[1] "ofn"        "-oTPAAD-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/PAAD-TP/15087151/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/15107801/PAAD-TP.mergedcluster.txt"

nPatients in clinical file=174, in cluster file=185, common to both=174
[1]  10 174
[1] "CN_CNMF"
[1] 3
 1  2  3 
81 68 24 
 1  2  3 
81 68 24 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
42 46 46 39 
 1  2  3  4 
42 46 46 39 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
35 19 16 18 16 
 1  2  3  4  5 
35 19 16 18 16 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
11 19 23 15 11 18  7 
 1  2  3  4  5  6  7 
11 19 23 15 11 18  7 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
75 47 45 
 1  2  3 
75 47 45 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
73 67 27 
 1  2  3 
73 67 27 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
61 39 34 33 
 1  2  3  4 
61 39 34 33 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
94 41 32 
 1  2  3 
94 41 32 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
63 65 36 
 1  2  3 
63 65 36 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
79 46 39 
 1  2  3 
79 46 39 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "NUMBER_PACK_YEARS_SMOKED"              
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 174 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=88,	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=101,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "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] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 174 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "COMPLETENESS_OF_RESECTION"    
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  8  21 140   4 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  8  21 140   4 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  8  21 140   4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  8  21 140   4 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=30, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=29, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=16, 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 40 39
  subtype2 27 41
  subtype3 12 12
subtype1 subtype2 subtype3 
      79       68       24 
subtype1 subtype2 subtype3 
      39       41       12 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR 
        2.17        20.61        19.96        15.91        11.84        14.40 
TCGA-2J-AABV TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IJ TCGA-3A-A9IR TCGA-3A-A9IX 
       21.44        53.00        23.61        60.95        50.70        34.09 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
       75.12        71.74         9.70        19.46         7.10         7.66 
TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPS TCGA-FB-AAPY 
       19.27         5.88        14.76        11.61         7.50        34.82 
TCGA-FZ-5919 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N TCGA-HZ-7920 
       24.36        36.20        20.35        17.79        13.84         7.76 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        0.26        27.62        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        0.69         9.83        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
       16.14        10.85         1.08        49.38        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 
       19.82        41.33        43.79        15.81        21.30        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-AAUM TCGA-IB-AAUP 
        2.47        12.00         7.20        20.88         0.26        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         9.44        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       12.46        10.29        13.68        15.32         9.40         0.30 
TCGA-US-A774 TCGA-US-A77E TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
       22.85        14.14        18.67        13.81        12.99        11.51 
TCGA-Z5-AAPL 
        0.69 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI 
       23.97         9.63         2.63        22.22        22.26        31.86 
TCGA-2J-AABO TCGA-2J-AABT TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        10.49         9.11         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       12.95         9.60        20.84        24.26        28.73        15.06 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T 
       10.13        12.39        10.98        17.00        24.07        12.43 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FB-AAQ6 
       37.15        12.53        15.55         5.03         1.02         8.02 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5924 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7919 
        2.01         5.10        15.78        12.89        22.06        19.50 
TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
        0.13        17.92        10.13         6.38        21.60         5.26 
TCGA-IB-7644 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7893 TCGA-IB-A5SP 
       12.95        23.80         4.04         3.62         3.85        15.85 
TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUU 
       15.12        21.90        15.88         4.73         7.86         8.05 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-S4-A8RM 
        9.14        12.92        19.20         8.78        15.45        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL 
       17.26        23.08        16.80         0.39        12.03        13.32 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

$subtype3
TCGA-2J-AABF TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       22.72        45.47         7.36        84.10        68.52        63.85 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-FB-AAQ1 
       30.64        31.79         3.12        15.95        23.54         4.04 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8005 TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7654 
       21.73         0.92         3.95         0.23         4.77        15.65 
TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A6UG TCGA-IB-A7LX TCGA-Q3-AA2A TCGA-US-A776 
       19.66        17.16         1.35         8.22         3.12        27.75 

subtype1 subtype2 subtype3 
    0.26     0.13     0.23 
subtype1 subtype2 subtype3 
   75.12    66.28    84.10 
subtype1 subtype2 subtype3 
  14.400   12.935   16.555 
[1] "0.3 - 75.1 (14.4)" "0.1 - 66.3 (12.9)" "0.2 - 84.1 (16.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        4        6        11        55         3        2
  subtype2       0        2        1        14        47         2        2
  subtype3       1        0        6         1        15         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         4        2        0
  STAGE IB         6        1        6
  STAGE IIA       11       14        1
  STAGE IIB       55       47       15
  STAGE III        3        2        0
  STAGE IV         2        2        0
[1] 7 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  5 11 62  3
  subtype2  2  3 62  1
  subtype3  1  7 15  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        2        1
  T2       11        3        7
  T3       62       62       15
  T4        3        1        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"
D1V5, binary
          cls
clus        0  1
  subtype1 21 59
  subtype2 19 49
  subtype3  5 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   59
  subtype2   19   49
  subtype3    5   16
   clus
vv  subtype1 subtype2 subtype3
  0       21       19        5
  1       59       49       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 40  2
  subtype2 32  2
  subtype3  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    2
  subtype2   32    2
  subtype3    8    0
   clus
vv  subtype1 subtype2 subtype3
  0       40       32        8
  1        2        2        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"
D1V7, binary
          cls
clus        0  1
  subtype1 41 40
  subtype2 32 36
  subtype3  5 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   40
  subtype2   32   36
  subtype3    5   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       41       32        5
  MALE         40       36       19
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  68
  subtype2                                  61
  subtype3                                  16
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                     6
  subtype3                                     7
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                0
  subtype3                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D1V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    68       61       16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        6        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        0        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        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"
D1V9, continuous
D1V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 58 17  1  1
  subtype2 37 25  1  1
  subtype3 13  9  0  2
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       58       37       13
  R1       17       25        9
  R2        1        1        0
  RX        1        1        2
[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"
D1V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         5    73
  subtype2     2                         2    62
  subtype3     0                         0    23
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        0
  BLACK OR AFRICAN AMERICAN        5        2        0
  WHITE                           73       62       23
[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"
D1V14, binary
          cls
clus        0  1
  subtype1  2 68
  subtype2  1 47
  subtype3  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   68
  subtype2    1   47
  subtype3    0   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       68       47       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 15 27
  subtype2 29 17
  subtype3 15 30
  subtype4 21 17
subtype1 subtype2 subtype3 subtype4 
      42       46       45       38 
subtype1 subtype2 subtype3 subtype4 
      27       17       30       17 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO 
        2.17         2.63        22.72        22.26        31.86        14.47 
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9IH TCGA-3A-A9J0 
        4.70        12.95         9.60        53.00        28.73        12.39 
TCGA-3E-AAAZ TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAQ0 
       71.74        14.76        12.43        15.95        37.15        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ6 TCGA-FZ-5920 TCGA-FZ-5923 TCGA-HZ-7926 
        4.04         5.03         8.02         2.01        20.35        17.03 
TCGA-HZ-8005 TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7886 
        3.95         0.23         4.77        21.90        19.82         4.04 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUN 
       15.81        19.66        17.16        21.90         1.35         4.73 
TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A77E TCGA-US-A77G TCGA-YY-A8LH 
        8.78        21.24        17.26        14.14         0.39        66.28 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQI 
       23.97        20.61        15.91        14.40        21.44         3.39 
TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       45.47        20.84        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-6880 
       50.70        30.64        31.79        34.09        75.12         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FZ-5922 TCGA-FZ-5926 
       19.46         7.10        19.27        11.93        36.20        17.79 
TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 
       13.84         0.92         7.76        27.62        12.03         0.69 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O 
       12.43        14.93         4.96        21.70        16.14         5.26 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUW TCGA-LB-A8F3 
       15.35        23.80         0.26         9.44         7.56        12.46 
TCGA-LB-A9Q5 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-XD-AAUG 
       10.29         9.40         0.30        13.81 

