.63 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  39.250   33.680   29.100   34.505   42.510   73.005   78.410 
[1] "9.5 - 152.2 (39.2)"  "14.6 - 121.2 (33.7)" "12.0 - 83.8 (29.1)" 
[4] "0.0 - 79.1 (34.5)"   "4.1 - 91.3 (42.5)"   "18.1 - 99.9 (73.0)" 
[7] "39.6 - 153.6 (78.4)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3       10         3        3
  subtype2       2       11         5        0
  subtype3       0        5         2        6
  subtype4       0        5         6        7
  subtype5       3        4         1        1
  subtype6       1        4         1        0
  subtype7       0        4         0        1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          3        2        0        0        3        1        0
  STAGE II        10       11        5        5        4        4        4
  STAGE III        3        5        2        6        1        1        0
  STAGE IV         3        0        6        7        1        0        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 11  3  2
  subtype2  2 12  2  2
  subtype3  0  6  2  5
  subtype4  0  7  3  8
  subtype5  3  4  0  2
  subtype6  1  4  1  0
  subtype7  0  4  0  1
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        3        2        0        0        3        1        0
  T2       11       12        6        7        4        4        4
  T3        3        2        2        3        0        1        0
  T4        2        2        5        8        2        0        1
[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"
D1V5, binary
          cls
clus        0  1
  subtype1 18  1
  subtype2 17  1
  subtype3  8  5
  subtype4 15  3
  subtype5  9  0
  subtype6  6  0
  subtype7  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   17    1
  subtype3    8    5
  subtype4   15    3
  subtype5    9    0
  subtype6    6    0
  subtype7    5    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       18       17        8       15        9        6        5
  1        1        1        5        3        0        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"
D1V6, binary
          cls
clus        0  1
  subtype1 15  4
  subtype2 12  6
  subtype3  7  6
  subtype4 13  5
  subtype5  6  5
  subtype6  4  2
  subtype7  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    4
  subtype2   12    6
  subtype3    7    6
  subtype4   13    5
  subtype5    6    5
  subtype6    4    2
  subtype7    2    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       15       12        7       13        6        4        2
  MALE          4        6        6        5        5        2        3
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 14  4
  subtype2 14  4
  subtype3 10  2
  subtype4 13  5
  subtype5  8  2
  subtype6  6  0
  subtype7  4  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    4
  subtype2   14    4
  subtype3   10    2
  subtype4   13    5
  subtype5    8    2
  subtype6    6    0
  subtype7    4    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        14       14       10       13        8        6        4
  YES        4        4        2        5        2        0        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     0
  subtype5                                     0
  subtype6                                     1
  subtype7                                     0
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
  subtype6                                        2
  subtype7                                        1
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   19
  subtype2                                   17
  subtype3                                   13
  subtype4                                   18
  subtype5                                   11
  subtype6                                    3
  subtype7                                    4
D1V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        0        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        1        0        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           19       17       13       18
                                          clus
vv                                         subtype5 subtype6 subtype7
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        1        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        2        1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           11        3        4
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 16  1  2  0
  subtype2 15  1  0  2
  subtype3  7  1  4  0
  subtype4  8  2  6  2
  subtype5  6  2  0  1
  subtype6  6  0  0  0
  subtype7  5  0  0  0
D1V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       16       15        7        8        6        6        5
  R1        1        1        1        2        2        0        0
  R2        2        0        4        6        0        0        0
  RX        0        2        0        2        1        0        0
[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"
D1V10, continuous
[1] "Remove cluster labels:" "subtype6"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        5        6        7        3        2        2 
 [1] "subtype5" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
 [7] "subtype1" "subtype3" "subtype3" "subtype2" "subtype4" "subtype3"
[13] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype2" "subtype4" "subtype1" "subtype4" "subtype2"
[25] "subtype3" "subtype5" "subtype5"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    16
  subtype2     0                         0    16
  subtype3     0                         0    12
  subtype4     0                         0    17
  subtype5     1                         0     8
  subtype6     0                         0     4
  subtype7     0                         0     3
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0        0
  WHITE                           16       16       12       17        8
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        0        0
  WHITE                            4        3
[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"
D1V12, binary
          cls
clus       0 1
  subtype1 3 9
  subtype2 1 9
  subtype3 2 6
  subtype4 2 8
  subtype5 0 3
  subtype6 0 0
  subtype7 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    9
  subtype2    1    9
  subtype3    2    6
  subtype4    2    8
  subtype5    0    3
  subtype6    0    0
  subtype7    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  HISPANIC OR LATINO            3        1        2        2        0        0
  NOT HISPANIC OR LATINO        9        9        6        8        3        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  4 12
  subtype2 10  4
  subtype3  5  3
  subtype4 10  8
  subtype5  8  1
  subtype6 13  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      16       14        8       18        9       13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12        4        3        8        1        0 
$subtype1
TCGA-OR-A5K0 TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM 
       33.83        44.55        13.91        16.11        69.21        18.48 
TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KV 
       15.25        18.15        32.68        16.37        11.31       127.50 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-OR-A5LE 
       44.84         4.11        39.35        21.76 

$subtype2
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB 
       43.30        12.59        55.13        88.87        19.04        18.12 
TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JV TCGA-OR-A5KT TCGA-OR-A5L3 TCGA-OR-A5LK 
       49.22        39.25        66.51        95.18       152.15        90.08 
TCGA-PA-A5YG TCGA-PK-A5H9 
       24.85        20.25 

$subtype3
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JS TCGA-OR-A5K6 TCGA-OR-A5KW TCGA-OR-A5LC 
       68.75        30.31        12.59        49.08        68.25         5.23 
TCGA-OR-A5LG TCGA-OR-A5LL 
       52.24        53.03 

$subtype4
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JG 
       39.58        42.51        12.00        44.45        57.53        17.79 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JW TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5KY 
       76.64        16.11        72.39        24.62       153.63        12.85 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF TCGA-PK-A5HA 
       61.08        79.07        36.03        38.50         6.81        39.48 