$subtype3
TCGA-2J-AAB6 TCGA-2J-AABE TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9IB TCGA-3A-A9IC 
        9.63        22.22         9.11        22.49         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-F2-6879 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 
       15.06        10.13        10.98         3.12        17.00        24.07 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ3 TCGA-FZ-5924 TCGA-H6-8124 TCGA-H8-A6C1 
       12.53        23.54         1.02        15.78        12.89        22.06 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49I 
       21.73        19.50         0.13         9.83        17.92        10.13 
TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7654 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A5SS 
       21.60        12.95        15.65         3.85        15.85        15.12 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX 
        8.22        15.88         7.86         8.05         9.14        12.92 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
       15.45         3.12        15.32        23.08        27.75        16.80 
TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY 
       13.32        11.51        12.76 

$subtype4
TCGA-2J-AABA TCGA-2J-AABP TCGA-2J-AABT TCGA-3A-A9I7 TCGA-F2-A44G TCGA-FB-A4P5 
       19.96        11.84        10.49        23.61         7.66         5.88 
TCGA-FB-A7DR TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FZ-5919 TCGA-HZ-7923 TCGA-HZ-7925 
       11.61         7.50        34.82        24.36         0.26        20.19 
TCGA-HZ-8001 TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7645 TCGA-IB-7885 
       23.21         6.38        10.85         1.08        49.38        41.33 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
        3.62        43.79        21.30        15.98         2.47        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        7.20        20.88        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A77J TCGA-XD-AAUH 
       13.28        19.20        13.68        22.85        18.67        12.99 
TCGA-XD-AAUI TCGA-Z5-AAPL 
       12.03         0.69 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.26     0.13     0.26 
subtype1 subtype2 subtype3 subtype4 
   71.74    84.10    27.75    49.38 
subtype1 subtype2 subtype3 subtype4 
  14.615   15.630   13.320   12.510 
[1] "0.2 - 71.7 (14.6)" "0.3 - 84.1 (15.6)" "0.1 - 27.8 (13.3)"
[4] "0.3 - 49.4 (12.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        3        4         5        28         1        1
  subtype2       1        3        7         6        26         1        1
  subtype3       0        0        1        10        32         1        2
  subtype4       0        0        1         5        31         2        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        0        0
  STAGE IA         3        3        0        0
  STAGE IB         4        7        1        1
  STAGE IIA        5        6       10        5
  STAGE IIB       28       26       32       31
  STAGE III        1        1        1        2
  STAGE IV         1        1        2        0
[1] 7 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  4 33  2
  subtype2  5 12 28  0
  subtype3  0  2 44  0
  subtype4  0  3 34  2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        5        0        0
  T2        4       12        2        3
  T3       33       28       44       34
  T4        2        0        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"
D2V5, binary
          cls
clus        0  1
  subtype1 13 29
  subtype2 15 28
  subtype3 11 35
  subtype4  6 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   29
  subtype2   15   28
  subtype3   11   35
  subtype4    6   32
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       13       15       11        6
  1       29       28       35       32
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 20  1
  subtype2 18  1
  subtype3 18  2
  subtype4 23  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   18    1
  subtype3   18    2
  subtype4   23    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       20       18       18       23
  1        1        1        2        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 10 32
  subtype2 22 24
  subtype3 21 25
  subtype4 24 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   32
  subtype2   22   24
  subtype3   21   25
  subtype4   24   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       22       21       24
  MALE         32       24       25       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  38
  subtype2                                  33
  subtype3                                  39
  subtype4                                  35
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                    11
  subtype3                                     5
  subtype4                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                2
  subtype3                                                1
  subtype4                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   0
  subtype4                                   1
D2V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    38       33       39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4       11        5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        2        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        0
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     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"
D2V9, continuous
D2V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 23 16  0  2
  subtype2 32 11  0  0
  subtype3 27 13  1  2
  subtype4 26 11  1  0
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       23       32       27       26
  R1       16       11       13       11
  R2        0        0        1        1
  RX        2        0        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"
D2V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    39
  subtype2     1                         2    42
  subtype3     1                         1    44
  subtype4     1                         2    34
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        1        1
  BLACK OR AFRICAN AMERICAN        2        2        1        2
  WHITE                           39       42       44       34
[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"
D2V14, binary
          cls
clus        0  1
  subtype1  1 31
  subtype2  0 37
  subtype3  1 37
  subtype4  1 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   31
  subtype2    0   37
  subtype3    1   37
  subtype4    1   31
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        1        1
  NOT HISPANIC OR LATINO       31       37       37       31
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 15 20
  subtype2  7 12
  subtype3 11  5
  subtype4  7 11
  subtype5  6 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      35       19       16       18       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       12        5       11       10 
$subtype1
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9IH TCGA-3E-AAAZ TCGA-F2-6879 
        4.70         3.39         9.60        28.73        71.74        10.98 
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FZ-5920 TCGA-HZ-7919 
       17.00         5.88        11.93        14.76         2.01        19.50 
TCGA-HZ-7922 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7890 
        0.13        23.80        15.65         4.04        15.81        19.66 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-AAUN 
        3.85        17.16        12.00        15.85         7.20         4.73 
TCGA-IB-AAUP TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RM 
       14.17         8.05        12.92        12.46         8.78        21.24 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A779 TCGA-YB-A89D TCGA-YY-A8LH 
       17.26        23.08        16.80        11.51        66.28 

$subtype2
TCGA-2L-AAQJ TCGA-F2-A44G TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HZ-7925 
       12.95         7.66        24.36         5.10        22.06        20.19 
TCGA-HZ-8638 TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5ST 
        4.96        12.95        15.35        41.33         2.47        20.88 
TCGA-IB-A7M4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 TCGA-US-A77E 
       15.88        10.29        19.20        15.45        15.32        14.14 
TCGA-YH-A8SY 
       12.76 