$subtype5
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5L8 TCGA-OR-A5LA 
       99.88        66.25        67.59        36.26        29.10        23.64 
TCGA-OR-A5LH TCGA-OR-A5LN TCGA-OR-A5LP 
       78.41        77.00        61.05 

$subtype6
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
      121.25        29.82        31.23        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LR TCGA-OR-A5LT 
       35.57        31.79        28.31        28.64        28.04        18.05 
TCGA-PK-A5H8 
      119.11 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.11    12.59     5.23     6.81    23.64    18.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  127.50   152.15    68.75   153.63    99.88   121.25 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   20.12    46.26    50.66    39.53    66.25    31.23 
[1] "4.1 - 127.5 (20.1)"  "12.6 - 152.2 (46.3)" "5.2 - 68.8 (50.7)"  
[4] "6.8 - 153.6 (39.5)"  "23.6 - 99.9 (66.2)"  "18.1 - 121.2 (31.2)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        6         6        3
  subtype2       4        5         1        4
  subtype3       0        3         3        2
  subtype4       2        7         2        5
  subtype5       1        8         0        0
  subtype6       1        8         4        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          1        4        0        2        1        1
  STAGE II         6        5        3        7        8        8
  STAGE III        6        1        3        2        0        4
  STAGE IV         3        4        2        5        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  8  3  4
  subtype2  4  5  2  3
  subtype3  0  4  2  2
  subtype4  2  8  0  6
  subtype5  1  8  0  0
  subtype6  1  8  2  2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        4        0        2        1        1
  T2        8        5        4        8        8        8
  T3        3        2        2        0        0        2
  T4        4        3        2        6        0        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 12  4
  subtype2 14  0
  subtype3  7  1
  subtype4 12  4
  subtype5  9  0
  subtype6 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    4
  subtype2   14    0
  subtype3    7    1
  subtype4   12    4
  subtype5    9    0
  subtype6   13    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       12       14        7       12        9       13
  1        4        0        1        4        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 11  5
  subtype2  8  6
  subtype3  7  1
  subtype4  7 11
  subtype5  9  0
  subtype6  5  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    5
  subtype2    8    6
  subtype3    7    1
  subtype4    7   11
  subtype5    9    0
  subtype6    5    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       11        8        7        7        9        5
  MALE          5        6        1       11        0        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 11  5
  subtype2 11  2
  subtype3  6  2
  subtype4 13  3
  subtype5  8  1
  subtype6  9  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    5
  subtype2   11    2
  subtype3    6    2
  subtype4   13    3
  subtype5    8    1
  subtype6    9    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        11       11        6       13        8        9
  YES        5        2        2        3        1        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     0
  subtype5                                     1
  subtype6                                     0
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        1
  subtype6                                        1
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   16
  subtype2                                   13
  subtype3                                    8
  subtype4                                   18
  subtype5                                    7
  subtype6                                   12
D2V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        0        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        1        0        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           16       13        8       18
                                          clus
vv                                         subtype5 subtype6
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           1        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        1        1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            7       12
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 10  2  2  2
  subtype2 10  1  3  0
  subtype3  5  1  1  1
  subtype4 10  1  3  1
  subtype5  9  0  0  0
  subtype6 10  1  0  2
D2V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       10       10        5       10        9       10
  R1        2        1        1        1        0        1
  R2        2        3        1        3        0        0
  RX        2        0        1        1        0        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        4        4        8        2        4 
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [7] "subtype4" "subtype4" "subtype6" "subtype2" "subtype6" "subtype1"
[13] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype4"
[19] "subtype6" "subtype3" "subtype3" "subtype4" "subtype4" "subtype6"
[25] "subtype4" "subtype4"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    16
  subtype2     1                         1    11
  subtype3     0                         0     7
  subtype4     0                         0    13
  subtype5     0                         0     7
  subtype6     0                         0    11
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        0        0        0
  BLACK OR AFRICAN AMERICAN        0        1        0        0        0
  WHITE                           16       11        7       13        7
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           11
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
          cls
clus       0 1
  subtype1 2 5
  subtype2 3 6
  subtype3 1 4
  subtype4 2 6
  subtype5 0 3
  subtype6 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    5
  subtype2    3    6
  subtype3    1    4
  subtype4    2    6
  subtype5    0    3
  subtype6    0    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        3        1        2        0        0
  NOT HISPANIC OR LATINO        5        6        4        6        3        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  6  4
  subtype2  9  2
  subtype3 10  1
  subtype4  7  7
subtype1 subtype2 subtype3 subtype4 
      10       11       11       14 
subtype1 subtype2 subtype3 subtype4 
       4        2        1        7 
$subtype1
TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59        55.13        19.04        29.82        18.15        27.02 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5LK TCGA-OU-A5PI 
      153.63        44.84        90.08        38.50 

$subtype2
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K8 
       68.75        30.31        15.25        72.39        49.08        24.62 
TCGA-OR-A5KW TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LT TCGA-PK-A5H9 
       68.25        52.24        53.03        18.05        20.25 

$subtype3
TCGA-OR-A5J6 TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5LH 
       88.87       121.25        66.51       108.13       113.92        78.41 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5HA 
       77.00        61.05        24.85       119.11        39.48 