$subtype3
TCGA-2L-AAQM TCGA-F2-6880 TCGA-FB-A78T TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H6-A45N 
       45.47         9.70        12.43        20.35        17.79        13.84 
TCGA-HZ-7924 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A4BK TCGA-IB-7651 TCGA-IB-7891 
       27.62         0.69        14.93        21.60        19.82        21.30 
TCGA-IB-A6UF TCGA-IB-AAUM TCGA-US-A776 TCGA-US-A77G 
       21.90         0.26        27.75         0.39 

$subtype4
TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IN TCGA-3A-A9IU TCGA-3A-A9IX TCGA-FZ-5922 
       53.00         7.36        68.52        15.06        34.09        36.20 
TCGA-HZ-7918 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-8002 TCGA-HZ-8315 TCGA-IB-7888 
        0.92         7.76         0.26        12.03         9.83        43.79 
TCGA-IB-A5SS TCGA-IB-AAUO TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A774 TCGA-US-A77J 
       15.12         7.86        13.28         9.40        22.85        18.67 

$subtype5
TCGA-3A-A9IZ TCGA-FB-A545 TCGA-FZ-5924 TCGA-HZ-8001 TCGA-HZ-8005 TCGA-HZ-A4BH 
       10.13        24.07        15.78        23.21         3.95         6.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7887 TCGA-IB-A7LX TCGA-IB-AAUS TCGA-IB-AAUW 
        4.77        21.90         3.62         8.22         7.40         7.56 
TCGA-L1-A7W4 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-XD-AAUL 
        9.14        13.68         3.12        13.32 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     2.47     0.26     0.26     3.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
   71.74    41.33    45.47    68.52    24.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.920   15.320   18.805   14.170    8.680 
[1] "0.1 - 71.7 (12.9)" "2.5 - 41.3 (15.3)" "0.3 - 45.5 (18.8)"
[4] "0.3 - 68.5 (14.2)" "3.1 - 24.1 (8.7)" 
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        4         6        24         0        0
  subtype2        1        0         2        12         3        1
  subtype3        1        0         2        11         1        1
  subtype4        2        2         4        10         0        0
  subtype5        0        1         1        13         1        0
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE IA         1        1        1        2        0
  STAGE IB         4        0        0        2        1
  STAGE IIA        6        2        2        4        1
  STAGE IIB       24       12       11       10       13
  STAGE III        0        3        1        0        1
  STAGE IV         0        1        1        0        0
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  5 29  0
  subtype2  1  0 16  2
  subtype3  1  1 13  1
  subtype4  3  2 13  0
  subtype5  0  0 15  1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        1        3        0
  T2        5        0        1        2        0
  T3       29       16       13       13       15
  T4        0        2        1        0        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 11 24
  subtype2  4 15
  subtype3  3 13
  subtype4  7 10
  subtype5  2 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   24
  subtype2    4   15
  subtype3    3   13
  subtype4    7   10
  subtype5    2   14
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       11        4        3        7        2
  1       24       15       13       10       14
[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"
D3V6, binary
          cls
clus        0  1
  subtype1 19  0
  subtype2  7  1
  subtype3  7  1
  subtype4  6  0
  subtype5  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    0
  subtype2    7    1
  subtype3    7    1
  subtype4    6    0
  subtype5    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       19        7        7        6        8
  1        0        1        1        0        0
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 14 21
  subtype2 15  4
  subtype3  7  9
  subtype4  8 10
  subtype5  6 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   21
  subtype2   15    4
  subtype3    7    9
  subtype4    8   10
  subtype5    6   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       14       15        7        8        6
  MALE         21        4        9       10       10
[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       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  34
  subtype2                                  14
  subtype3                                  11
  subtype4                                  17
  subtype5                                  16
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     3
  subtype3                                     4
  subtype4                                     1
  subtype5                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                1
  subtype4                                                0
  subtype5                                                0
D3V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    34       14       11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        3        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        1        1
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    17       16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       9        7        4        5        2 
 [1] "subtype4" "subtype4" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[13] "subtype3" "subtype2" "subtype1" "subtype4" "subtype3" "subtype2"
[19] "subtype4" "subtype1" "subtype2" "subtype1" "subtype1" "subtype4"
[25] "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1 20 12  0  1
  subtype2  8  7  0  0
  subtype3 12  3  0  0
  subtype4 15  3  0  0
  subtype5  6  7  1  1
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       20        8       12       15        6
  R1       12        7        3        3        7
  R2        0        0        0        0        1
  RX        1        0        0        0        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    30
  subtype2     0                         0    16
  subtype3     0                         0    16
  subtype4     0                         1    17
  subtype5     0                         0    16
D3V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        3        0        0        1        0
  WHITE                           30       16       16       17       16
[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"
D3V14, binary
          cls
clus        0  1
  subtype1  1 26
  subtype2  0 15
  subtype3  0 14
  subtype4  0 18
  subtype5  1 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   26
  subtype2    0   15
  subtype3    0   14
  subtype4    0   18
  subtype5    1   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        0        0        1
  NOT HISPANIC OR LATINO       26       15       14       18       14
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  6  5
  subtype2  8 11
  subtype3 11 12
  subtype4 12  3
  subtype5  6  5
  subtype6  1 17
  subtype7  2  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      11       19       23       15       11       18        7 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       5       11       12        3        5       17        5 
$subtype1
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-3A-A9IH TCGA-FB-A4P5 TCGA-HZ-7919 TCGA-IB-7652 
        4.70         3.39        28.73         5.88        19.50        23.80 
TCGA-IB-A5SP TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-YY-A8LH 
       15.85        21.24        17.26        23.08        66.28 

$subtype2
TCGA-2L-AAQJ TCGA-F2-A44G TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HZ-7925 
       12.95         7.66        24.36         5.10        22.06        20.19 
TCGA-HZ-8001 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-8126 
       23.21        12.95         4.77        15.35        41.33         2.47 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 
       20.88        15.88        10.29        19.20        15.45        15.32 
TCGA-YH-A8SY 
       12.76 

$subtype3
TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9IX TCGA-3E-AAAZ TCGA-FB-A4P6 TCGA-FB-A5VM 
        9.60        53.00        34.09        71.74        11.93        14.76 
TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-8315 TCGA-HZ-8638 TCGA-IB-7886 TCGA-IB-7890 
        0.13        27.62         9.83         4.96         4.04        19.66 
TCGA-IB-8127 TCGA-IB-A5SQ TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUU 
       17.16         7.20         4.73         7.86        14.17         8.05 
TCGA-LB-A7SX TCGA-RB-AA9M TCGA-US-A774 TCGA-US-A77E TCGA-YB-A89D 
       12.92         9.40        22.85        14.14        11.51 