$subtype4
TCGA-OR-A5K0 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JS TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        16.11        44.45        12.59        35.57        16.37 
TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LM 
       46.49        12.85         4.11        39.35        36.33        61.08 
TCGA-OR-A5LO TCGA-OR-A5LS 
       79.07        36.03 

subtype1 subtype2 subtype3 subtype4 
   12.59    15.25    24.85     4.11 
subtype1 subtype2 subtype3 subtype4 
  153.63    72.39   121.25    79.07 
subtype1 subtype2 subtype3 subtype4 
   34.16    49.08    78.41    35.80 
[1] "12.6 - 153.6 (34.2)" "15.2 - 72.4 (49.1)"  "24.9 - 121.2 (78.4)"
[4] "4.1 - 79.1 (35.8)"  
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        4         2        4
  subtype2       0        6         4        1
  subtype3       2        9         0        0
  subtype4       0        7         4        3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        0        2        0
  STAGE II         4        6        9        7
  STAGE III        2        4        0        4
  STAGE IV         4        1        0        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  6  2  2
  subtype2  0  7  3  1
  subtype3  2  9  0  0
  subtype4  0  8  2  4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        0        2        0
  T2        6        7        9        8
  T3        2        3        0        2
  T4        2        1        0        4
[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"
D3V5, binary
          cls
clus        0  1
  subtype1  7  3
  subtype2 10  1
  subtype3 11  0
  subtype4 12  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    3
  subtype2   10    1
  subtype3   11    0
  subtype4   12    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7       10       11       12
  1        3        1        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"
D3V6, binary
          cls
clus        0  1
  subtype1  7  3
  subtype2  6  5
  subtype3  4  7
  subtype4 11  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    3
  subtype2    6    5
  subtype3    4    7
  subtype4   11    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7        6        4       11
  MALE          3        5        7        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"
D3V7, binary
          cls
clus        0  1
  subtype1  6  4
  subtype2  9  2
  subtype3 11  0
  subtype4 11  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    4
  subtype2    9    2
  subtype3   11    0
  subtype4   11    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        9       11       11
  YES        4        2        0        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"
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        1
  subtype2                                        0
  subtype3                                        1
  subtype4                                        0
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                    9
  subtype2                                   11
  subtype3                                   10
  subtype4                                   14
D3V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        1        0        1        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            9       11       10       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  6  0  3  0
  subtype2  9  1  0  1
  subtype3 10  0  0  1
  subtype4  8  2  2  2
D3V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        6        9       10        8
  R1        0        1        0        2
  R2        3        0        0        2
  RX        0        1        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     9
  subtype2     1                         0     8
  subtype3     0                         1     7
  subtype4     0                         0    11
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0
  WHITE                            9        8        7       11
[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"
D3V12, binary
          cls
clus       0 1
  subtype1 2 4
  subtype2 1 5
  subtype3 1 3
  subtype4 2 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    4
  subtype2    1    5
  subtype3    1    3
  subtype4    2    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        1        2
  NOT HISPANIC OR LATINO        4        5        3        5
[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 3 5
  subtype2 4 3
  subtype3 7 0
  subtype4 2 1
  subtype5 1 3
  subtype6 4 0
  subtype7 6 1
  subtype8 5 1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       8        7        7        3        4        4        7        6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       5        3        0        1        3        0        1        1 
$subtype1
TCGA-OR-A5K0 TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-OR-A5LJ 
       33.83        55.13        44.45         4.11        39.35        36.33 
TCGA-OR-A5LO TCGA-OR-A5LS 
       79.07        36.03 

$subtype2
TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KW 
       68.75        30.31        16.37        24.62        46.49        68.25 
TCGA-OR-A5KY 
       12.85 

$subtype3
TCGA-OR-A5J6 TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5LK TCGA-OR-A5LP TCGA-PA-A5YG 
       88.87        29.82        27.02        90.08        61.05        24.85 
TCGA-PK-A5HA 
       39.48 

$subtype4
TCGA-OR-A5J7 TCGA-OR-A5JP TCGA-OR-A5KX 
       16.11        15.25        44.84 

$subtype5
TCGA-P6-A5OG TCGA-OR-A5J8 TCGA-OR-A5JY TCGA-OR-A5KU 
       12.59        19.04        18.15       153.63 

$subtype6
TCGA-OR-A5JR TCGA-OR-A5K1 TCGA-OR-A5LN TCGA-OR-A5LT 
      121.25       108.13        77.00        18.05 

$subtype7
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5LH TCGA-OR-A5LM 
       12.59        66.51       113.92        35.57        78.41        61.08 
TCGA-PK-A5H8 
      119.11 

$subtype8
TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OU-A5PI TCGA-PK-A5H9 
       72.39        49.08        52.24        53.03        38.50        20.25 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    4.11    12.85    24.85    15.25    12.59    18.05    12.59    20.25 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   79.07    68.75    90.08    44.84   153.63   121.25   119.11    72.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  37.840   30.310   39.480   16.110   18.595   92.565   66.510   50.660 
[1] "4.1 - 79.1 (37.8)"   "12.8 - 68.8 (30.3)"  "24.9 - 90.1 (39.5)" 
[4] "15.2 - 44.8 (16.1)"  "12.6 - 153.6 (18.6)" "18.1 - 121.2 (92.6)"
[7] "12.6 - 119.1 (66.5)" "20.2 - 72.4 (50.7)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        5         1        2
  subtype2       0        1         3        3
  subtype3       1        6         0        0
  subtype4       0        1         2        0
  subtype5       0        1         1        2
  subtype6       1        2         1        0
  subtype7       0        6         1        0
  subtype8       0        4         1        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          0        0        1        0        0        1        0
  STAGE II         5        1        6        1        1        2        6
  STAGE III        1        3        0        2        1        1        1
  STAGE IV         2        3        0        0        2        0        0
           clus
vv          subtype8
  STAGE I          0
  STAGE II         4
  STAGE III        1
  STAGE IV         1
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  6  1  1
  subtype2  0  2  2  3
  subtype3  1  6  0  0
  subtype4  0  2  1  0
  subtype5  0  1  1  2
  subtype6  1  2  1  0
  subtype7  0  6  0  1
  subtype8  0  5  1  0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        0        0        1        0        0        1        0        0
  T2        6        2        6        2        1        2        6        5
  T3        1        2        0        1        1        1        0        1
  T4        1        3        0        0        2        0        1        0
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus       0 1
  subtype1 7 1
  subtype2 5 2
  subtype3 7 0
  subtype4 2 1
  subtype5 3 1
  subtype6 4 0
  subtype7 7 0
  subtype8 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    5    2
  subtype3    7    0
  subtype4    2    1
  subtype5    3    1
  subtype6    4    0
  subtype7    7    0
  subtype8    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0        7        5        7        2        3        4        7        5
  1        1        2        0        1        1        0        0        1
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus       0 1
  subtype1 6 2
  subtype2 6 1
  subtype3 3 4
  subtype4 2 1
  subtype5 3 1
  subtype6 1 3
  subtype7 3 4
  subtype8 4 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    2
  subtype2    6    1
  subtype3    3    4
  subtype4    2    1
  subtype5    3    1
  subtype6    1    3
  subtype7    3    4
  subtype8    4    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        6        6        3        2        3        1        3
  MALE          2        1        4        1        1        3        4
        clus
vv       subtype8
  FEMALE        4
  MALE          2
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus       0 1
  subtype1 8 0
  subtype2 5 2
  subtype3 5 2
  subtype4 3 0
  subtype5 2 2
  subtype6 4 0
  subtype7 5 2
  subtype8 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2    5    2
  subtype3    5    2
  subtype4    3    0
  subtype5    2    2
  subtype6    4    0
  subtype7    5    2
  subtype8    5    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         8        5        5        3        2        4        5        5
  YES        0        2        2        0        2        0        2        1
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
  subtype4                                        0
  subtype5                                        0
  subtype6                                        0
  subtype7                                        1
  subtype8                                        0
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                    8
  subtype2                                    7
  subtype3                                    6
  subtype4                                    3
  subtype5                                    4
  subtype6                                    4
  subtype7                                    6
  subtype8                                    6
D4V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        1        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            8        7        6        3
                                          clus
vv                                         subtype5 subtype6 subtype7 subtype8
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        1        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            4        4        6        6
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  4  0  2  2
  subtype2  5  1  1  0
  subtype3  7  0  0  0
  subtype4  2  1  0  0
  subtype5  2  0  2  0
  subtype6  3  0  0  1
  subtype7  6  1  0  0
  subtype8  4  0  0  1
D4V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0        4        5        7        2        2        3        6        4
  R1        0        1        0        1        0        0        1        0
  R2        2        1        0        0        2        0        0        0
  RX        2        0        0        0        0        1        0        1
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
[4] "subtype6"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        4        3        1        4        2        2        3 
 [1] "subtype5" "subtype2" "subtype5" "subtype3" "subtype5" "subtype2"
 [7] "subtype5" "subtype2" "subtype2" "subtype8" "subtype8" "subtype3"
[13] "subtype8" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     6
  subtype2     0                         0     7
  subtype3     0                         1     3
  subtype4     0                         0     3
  subtype5     0                         0     4
  subtype6     0                         0     2
  subtype7     0                         0     6
  subtype8     1                         0     4
D4V11, multiclass
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       6        7        4        3        4        2        6        5 
 [1] "subtype1" "subtype5" "subtype1" "subtype2" "subtype3" "subtype4"
 [7] "subtype5" "subtype1" "subtype2" "subtype4" "subtype7" "subtype3"
[13] "subtype7" "subtype8" "subtype5" "subtype3" "subtype7" "subtype7"
[19] "subtype2" "subtype8" "subtype2" "subtype2" "subtype5" "subtype2"
[25] "subtype4" "subtype2" "subtype1" "subtype1" "subtype8" "subtype7"
[31] "subtype1" "subtype8" "subtype3" "subtype7" "subtype8"
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                            6        7        3        3        4
                           clus
vv                          subtype7 subtype8
  ASIAN                            0        1
  BLACK OR AFRICAN AMERICAN        0        0
  WHITE                            6        4
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus       0 1
  subtype1 2 3
  subtype2 1 4
  subtype3 1 1
  subtype4 1 1
  subtype5 1 2
  subtype6 0 0
  subtype7 0 2
  subtype8 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2    1    4
  subtype3    1    1
  subtype4    1    1
  subtype5    1    2
  subtype6    0    0
  subtype7    0    2
  subtype8    0    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  HISPANIC OR LATINO            2        1        1        1        1        0
  NOT HISPANIC OR LATINO        3        4        1        1        2        2
                        clus
vv                       subtype8
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        4
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  9 15
  subtype2  7  8
  subtype3 13  4
  subtype4 22  1
subtype1 subtype2 subtype3 subtype4 
      24       15       17       23 
subtype1 subtype2 subtype3 subtype4 
      15        8        4        1 
$subtype1
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       33.83        12.59        44.55        16.11        19.04        18.12 
TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 
       69.21        18.48        15.25        12.59        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       16.37        49.08        11.31        95.18       127.50        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
        4.11       152.15         5.23        39.35        21.76        52.24 

$subtype2
TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ 
       39.58        55.13        12.00        44.45        66.25        16.11 
TCGA-OR-A5JX TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LJ TCGA-OR-A5LO 
       31.23       153.63        12.85        29.10        36.33        79.07 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF 
       36.03        38.50         6.81 

$subtype3
TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JL 
       42.51        68.75        30.31        57.53        17.79        67.59 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO 
       66.51        72.39       113.92        35.57        24.62        46.49 
TCGA-OR-A5KW TCGA-OR-A5L4 TCGA-OR-A5LH TCGA-OR-A5LM TCGA-PK-A5H8 
       68.25        31.79        78.41        61.08       119.11 