$subtype4
TCGA-2L-AAQM TCGA-3A-A9IN TCGA-F2-6880 TCGA-FB-A78T TCGA-FZ-5923 TCGA-FZ-5926 
       45.47        68.52         9.70        12.43        20.35        17.79 
TCGA-HZ-7918 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A4BK TCGA-IB-7891 TCGA-IB-A6UF 
        0.92         0.69        14.93        21.60        21.30        21.90 
TCGA-IB-AAUM TCGA-US-A776 TCGA-US-A77G 
        0.26        27.75         0.39 

$subtype5
TCGA-3A-A9IB TCGA-3A-A9IU TCGA-FZ-5922 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-A4BH 
        7.36        15.06        36.20         7.76         0.26         6.38 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-XD-AAUL 
       13.28         7.56        13.68         3.12        13.32 

$subtype6
TCGA-3A-A9IZ TCGA-FB-A545 TCGA-FZ-5924 TCGA-H6-A45N TCGA-HZ-8002 TCGA-HZ-8005 
       10.13        24.07        15.78        13.84        12.03         3.95 
TCGA-IB-7647 TCGA-IB-7654 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-A5SO 
       21.90        15.65         3.62        43.79        15.81        12.00 
TCGA-IB-A5SS TCGA-IB-A7LX TCGA-IB-AAUS TCGA-L1-A7W4 TCGA-US-A779 TCGA-US-A77J 
       15.12         8.22         7.40         9.14        16.80        18.67 

$subtype7
TCGA-F2-6879 TCGA-F2-A8YN TCGA-FZ-5920 TCGA-IB-7651 TCGA-IB-7893 TCGA-LB-A8F3 
       10.98        17.00         2.01        19.82         3.85        12.46 
TCGA-OE-A75W 
        8.78 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    3.39     2.47     0.13     0.26     0.26     3.62     2.01 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   66.28    41.33    71.74    68.52    36.20    43.79    19.82 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   19.50    15.35    11.93    17.79     7.76    14.48    10.98 
[1] "3.4 - 66.3 (19.5)" "2.5 - 41.3 (15.3)" "0.1 - 71.7 (11.9)"
[4] "0.3 - 68.5 (17.8)" "0.3 - 36.2 (7.8)"  "3.6 - 43.8 (14.5)"
[7] "2.0 - 19.8 (11.0)"
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        0         1         9         0        0
  subtype2        0        0         2        12         4        1
  subtype3        3        4         3        13         0        0
  subtype4        1        1         1        10         1        1
  subtype5        0        2         3         6         0        0
  subtype6        0        0         1        17         0        0
  subtype7        0        0         4         3         0        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE IA         1        0        3        1        0        0        0
  STAGE IB         0        0        4        1        2        0        0
  STAGE IIA        1        2        3        1        3        1        4
  STAGE IIB        9       12       13       10        6       17        3
  STAGE III        0        4        0        1        0        0        0
  STAGE IV         0        1        0        1        0        0        0
[1] 6 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  0 10  0
  subtype2  0  0 16  3
  subtype3  4  4 15  0
  subtype4  1  2 11  1
  subtype5  0  1 10  0
  subtype6  0  1 17  0
  subtype7  0  0  7  0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        1        0        4        1        0        0        0
  T2        0        0        4        2        1        1        0
  T3       10       16       15       11       10       17        7
  T4        0        3        0        1        0        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"
D4V5, binary
          cls
clus        0  1
  subtype1  2  9
  subtype2  4 15
  subtype3 10 13
  subtype4  2 12
  subtype5  4  7
  subtype6  1 17
  subtype7  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    9
  subtype2    4   15
  subtype3   10   13
  subtype4    2   12
  subtype5    4    7
  subtype6    1   17
  subtype7    4    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        2        4       10        2        4        1        4
  1        9       15       13       12        7       17        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"
D4V6, binary
          cls
clus        0  1
  subtype1  3  0
  subtype2  8  1
  subtype3  9  0
  subtype4  7  1
  subtype5  3  0
  subtype6 11  0
  subtype7  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    8    1
  subtype3    9    0
  subtype4    7    1
  subtype5    3    0
  subtype6   11    0
  subtype7    6    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        3        8        9        7        3       11        6
  1        0        1        0        1        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"
D4V7, binary
          cls
clus        0  1
  subtype1  7  4
  subtype2 14  5
  subtype3  9 14
  subtype4  5 10
  subtype5  3  8
  subtype6 10  8
  subtype7  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    4
  subtype2   14    5
  subtype3    9   14
  subtype4    5   10
  subtype5    3    8
  subtype6   10    8
  subtype7    2    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        7       14        9        5        3       10        2
  MALE          4        5       14       10        8        8        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  11
  subtype2                                  16
  subtype3                                  21
  subtype4                                  10
  subtype5                                  11
  subtype6                                  17
  subtype7                                   6
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     0
  subtype2                                     2
  subtype3                                     1
  subtype4                                     4
  subtype5                                     0
  subtype6                                     1
  subtype7                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                1
  subtype4                                                1
  subtype5                                                0
  subtype6                                                0
  subtype7                                                0
D4V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    11       16       21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        2        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0        1
                                                  clus
vv                                                 subtype4 subtype5 subtype6
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    10       11       17
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        0        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        0        0
                                                  clus
vv                                                 subtype7
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0
[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"
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "subtype6"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       3        7        7        3        3        2        2 
 [1] "subtype5" "subtype3" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype4"
[13] "subtype2" "subtype3" "subtype4" "subtype2" "subtype5" "subtype3"
[19] "subtype2" "subtype1" "subtype3" "subtype5" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1  5  6  0  0
  subtype2  8  7  0  0
  subtype3 12  8  0  1
  subtype4 11  4  0  0
  subtype5  9  1  0  1
  subtype6 10  5  1  0
  subtype7  6  1  0  0
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0        5        8       12       11        9       10        6
  R1        6        7        8        4        1        5        1
  R2        0        0        0        0        0        1        0
  RX        0        0        1        0        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"
D4V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    10
  subtype2     0                         0    16
  subtype3     0                         1    21
  subtype4     0                         0    15
  subtype5     0                         0    11
  subtype6     0                         1    17
  subtype7     0                         2     5
D4V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                           10       16       21       15       11
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        1        2
  WHITE                           17        5
[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"
D4V14, binary
          cls
clus        0  1
  subtype1  0  7
  subtype2  0 15
  subtype3  1 20
  subtype4  0 13
  subtype5  0 10
  subtype6  1 16
  subtype7  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    7
  subtype2    0   15
  subtype3    1   20
  subtype4    0   13
  subtype5    0   10
  subtype6    1   16
  subtype7    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        1        0        0        1
  NOT HISPANIC OR LATINO        7       15       20       13       10       16
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        6
[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 30 44
  subtype2 23 24
  subtype3 27 17
subtype1 subtype2 subtype3 
      74       47       44 
subtype1 subtype2 subtype3 
      44       24       17 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABT 
        2.17         2.63        19.96        22.22        31.86        10.49 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IB 
        9.11         4.70        22.49        12.95        23.61         7.36 
TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 
       24.26        15.06        10.13        12.39        71.74        10.98 
TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ 
        7.66        17.00        24.07        11.61        15.95        37.15 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-H6-8124 
       12.53        23.54        15.55         1.02         8.02        12.89 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7925 
       22.06        21.73        19.50         0.13        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49I 
       17.03         3.95         9.83        17.92         4.96        10.13 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 
        1.08         0.23        12.95         4.77        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7LX 
        3.62         3.85        17.16        15.12        20.88         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUS TCGA-L1-A7W4 TCGA-LB-A7SX 
       15.88         7.86        14.17         7.40         9.14        12.92 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.20         8.78        15.45        13.68         3.12        15.32 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUL TCGA-YH-A8SY 
       21.24        17.26        27.75        14.14        13.32        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR 
       23.97        20.61        22.72        22.26        15.91        14.40 
TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IX TCGA-3E-AAAY 
       21.44         3.39         9.60        20.84        34.09        75.12 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 TCGA-FB-A78T 
        9.70        19.46        19.27         3.12        11.93        12.43 
TCGA-FB-AAPY TCGA-FB-AAQ1 TCGA-HZ-7918 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A4BK 
       34.82         4.04         0.92        12.43        21.70        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
        5.26        10.85        15.35        19.82        23.80        15.65 
TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
       15.81        21.30        15.85        21.90         1.35         0.26 
TCGA-IB-AAUN TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        4.73         9.44         8.05         7.56        12.46        10.29 
TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G 
        0.30        23.08        22.85        16.80         0.39 