$subtype4
TCGA-OR-A5L5 TCGA-OR-A5J6 TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JO 
       43.30        88.87        99.88        76.64        49.22        39.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5L6 
       36.26       121.25        29.82        27.02       108.13        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP 
       28.64        23.64        90.08        53.03        77.00        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       28.04        18.05        24.85        20.25        39.48 

subtype1 subtype2 subtype3 subtype4 
    4.11     6.81    17.79    18.05 
subtype1 subtype2 subtype3 subtype4 
  152.15   153.63   119.11   121.25 
subtype1 subtype2 subtype3 subtype4 
   20.40    36.33    61.08    39.48 
[1] "4.1 - 152.2 (20.4)"  "6.8 - 153.6 (36.3)"  "17.8 - 119.1 (61.1)"
[4] "18.1 - 121.2 (39.5)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3        8         8        5
  subtype2       0        6         3        6
  subtype3       1        7         4        3
  subtype4       5       16         1        1
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          3        0        1        5
  STAGE II         8        6        7       16
  STAGE III        8        3        4        1
  STAGE IV         5        6        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 10  4  7
  subtype2  0  8  2  5
  subtype3  1  8  1  5
  subtype4  5 16  1  1
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        0        1        5
  T2       10        8        8       16
  T3        4        2        1        1
  T4        7        5        5        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 21  3
  subtype2 11  4
  subtype3 13  2
  subtype4 23  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    3
  subtype2   11    4
  subtype3   13    2
  subtype4   23    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       21       11       13       23
  1        3        4        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, binary
          cls
clus        0  1
  subtype1 16  8
  subtype2 11  4
  subtype3  8  9
  subtype4 13 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    8
  subtype2   11    4
  subtype3    8    9
  subtype4   13   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       16       11        8       13
  MALE          8        4        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"
D5V7, binary
          cls
clus        0  1
  subtype1 16  7
  subtype2 12  3
  subtype3 11  4
  subtype4 20  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    7
  subtype2   12    3
  subtype3   11    4
  subtype4   20    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        16       12       11       20
  YES        7        3        4        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"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     1
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
  subtype4                                        2
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   24
  subtype2                                   15
  subtype3                                   16
  subtype4                                   20
D5V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        0        1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        1        2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           24       15       16       20
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 15  3  3  3
  subtype2  8  0  5  1
  subtype3 11  3  0  1
  subtype4 21  0  1  1
D5V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       15        8       11       21
  R1        3        0        3        0
  R2        3        5        0        1
  RX        3        1        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    24
  subtype2     0                         0    13
  subtype3     0                         0    15
  subtype4     1                         1    14
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                           24       13       15       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"
D5V12, binary
          cls
clus        0  1
  subtype1  2 11
  subtype2  3  7
  subtype3  1  6
  subtype4  1  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   11
  subtype2    3    7
  subtype3    1    6
  subtype4    1    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        1        1
  NOT HISPANIC OR LATINO       11        7        6        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  8 15
  subtype2 15  9
  subtype3  4  3
  subtype4 24  1
subtype1 subtype2 subtype3 subtype4 
      23       24        7       25 
subtype1 subtype2 subtype3 subtype4 
      15        9        3        1 
$subtype1
TCGA-OR-A5K0 TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM 
       33.83        44.55        55.13        16.11        69.21        18.48 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 
       15.25        12.59        18.15        32.68        16.37        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LC 
       11.31       127.50        44.84         4.11       152.15         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LL 
       39.35        21.76        52.24        36.33        53.03 

$subtype2
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       39.58        42.51        68.75        12.00        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JW 
       57.53        66.25        17.79        16.11        49.22        72.39 
TCGA-OR-A5JX TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       31.23        24.62        46.49       153.63        68.25        12.85 
TCGA-OR-A5L8 TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF 
       29.10        61.08        79.07        36.03        38.50         6.81 

$subtype3
TCGA-P6-A5OG TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5KT 
       12.59        88.87        19.04        18.12        39.25        95.18 
TCGA-PK-A5H9 
       20.25 

$subtype4
TCGA-OR-A5L5 TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR 
       43.30        99.88        76.64        67.59        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       29.82        66.51        27.02       108.13       113.92        35.57 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LH TCGA-OR-A5LK 
       31.79        28.31        28.64        23.64        78.41        90.08 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H8 
       77.00        61.05        28.04        18.05        24.85       119.11 
TCGA-PK-A5HA 
       39.48 

subtype1 subtype2 subtype3 subtype4 
    4.11     6.81    12.59    18.05 
subtype1 subtype2 subtype3 subtype4 
  152.15   153.63    95.18   121.25 
subtype1 subtype2 subtype3 subtype4 
  33.830   41.045   20.250   43.300 
[1] "4.1 - 152.2 (33.8)"  "6.8 - 153.6 (41.0)"  "12.6 - 95.2 (20.2)" 
[4] "18.1 - 121.2 (43.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2        9         7        5
  subtype2       0        9         5        8
  subtype3       2        2         1        2
  subtype4       5       17         3        0
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        2        5
  STAGE II         9        9        2       17
  STAGE III        7        5        1        3
  STAGE IV         5        8        2        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 12  4  5
  subtype2  0 11  2  9
  subtype3  2  2  1  2
  subtype4  5 17  1  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        0        2        5
  T2       12       11        2       17
  T3        4        2        1        1
  T4        5        9        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 19  4
  subtype2 17  5
  subtype3  7  0
  subtype4 25  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    4
  subtype2   17    5
  subtype3    7    0
  subtype4   25    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       19       17        7       25
  1        4        5        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"
D6V6, binary
          cls
clus        0  1
  subtype1 17  6
  subtype2 13 11
  subtype3  5  2
  subtype4 13 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    6
  subtype2   13   11
  subtype3    5    2
  subtype4   13   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       13        5       13
  MALE          6       11        2       12
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 17  6
  subtype2 15  7
  subtype3  5  1
  subtype4 22  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    6
  subtype2   15    7
  subtype3    5    1
  subtype4   22    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       15        5       22
  YES        6        7        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"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     1
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        0
  subtype4                                        3
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   23
  subtype2                                   24
  subtype3                                    7
  subtype4                                   21
D6V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        0        1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        0        3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           23       24        7       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"
          vv
clus       R0 R1 R2 RX
  subtype1 14  2  4  3
  subtype2 14  2  4  1
  subtype3  5  1  1  0
  subtype4 22  1  0  2
D6V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       14       14        5       22
  R1        2        2        1        1
  R2        4        4        1        0
  RX        3        1        0        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       8       10        2        7 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype4"
 [7] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype1"
[19] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[25] "subtype4"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    22
  subtype2     0                         0    20
  subtype3     1                         1     5
  subtype4     0                         0    19
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0
  WHITE                           22       20        5       19
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
          cls
clus        0  1
  subtype1  2 10
  subtype2  3  9
  subtype3  2  3
  subtype4  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   10
  subtype2    3    9
  subtype3    2    3
  subtype4    0    8
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        2        0
  NOT HISPANIC OR LATINO       10        9        3        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 18 13
  subtype2 10 14
  subtype3 23  2
subtype1 subtype2 subtype3 
      31       24       25 
subtype1 subtype2 subtype3 
      13       14        2 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA 
       44.55        68.75        12.00        88.87        16.11        30.31 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JS 
       69.21        17.79        49.22        67.59        15.25        12.59 
TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KW 
       32.68        35.57        49.08        11.31        46.49        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE 
       44.84         4.11        31.79        29.10        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-P6-A5OF TCGA-PK-A5H8 
       52.24        61.08        79.07        36.03         6.81       119.11 
TCGA-PK-A5H9 
       20.25 