$subtype3
TCGA-2J-AAB6 TCGA-2J-AABO TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IH 
        9.63        14.47        11.84        45.47        53.00        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IV TCGA-F2-7276 TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-FB-AAQ2 
       31.79         7.10         5.88        14.76         7.50         5.03 
TCGA-H6-A45N TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       13.84         7.76         0.26        23.21        12.03         0.69 
TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 
       14.93        16.14         6.38        49.38        21.90        43.79 
TCGA-IB-7890 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-AAUQ 
       19.66        15.98         2.47        12.00         7.20         6.02 
TCGA-IB-AAUR TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       11.11        13.28         9.40        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-YB-A89D 
       12.03        11.51 

subtype1 subtype2 subtype3 
    0.13     0.26     0.26 
subtype1 subtype2 subtype3 
   71.74    75.12    84.10 
subtype1 subtype2 subtype3 
  13.135   15.650   13.825 
[1] "0.1 - 71.7 (13.1)" "0.3 - 75.1 (15.7)" "0.3 - 84.1 (13.8)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        2        16        51         2        2
  subtype2       0        1        2         6        38         0        0
  subtype3       1        3        9         3        25         2        1
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         2        1        3
  STAGE IB         2        2        9
  STAGE IIA       16        6        3
  STAGE IIB       51       38       25
  STAGE III        2        0        2
  STAGE IV         2        0        1
[1] 7 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  2 70  1
  subtype2  1  9 37  0
  subtype3  5 10 27  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        1        5
  T2        2        9       10
  T3       70       37       27
  T4        1        0        2
[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"
D5V5, binary
          cls
clus        0  1
  subtype1 20 54
  subtype2  9 38
  subtype3 15 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   54
  subtype2    9   38
  subtype3   15   27
   clus
vv  subtype1 subtype2 subtype3
  0       20        9       15
  1       54       38       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 30  2
  subtype2 28  0
  subtype3 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    2
  subtype2   28    0
  subtype3   17    1
   clus
vv  subtype1 subtype2 subtype3
  0       30       28       17
  1        2        0        1
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 34 41
  subtype2 19 28
  subtype3 22 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   41
  subtype2   19   28
  subtype3   22   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       19       22
  MALE         41       28       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  63
  subtype2                                  42
  subtype3                                  34
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     8
  subtype2                                     4
  subtype3                                    10
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   1
D5V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    63       42       34
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   8        4       10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        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"
D5V9, continuous
D5V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 42 25  1  3
  subtype2 27 17  0  1
  subtype3 34  9  1  0
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       42       27       34
  R1       25       17        9
  R2        1        0        1
  RX        3        1        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"
D5V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    69
  subtype2     1                         2    43
  subtype3     0                         1    42
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        0
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           69       43       42
[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"
D5V14, binary
          cls
clus        0  1
  subtype1  2 61
  subtype2  0 33
  subtype3  1 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   61
  subtype2    0   33
  subtype3    1   36
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        1
  NOT HISPANIC OR LATINO       61       33       36
[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(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 33 39
  subtype2 29 38
  subtype3 18  8
subtype1 subtype2 subtype3 
      72       67       26 
subtype1 subtype2 subtype3 
      39       38        8 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
        2.17        23.97        20.61        22.72        22.26        15.91 
TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I9 
       14.47        14.40        21.44         3.39         9.60        20.84 
TCGA-3A-A9IB TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 
        7.36        15.06        34.09        10.13        75.12         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 
       19.46         7.10         7.66        19.27         3.12         5.88 
TCGA-FB-A4P6 TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 
       11.93        12.43         7.50        34.82        23.54         4.04 
TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 
        1.02        13.84        22.06         0.92        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-A49G 
       17.03        12.03         0.69         9.83        12.43        21.70 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       16.14        21.60         5.26        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
       15.65         4.04        15.81        21.30         2.47        17.16 
TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUS 
       15.85        21.90         1.35         0.26         4.73         7.40 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-RL-AAAS 
        9.44         8.05         7.56        12.46        10.29         0.30 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL 
       23.08        22.85        16.80         0.39        12.03        13.32 

$subtype2
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABP 
        9.63         2.63        19.96        22.22        31.86        11.84 
TCGA-2J-AABT TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 
       10.49         9.11         4.70        22.49        12.95        23.61 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN 
       24.26        28.73        12.39        71.74        10.98        17.00 
TCGA-FB-A545 TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAQ0 
       24.07        11.61        15.95        37.15        12.53        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ6 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7924 TCGA-HZ-7925 
        5.03         8.02        12.89        21.73        27.62        20.19 
TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A77Q 
        3.95        17.92         4.96        10.13        10.85         1.08 
TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7890 
        0.23        12.95         4.77        41.33         3.62        19.66 
TCGA-IB-7893 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO 
        3.85        15.12        20.88         8.22        15.88         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 
       14.17         6.02        11.11         9.14        12.92        19.20 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM 
        8.78        15.45        13.68         3.12        15.32        21.24 
TCGA-S4-A8RO TCGA-US-A776 TCGA-US-A77E TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       17.26        27.75        14.14        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