$subtype2
TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J4 
       33.83        39.58        12.59        42.51        55.13        13.91 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JM 
       19.04        44.45        18.12        66.25        16.11        18.48 
TCGA-OR-A5JY TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       18.15        16.37        24.62        95.18       153.63       127.50 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OU-A5PI 
       12.85       152.15         5.23        36.33        53.03        38.50 

$subtype3
TCGA-OR-A5L5 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JQ 
       43.30        57.53        99.88        76.64        39.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
      121.25        29.82        66.51        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LH 
      108.13       113.92        28.31        28.64        23.64        78.41 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       90.08        77.00        61.05        28.04        18.05        24.85 
TCGA-PK-A5HA 
       39.48 

subtype1 subtype2 subtype3 
    4.11     5.23    18.05 
subtype1 subtype2 subtype3 
  119.11   153.63   121.25 
subtype1 subtype2 subtype3 
   36.03    35.08    43.30 
[1] "4.1 - 119.1 (36.0)"  "5.2 - 153.6 (35.1)"  "18.1 - 121.2 (43.3)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2       14        11        4
  subtype2       2        6         3       12
  subtype3       5       17         2        0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          2        2        5
  STAGE II        14        6       17
  STAGE III       11        3        2
  STAGE IV         4       12        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 16  3 10
  subtype2  2  9  4  8
  subtype3  5 17  2  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        2        5
  T2       16        9       17
  T3        3        4        2
  T4       10        8        0
[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"
D7V5, binary
          cls
clus        0  1
  subtype1 28  3
  subtype2 16  7
  subtype3 24  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    3
  subtype2   16    7
  subtype3   24    0
   clus
vv  subtype1 subtype2 subtype3
  0       28       16       24
  1        3        7        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, binary
          cls
clus        0  1
  subtype1 20 11
  subtype2 18  6
  subtype3 11 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   11
  subtype2   18    6
  subtype3   11   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       18       11
  MALE         11        6       14
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 25  5
  subtype2 15  8
  subtype3 20  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    5
  subtype2   15    8
  subtype3   20    4
     clus
vv    subtype1 subtype2 subtype3
  NO        25       15       20
  YES        5        8        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     1
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        3
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   31
  subtype2                                   24
  subtype3                                   21
D7V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           31       24       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"
          vv
clus       R0 R1 R2 RX
  subtype1 20  4  2  5
  subtype2 12  2  8  0
  subtype3 23  0  0  1
D7V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       20       12       23
  R1        4        2        0
  R2        2        8        0
  RX        5        0        1
[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, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    26
  subtype2     0                         0    22
  subtype3     0                         0    19
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        0
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           26       22       19
[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"
D7V12, binary
          cls
clus        0  1
  subtype1  4 13
  subtype2  4 11
  subtype3  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   13
  subtype2    4   11
  subtype3    0    6
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        0
  NOT HISPANIC OR LATINO       13       11        6
[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  8  9
  subtype2 20  7
  subtype3 12  0
  subtype4  9 11
  subtype5  2  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       27       12       20        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9        7        0       11        2 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JC 
       44.55        68.75        13.91        12.00        30.31        57.53 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JX TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KW 
       16.11        49.22        31.23       113.92        35.57        68.25 
TCGA-OR-A5KZ TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-P6-A5OF 
        4.11        52.24        61.08        79.07         6.81 

$subtype2
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD 
       33.83        12.59        55.13        44.45        18.12        99.88 
TCGA-OR-A5JF TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       66.25        18.48        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K8 TCGA-OR-A5KU 
       72.39        18.15        27.02       108.13        24.62       153.63 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LP 
       12.85        28.31        28.64        78.41        90.08        61.05 
TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HA 
       28.04        24.85        39.48 

$subtype3
TCGA-OR-A5L5 TCGA-OR-A5J6 TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5KO 
       43.30        88.87        76.64        67.59        39.25        46.49 
TCGA-OR-A5L4 TCGA-OR-A5LA TCGA-OR-A5LN TCGA-OR-A5LT TCGA-PK-A5H8 TCGA-PK-A5H9 
       31.79        23.64        77.00        18.05       119.11        20.25 

$subtype4
TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JP 
       42.51        16.11        19.04        69.21        17.79        15.25 
TCGA-OR-A5JS TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV 
       12.59        32.68        16.37        11.31        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       44.84       152.15        29.10         5.23        39.35        21.76 
TCGA-OR-A5LJ TCGA-OR-A5LS 
       36.33        36.03 