$subtype3
TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO 
       45.47        53.00        60.95        84.10        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-A5VM TCGA-HZ-7920 TCGA-HZ-7923 
       50.70        30.64        31.79        14.76         7.76         0.26 
TCGA-HZ-8001 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 
       23.21        14.93         6.38        49.38        21.90        43.79 
TCGA-IB-7897 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A77J 
       15.98        12.00         7.20        13.28         9.40        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH 
       13.81        12.99 

subtype1 subtype2 subtype3 
    0.13     0.23     0.26 
subtype1 subtype2 subtype3 
   75.12    71.74    84.10 
subtype1 subtype2 subtype3 
  12.890   12.950   20.285 
[1] "0.1 - 75.1 (12.9)" "0.2 - 71.7 (12.9)" "0.3 - 84.1 (20.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        2         9        60         1        0
  subtype2       0        3        3        14        43         2        2
  subtype3       1        2        8         2        11         1        1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         1        3        2
  STAGE IB         2        3        8
  STAGE IIA        9       14        2
  STAGE IIB       60       43       11
  STAGE III        1        2        1
  STAGE IV         0        2        1
[1] 7 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  1 11 60  1
  subtype2  3  2 61  1
  subtype3  4  8 13  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        3        4
  T2       11        2        8
  T3       60       61       13
  T4        1        1        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"
D6V5, binary
          cls
clus        0  1
  subtype1 12 61
  subtype2 20 46
  subtype3 12 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   61
  subtype2   20   46
  subtype3   12   12
   clus
vv  subtype1 subtype2 subtype3
  0       12       20       12
  1       61       46       12
[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"
D6V6, binary
          cls
clus        0  1
  subtype1 37  0
  subtype2 29  2
  subtype3  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    0
  subtype2   29    2
  subtype3    9    1
   clus
vv  subtype1 subtype2 subtype3
  0       37       29        9
  1        0        2        1
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 33 40
  subtype2 30 37
  subtype3 12 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   40
  subtype2   30   37
  subtype3   12   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       30       12
  MALE         40       37       15
[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       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  66
  subtype2                                  55
  subtype3                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     7
  subtype3                                     9
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                3
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
D6V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    66       55       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        7        9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        3        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        1        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"
D6V9, continuous
D6V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 42 26  0  2
  subtype2 39 21  1  2
  subtype3 22  4  1  0
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       42       39       22
  R1       26       21        4
  R2        0        1        1
  RX        2        2        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"
D6V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    68
  subtype2     2                         2    61
  subtype3     0                         1    25
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        0
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           68       61       25
[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"
D6V14, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  1 52
  subtype3  1 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    1   52
  subtype3    1   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        1
  NOT HISPANIC OR LATINO       56       52       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 24 36
  subtype2 22 17
  subtype3 15 19
  subtype4 19 13
subtype1 subtype2 subtype3 subtype4 
      60       39       34       32 
subtype1 subtype2 subtype3 subtype4 
      36       17       19       13 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABF 
        2.17        23.97         9.63         2.63        22.22        22.72 
TCGA-2J-AABI TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IC 
       31.86         9.11         4.70        12.95        23.61        24.26 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A8YN 
       15.06        10.13        12.39        10.98         7.66        17.00 
TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       24.07        15.95        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
        1.02         8.02        12.89        22.06        21.73        19.50 
TCGA-HZ-7924 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A8P1 TCGA-IB-7644 
       27.62        17.92        10.13        21.60         0.23        12.95 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7LX TCGA-IB-A7M4 
        4.04         3.62        17.16        15.12         8.22        15.88 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUU TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
        4.73         7.86         8.05        12.92        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       15.45         3.12        15.32        21.24        17.26        23.08 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUL TCGA-YH-A8SY TCGA-YY-A8LH 
       27.75        16.80        14.14        13.32        12.76        66.28 

$subtype2
TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQI TCGA-3A-A9I9 
       20.61        22.26        14.40        21.44         3.39        20.84 
TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-F2-A7TX 
       34.09        75.12         9.70        19.46        19.27         3.12 
TCGA-FB-A4P6 TCGA-FB-A78T TCGA-FB-AAQ1 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8003 
       11.93        12.43         4.04         0.92         0.13         0.69 
TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 
        9.83        21.70        16.14         5.26        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SP 
       23.80        15.65        15.81        21.30         2.47        15.85 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-LB-A9Q5 
       21.90         1.35         0.26         9.44        12.46        10.29 
TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A77G 
        0.30        22.85         0.39 

$subtype3
TCGA-2J-AABA TCGA-2J-AABP TCGA-2J-AABT TCGA-2L-AAQE TCGA-3A-A9IB TCGA-3E-AAAZ 
       19.96        11.84        10.49        22.49         7.36        71.74 
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPS TCGA-HZ-7925 TCGA-HZ-7926 
        5.88        14.76        11.61         7.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8638 TCGA-HZ-A4BH 
       23.21        12.03         3.95        12.43         4.96         6.38 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7893 
       10.85         1.08        49.38         4.77        41.33         3.85 
TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUW TCGA-L1-A7W4 
       20.88        14.17        11.11         7.40         7.56         9.14 
TCGA-Q3-A5QY TCGA-US-A77J TCGA-XD-AAUI TCGA-Z5-AAPL 
       13.68        18.67        12.03         0.69 