$subtype5
TCGA-OR-A5LB TCGA-OR-A5K6 TCGA-OR-A5LL TCGA-OU-A5PI 
       39.58        49.08        53.03        38.50 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.11    12.59    18.05     5.23    38.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
  113.92   153.63   119.11   152.15    53.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  44.550   36.260   44.895   30.890   44.330 
[1] "4.1 - 113.9 (44.5)"  "12.6 - 153.6 (36.3)" "18.1 - 119.1 (44.9)"
[4] "5.2 - 152.2 (30.9)"  "38.5 - 53.0 (44.3)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        5         7        4
  subtype2       2       19         0        6
  subtype3       4        5         2        1
  subtype4       3        6         7        3
  subtype5       0        2         0        2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        2        4        3        0
  STAGE II         5       19        5        6        2
  STAGE III        7        0        2        7        0
  STAGE IV         4        6        1        3        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  6  4  6
  subtype2  2 19  1  5
  subtype3  4  5  1  2
  subtype4  3  9  3  4
  subtype5  0  3  0  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        2        4        3        0
  T2        6       19        5        9        3
  T3        4        1        1        3        0
  T4        6        5        2        4        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 13  3
  subtype2 25  2
  subtype3 12  0
  subtype4 15  4
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    3
  subtype2   25    2
  subtype3   12    0
  subtype4   15    4
  subtype5    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       25       12       15        3
  1        3        2        0        4        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"
D8V6, binary
          cls
clus        0  1
  subtype1  7 10
  subtype2 16 11
  subtype3  9  3
  subtype4 14  6
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   10
  subtype2   16   11
  subtype3    9    3
  subtype4   14    6
  subtype5    3    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        7       16        9       14        3
  MALE         10       11        3        6        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"
D8V7, binary
          cls
clus        0  1
  subtype1 12  4
  subtype2 20  6
  subtype3 12  0
  subtype4 13  6
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    4
  subtype2   20    6
  subtype3   12    0
  subtype4   13    6
  subtype5    3    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        12       20       12       13        3
  YES        4        6        0        6        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"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     1
  subtype3                                     0
  subtype4                                     0
  subtype5                                     0
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        1
  subtype2                                        2
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   16
  subtype2                                   24
  subtype3                                   12
  subtype4                                   20
  subtype5                                    4
D8V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        1        0        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        1        2        0        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           16       24       12       20
                                          clus
vv                                         subtype5
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  7  2  4  3
  subtype2 20  2  4  1
  subtype3 11  0  0  1
  subtype4 14  2  2  1
  subtype5  3  0  0  0
D8V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7       20       11       14        3
  R1        2        2        0        2        0
  R2        4        4        0        2        0
  RX        3        1        1        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       10        2        6        2 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype4" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    15
  subtype2     0                         0    23
  subtype3     1                         1     8
  subtype4     0                         0    18
  subtype5     0                         0     3
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                           15       23        8       18        3
[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"
D8V12, binary
          cls
clus       0 1
  subtype1 3 4
  subtype2 2 8
  subtype3 1 6
  subtype4 2 9
  subtype5 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    4
  subtype2    2    8
  subtype3    1    6
  subtype4    2    9
  subtype5    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        1        2        0
  NOT HISPANIC OR LATINO        4        8        6        9        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1  6 10
  subtype2 10  9
  subtype3  9  8
  subtype4 24  2
subtype1 subtype2 subtype3 subtype4 
      16       19       17       26 
subtype1 subtype2 subtype3 subtype4 
      10        9        8        2 
$subtype1
TCGA-OR-A5K0 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5J9 
       33.83        42.51        44.55        13.91        19.04        44.45 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KV 
       18.48        15.25        18.15        32.68        16.37       127.50 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-OR-A5LE 
       44.84         4.11        39.35        21.76 

$subtype2
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JJ 
       39.58        12.59        55.13        18.12        66.25        16.11 
TCGA-OR-A5JS TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KT TCGA-OR-A5KU 
       12.59        72.39        49.08        24.62        95.18       153.63 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS 
       12.85       152.15         5.23        36.33        53.03        36.03 
TCGA-OU-A5PI 
       38.50 

$subtype3
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JE 
       68.75        12.00        88.87        16.11        30.31        69.21 
TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO 
       17.79        49.22        67.59        35.57        11.31        46.49 
TCGA-OR-A5KW TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LO TCGA-P6-A5OF 
       68.25        31.79        29.10        79.07         6.81 

$subtype4
TCGA-OR-A5L5 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JQ 
       43.30        57.53        99.88        76.64        39.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LG TCGA-OR-A5LH 
      113.92        28.31        28.64        23.64        52.24        78.41 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       90.08        77.00        61.05        28.04        18.05        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

subtype1 subtype2 subtype3 subtype4 
    4.11     5.23     6.81    18.05 
subtype1 subtype2 subtype3 subtype4 
  127.50   153.63    88.87   121.25 
subtype1 subtype2 subtype3 subtype4 
   27.22    38.50    35.57    41.39 
[1] "4.1 - 127.5 (27.2)"  "5.2 - 153.6 (38.5)"  "6.8 - 88.9 (35.6)"  
[4] "18.1 - 121.2 (41.4)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        6         6        3
  subtype2       2        8         0        9
  subtype3       2        4         7        4
  subtype4       5       17         3        0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        2        2        5
  STAGE II         6        8        4       17
  STAGE III        6        0        7        3
  STAGE IV         3        9        4        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  8  3  4
  subtype2  2 10  1  6
  subtype3  2  5  2  8
  subtype4  5 17  3  0
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        2        2        5
  T2        8       10        5       17
  T3        3        1        2        3
  T4        4        6        8        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 11  4
  subtype2 15  4
  subtype3 15  2
  subtype4 25  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    4
  subtype2   15    4
  subtype3   15    2
  subtype4   25    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       11       15       15       25
  1        4        4        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"
D9V6, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2 14  5
  subtype3 14  3
  subtype4 12 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2   14    5
  subtype3   14    3
  subtype4   12   14
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       14       14       12
  MALE          7        5        3       14
[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"
D9V7, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2 14  4
  subtype3 13  3
  subtype4 22  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2   14    4
  subtype3   13    3
  subtype4   22    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         9       14       13       22
  YES        7        4        3        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"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     1
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        0
  subtype4                                        3
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                   16
  subtype2                                   19
  subtype3                                   17
  subtype4                                   22
D9V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0        0        1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        0        0        3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           16       19       17       22
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 10  1  2  2
  subtype2 11  1  6  0
  subtype3  9  4  2  2
  subtype4 23  0  0  2
D9V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       10       11        9       23
  R1        1        1        4        0
  R2        2        6        2        0
  RX        2        0        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    15
  subtype2     0                         0    17
  subtype3     0                         1    15
  subtype4     1                         0    19
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        1        0
  WHITE                           15       17       15       19
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus        0  1
  subtype1  3  5
  subtype2  1 11
  subtype3  4  5
  subtype4  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    5
  subtype2    1   11
  subtype3    4    5
  subtype4    0    8
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        4        0
  NOT HISPANIC OR LATINO        5       11        5        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1  0  7
  subtype2 19  5
  subtype3  9  2
  subtype4  6  8
  subtype5  5  6
  subtype6 10  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7       24       11       14       11       11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7        5        2        8        6        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JJ TCGA-OR-A5KZ TCGA-OR-A5LO 
       44.55        13.91        12.00        16.11         4.11        79.07 
TCGA-P6-A5OF 
        6.81 

$subtype2
TCGA-OR-A5K0 TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JM TCGA-OR-A5JQ 
       33.83        55.13        44.45        66.25        18.48        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        29.82        66.51        72.39        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K8 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5L9 
      108.13        24.62       153.63        12.85        28.31        28.64 
TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HA 
       78.41        90.08        61.05        28.04        24.85        39.48 

$subtype3
TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL 
       68.75        88.87        30.31        17.79        49.22        67.59 
TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5L4 TCGA-OR-A5LG 
       35.57        46.49        68.25        31.79        52.24 

$subtype4
TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5K2 
       42.51        16.11        69.21        15.25        12.59        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5LC TCGA-OR-A5LD 
       16.37        11.31       127.50        44.84         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LS 
       21.76        36.03 

$subtype5
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5K6 TCGA-OR-A5KT 
       39.58        12.59        19.04        18.12        49.08        95.18 
TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OU-A5PI 
      152.15        29.10        36.33        53.03        38.50 

$subtype6
TCGA-OR-A5L5 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JX 
       43.30        57.53        99.88        76.64        39.25        31.23 
TCGA-OR-A5K3 TCGA-OR-A5LA TCGA-OR-A5LN TCGA-OR-A5LT TCGA-PK-A5H9 
      113.92        23.64        77.00        18.05        20.25 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.11    12.85    17.79     5.23    12.59    18.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   79.07   153.63    88.87   127.50   152.15   113.92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   13.91    37.87    49.22    27.22    38.50    43.30 
[1] "4.1 - 79.1 (13.9)"   "12.8 - 153.6 (37.9)" "17.8 - 88.9 (49.2)" 
[4] "5.2 - 127.5 (27.2)"  "12.6 - 152.2 (38.5)" "18.1 - 113.9 (43.3)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        3         2        2
  subtype2       2       18         0        4
  subtype3       1        1         5        4
  subtype4       1        5         6        1
  subtype5       2        3         1        5
  subtype6       3        5         2        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          0        2        1        1        2        3
  STAGE II         3       18        1        5        3        5
  STAGE III        2        0        5        6        1        2
  STAGE IV         2        4        4        1        5        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  3  1  3
  subtype2  2 18  1  3
  subtype3  1  2  2  6
  subtype4  1  7  2  3
  subtype5  2  5  1  3
  subtype6  3  5  2  0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        0        2        1        1        2        3
  T2        3       18        2        7        5        5
  T3        1        1        2        2        1        2
  T4        3        3        6        3        3        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  5  2
  subtype2 22  2
  subtype3  9  2
  subtype4 11  2
  subtype5  9  2
  subtype6 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    2
  subtype2   22    2
  subtype3    9    2
  subtype4   11    2
  subtype5    9    2
  subtype6   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        5       22        9       11        9       10
  1        2        2        2        2        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1  3  4
  subtype2 14 10
  subtype3  8  3
  subtype4 10  4
  subtype5  8  3
  subtype6  6  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    4
  subtype2   14   10
  subtype3    8    3
  subtype4   10    4
  subtype5    8    3
  subtype6    6    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        3       14        8       10        8        6
  MALE          4       10        3        4        3        5
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2 18  6
  subtype3  7  3
  subtype4  9  5
  subtype5  8  2
  subtype6  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   18    6
  subtype3    7    3
  subtype4    9    5
  subtype5    8    2
  subtype6    9    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         7       18        7        9        8        9
  YES        0        6        3        5        2        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  subtype1                                     0
  subtype2                                     1
  subtype3                                     0
  subtype4                                     0
  subtype5                                     0
  subtype6                                     0
          vv
clus       ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
  subtype6                                        2
          vv
clus       ADRENOCORTICAL CARCINOMA- USUAL TYPE
  subtype1                                    7
  subtype2                                   22
  subtype3                                   11
  subtype4                                   14
  subtype5                                   11
  subtype6                                    9
D10V8, multiclass
                                          clus
vv                                         subtype1 subtype2 subtype3 subtype4
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        1        0        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        1        0        0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE            7       22       11       14
                                          clus
vv                                         subtype5 subtype6
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE           0        0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE        0        2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE           11        9
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  2  0  3  2
  subtype2 19  1  3  1
  subtype3  5  3  1  2
  subtype4 10  1  1  1
  subtype5  7  1  2  0
  subtype6 10  0  0  0
D10V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        2       19        5       10        7       10
  R1        0        1        3        1        1        0
  R2        3        3        1        1        2        0
  RX        2        1        2        1        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     6
  subtype2     0                         0    20
  subtype3     0                         1    10
  subtype4     0                         0    12
  subtype5     0                         0    10
  subtype6     1                         0     8
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                            6       20       10       12       10
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            8
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus       0 1
  subtype1 2 2
  subtype2 2 7
  subtype3 2 4
  subtype4 1 5
  subtype5 1 8
  subtype6 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    2
  subtype2    2    7
  subtype3    2    4
  subtype4    1    5
  subtype5    1    8
  subtype6    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        2        2        1        1        0
  NOT HISPANIC OR LATINO        2        7        4        5        8        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