$subtype4
TCGA-2J-AABK TCGA-2J-AABO TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IH 
       15.91        14.47         9.60        45.47        53.00        28.73 
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       60.95        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IV TCGA-F2-7276 TCGA-FB-AAPQ TCGA-FB-AAQ2 TCGA-H6-A45N TCGA-HZ-7920 
       31.79         7.10        37.15         5.03        13.84         7.76 
TCGA-HZ-7923 TCGA-HZ-8519 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-7897 
        0.26        14.93        21.90        43.79        19.66        15.98 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-AAUQ TCGA-IB-AAUV TCGA-RB-AA9M TCGA-XD-AAUG 
       12.00         7.20         6.02        13.28         9.40        13.81 
TCGA-XD-AAUH TCGA-YB-A89D 
       12.99        11.51 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.13     0.69     0.26 
subtype1 subtype2 subtype3 subtype4 
   66.28    75.12    71.74    84.10 
subtype1 subtype2 subtype3 subtype4 
  15.090   14.400   11.725   15.420 
[1] "0.2 - 66.3 (15.1)" "0.1 - 75.1 (14.4)" "0.7 - 71.7 (11.7)"
[4] "0.3 - 84.1 (15.4)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        3        12        41         2        2
  subtype2       0        1        1         7        29         1        0
  subtype3       0        1        1         4        27         1        0
  subtype4       1        3        8         2        17         0        1
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        0        0        1
  STAGE IA         1        1        1        3
  STAGE IB         3        1        1        8
  STAGE IIA       12        7        4        2
  STAGE IIB       41       29       27       17
  STAGE III        2        1        1        0
  STAGE IV         2        0        0        1
[1] 7 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  1  5 54  1
  subtype2  1  6 31  1
  subtype3  1  2 30  1
  subtype4  5  8 19  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        1        1        5
  T2        5        6        2        8
  T3       54       31       30       19
  T4        1        1        1        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"
D7V5, binary
          cls
clus        0  1
  subtype1 17 44
  subtype2  9 30
  subtype3  6 27
  subtype4 12 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   44
  subtype2    9   30
  subtype3    6   27
  subtype4   12   18
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       17        9        6       12
  1       44       30       27       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 23  2
  subtype2 23  0
  subtype3 17  0
  subtype4 12  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    2
  subtype2   23    0
  subtype3   17    0
  subtype4   12    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       23       23       17       12
  1        2        0        0        1
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 26 35
  subtype2 19 20
  subtype3 17 17
  subtype4 13 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   35
  subtype2   19   20
  subtype3   17   17
  subtype4   13   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       26       19       17       13
  MALE         35       20       17       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  50
  subtype2                                  37
  subtype3                                  29
  subtype4                                  23
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                     1
  subtype3                                     2
  subtype4                                    10
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                1
  subtype3                                                2
  subtype4                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
D7V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    50       37       29
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        1        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1        2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        1
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                  10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     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"
D7V9, continuous
D7V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 34 22  0  2
  subtype2 23 14  0  0
  subtype3 22  9  1  1
  subtype4 24  6  1  1
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       34       23       22       24
  R1       22       14        9        6
  R2        0        0        1        1
  RX        2        0        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"
D7V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    57
  subtype2     1                         2    35
  subtype3     1                         1    31
  subtype4     0                         1    31
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        0
  BLACK OR AFRICAN AMERICAN        2        2        1        1
  WHITE                           57       35       31       31
[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"
D7V14, binary
          cls
clus        0  1
  subtype1  1 47
  subtype2  0 30
  subtype3  1 27
  subtype4  1 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   47
  subtype2    0   30
  subtype3    1   27
  subtype4    1   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        1        1
  NOT HISPANIC OR LATINO       47       30       27       26
[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(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 39 54
  subtype2 22 19
  subtype3 19 12
subtype1 subtype2 subtype3 
      93       41       31 
subtype1 subtype2 subtype3 
      54       19       12 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABT TCGA-2J-AABU 
       22.72        31.86        14.47        11.84        10.49         9.11 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
        4.70        22.49        12.95        23.61         7.36        24.26 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       15.06        10.13        12.39        71.74        10.98         7.66 
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        24.07        11.61        15.95        37.15        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ6 TCGA-H6-8124 
       34.82        23.54        15.55         4.04         8.02        12.89 
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7925 
       22.06        21.73        19.50         0.13        27.62        20.19 
TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49I 
       17.03         3.95         9.83        17.92         4.96        10.13 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 
       21.60        10.85         1.08         0.23        12.95         4.77 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
       19.82        41.33         4.04         3.62        19.66         3.85 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        12.00        15.85        15.12        20.88        21.90 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         4.73         7.86        14.17         6.02 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
        7.40         8.05         9.14        12.92        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45        13.68         3.12        15.32        21.24        17.26 
TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUL TCGA-YB-A89D 
       23.08        27.75        16.80        14.14        13.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28         0.69 

$subtype2
TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQI 
       20.61        22.26        15.91        14.40        21.44         3.39 
TCGA-3A-A9I9 TCGA-3A-A9IJ TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 
       20.84        60.95        34.09        75.12         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 TCGA-FB-A78T TCGA-FB-AAPS 
        7.10        19.27         3.12        11.93        12.43         7.50 
TCGA-FB-AAQ3 TCGA-HZ-7918 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G 
        1.02         0.92        12.03         0.69        12.43        21.70 
TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7654 TCGA-IB-7889 
       16.14         5.26        15.35        23.80        15.65        15.81 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUW 
       21.30         2.47         1.35         0.26         9.44         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A77G 
       12.46        10.29         0.30        22.85         0.39 

$subtype3
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IH TCGA-3A-A9IL TCGA-3A-A9IN 
        9.60        45.47        53.00        28.73        84.10        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-A4P5 TCGA-FB-A5VM 
       63.85        50.70        30.64        31.79         5.88        14.76 
TCGA-FB-AAQ2 TCGA-H6-A45N TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 
        5.03        13.84         7.76         0.26        23.21        14.93 
TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-A5SQ 
        6.38        49.38        21.90        43.79        15.98         7.20 
TCGA-IB-AAUR TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       11.11        13.28         9.40        18.67        13.81        12.99 
TCGA-XD-AAUI 
       12.03 

subtype1 subtype2 subtype3 
    0.13     0.26     0.26 
subtype1 subtype2 subtype3 
   71.74    75.12    84.10 
subtype1 subtype2 subtype3 
   13.68    12.43    14.93 
[1] "0.1 - 71.7 (13.7)" "0.3 - 75.1 (12.4)" "0.3 - 84.1 (14.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        4        18        66         2        2
  subtype2       0        1        2         5        32         1        0
  subtype3       1        3        7         2        16         1        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         2        1        3
  STAGE IB         4        2        7
  STAGE IIA       18        5        2
  STAGE IIB       66       32       16
  STAGE III        2        1        1
  STAGE IV         2        0        1
[1] 7 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  6 85  1
  subtype2  1  8 31  1
  subtype3  5  7 18  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        1        5
  T2        6        8        7
  T3       85       31       18
  T4        1        1        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"
D8V5, binary
          cls
clus        0  1
  subtype1 24 69
  subtype2  8 33
  subtype3 12 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   69
  subtype2    8   33
  subtype3   12   17
   clus
vv  subtype1 subtype2 subtype3
  0       24        8       12
  1       69       33       17
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 43  2
  subtype2 23  0
  subtype3  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    2
  subtype2   23    0
  subtype3    9    1
   clus
vv  subtype1 subtype2 subtype3
  0       43       23        9
  1        2        0        1
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 38 56
  subtype2 20 21
  subtype3 17 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   56
  subtype2   20   21
  subtype3   17   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       20       17
  MALE         56       21       15
[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       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  78
  subtype2                                  38
  subtype3                                  23
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                    11
  subtype2                                     2
  subtype3                                     9
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D8V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    78       38       23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                  11        2        9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        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"
D8V9, continuous
D8V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 54 32  1  3
  subtype2 27 12  0  0
  subtype3 22  7  1  1
D8V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       54       27       22
  R1       32       12        7
  R2        1        0        1
  RX        3        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"
D8V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    87
  subtype2     1                         2    37
  subtype3     0                         1    30
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        0
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           87       37       30
[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"
D8V14, binary
          cls
clus        0  1
  subtype1  2 71
  subtype2  0 32
  subtype3  1 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   71
  subtype2    0   32
  subtype3    1   27
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        1
  NOT HISPANIC OR LATINO       71       32       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 24 38
  subtype2 34 30
  subtype3 21 15
subtype1 subtype2 subtype3 
      62       64       36 
subtype1 subtype2 subtype3 
      38       30       15 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABP 
        2.17         9.63         2.63        22.22        31.86        11.84 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9IC TCGA-3A-A9IU 
        9.11         4.70        22.49        12.95        24.26        15.06 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 
       10.13        12.39        10.98         7.66        17.00        24.07 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.43        15.95        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ3 TCGA-FB-AAQ6 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
        1.02         8.02        12.89        22.06        19.50         0.13 
TCGA-HZ-7924 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-IB-7644 
       27.62         9.83        17.92        10.13         5.26        12.95 
TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-8127 
        4.77        19.82        41.33         4.04         3.62        17.16 
TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUO TCGA-L1-A7W4 
       15.12        21.90         8.22         4.73         7.86         9.14 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.92        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUL TCGA-YH-A8SY 
       15.32        21.24        27.75        14.14        13.32        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28         0.69 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR 
       23.97        20.61        19.96        15.91        14.47        14.40 
TCGA-2J-AABT TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IV 
       10.49        45.47        53.00        28.73        60.95        31.79 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 TCGA-FB-A4P6 
       75.12        71.74        19.46         7.10         5.88        11.93 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-H6-A45N TCGA-HZ-7918 
       14.76        11.61        37.15         7.50        13.84         0.92 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        7.76         0.26        20.19        17.03        23.21        12.03 
TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A4BH 
        0.69        12.43        14.93         4.96        21.70         6.38 
TCGA-HZ-A77P TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7654 
       10.85        49.38        21.90        15.35        23.80        15.65 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
       43.79        15.81        19.66        21.30         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUQ 
        2.47        12.00         7.20        20.88        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-RB-AA9M TCGA-RL-AAAS 
       11.11         7.40        13.28         7.56         9.40         0.30 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       18.67        13.81        12.99        12.03 

$subtype3
TCGA-2J-AABF TCGA-2J-AABH TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.72        22.26         3.39         9.60        23.61        20.84 
TCGA-3A-A9IB TCGA-3A-A9IL TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        84.10        68.52        63.85        50.70        30.64 
TCGA-3A-A9IX TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-HZ-7289 
       34.09        19.27         3.12         4.04         5.03        21.73 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-A5SP TCGA-IB-A6UG 
       16.14        21.60         1.08         0.23        15.85         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-LB-A9Q5 
       15.88         0.26         9.44         8.05        12.46        10.29 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-YB-A89D 
       17.26        23.08        22.85        16.80         0.39        11.51 

subtype1 subtype2 subtype3 
    0.13     0.26     0.23 
subtype1 subtype2 subtype3 
   66.28    75.12    84.10 
subtype1 subtype2 subtype3 
  12.935   14.435   16.010 
[1] "0.1 - 66.3 (12.9)" "0.3 - 75.1 (14.4)" "0.2 - 84.1 (16.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        2        14        42         2        2
  subtype2       0        4        7         6        45         2        1
  subtype3       1        1        4         5        24         0        0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         1        4        1
  STAGE IB         2        7        4
  STAGE IIA       14        6        5
  STAGE IIB       42       45       24
  STAGE III        2        2        0
  STAGE IV         2        1        0
[1] 7 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  1  4 57  1
  subtype2  5 11 47  2
  subtype3  2  6 27  0
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        5        2
  T2        4       11        6
  T3       57       47       27
  T4        1        2        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"
D9V5, binary
          cls
clus        0  1
  subtype1 18 45
  subtype2 17 47
  subtype3  9 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   45
  subtype2   17   47
  subtype3    9   24
   clus
vv  subtype1 subtype2 subtype3
  0       18       17        9
  1       45       47       24
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 29  2
  subtype2 35  1
  subtype3  9  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    2
  subtype2   35    1
  subtype3    9    0
   clus
vv  subtype1 subtype2 subtype3
  0       29       35        9
  1        2        1        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"
D9V7, binary
          cls
clus        0  1
  subtype1 32 31
  subtype2 30 35
  subtype3 13 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   31
  subtype2   30   35
  subtype3   13   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       30       13
  MALE         31       35       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  54
  subtype2                                  56
  subtype3                                  26
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     7
  subtype3                                     9
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                2
  subtype3                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D9V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    54       56       26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        7        9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        2        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        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"
D9V9, continuous
D9V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 36 22  1  1
  subtype2 43 16  1  1
  subtype3 23 11  0  2
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       36       43       23
  R1       22       16       11
  R2        1        1        0
  RX        1        1        2
[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"
D9V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    60
  subtype2     2                         3    57
  subtype3     0                         2    34
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        0
  BLACK OR AFRICAN AMERICAN        1        3        2
  WHITE                           60       57       34
[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"
D9V14, binary
          cls
clus        0  1
  subtype1  1 50
  subtype2  2 50
  subtype3  0 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   50
  subtype2    2   50
  subtype3    0   29
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        0
  NOT HISPANIC OR LATINO       50       50       29
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 33 46
  subtype2 22 23
  subtype3 24 14
subtype1 subtype2 subtype3 
      79       45       38 
subtype1 subtype2 subtype3 
      46       23       14 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABT TCGA-2J-AABU TCGA-2L-AAQA 
       31.86        14.47        11.84        10.49         9.11         4.70 
TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IZ 
       22.49        12.95        23.61         7.36        24.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 
       12.39        71.74        10.98         7.66        17.00        24.07 
TCGA-FB-A7DR TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       11.61        15.95        37.15        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ6 TCGA-H6-8124 TCGA-HZ-7289 
       15.55         4.04         5.03         8.02        12.89        21.73 
TCGA-HZ-7919 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8638 TCGA-HZ-A49I TCGA-HZ-A77P 
       19.50        27.62        20.19         4.96        10.13        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 
        1.08         0.23        12.95         4.77        41.33         4.04 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
       19.66         3.85        12.00        15.85        15.12        20.88 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 
        8.22        15.88         7.86         6.02         8.05         9.14 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.92        19.20         8.78        15.45        13.68         3.12 
TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
       15.32        21.24        17.26        23.08        27.75        16.80 
TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUL TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       14.14        13.81        13.32        11.51        12.76        66.28 
TCGA-Z5-AAPL 
        0.69 

$subtype2
TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-2L-AAQI 
       20.61        22.72        22.26        15.91        14.40         3.39 
TCGA-3A-A9I9 TCGA-3A-A9IU TCGA-3A-A9IX TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 
       20.84        15.06        34.09        19.27         3.12        11.93 
TCGA-FB-A78T TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 
       12.43         1.02        13.84        22.06         0.92         0.13 
TCGA-HZ-7926 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8636 TCGA-HZ-A49G 
       17.03         0.69         9.83        12.43        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       16.14        21.60         5.26        15.35        19.82        23.80 
TCGA-IB-7654 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
       15.65         3.62        15.81        21.30         2.47        17.16 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUT TCGA-LB-A8F3 
       21.90         1.35         0.26         4.73         9.44        12.46 
TCGA-LB-A9Q5 TCGA-US-A774 TCGA-US-A77G 
       10.29        22.85         0.39 

$subtype3
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I5 TCGA-3A-A9IH TCGA-3A-A9IJ TCGA-3A-A9IL 
        9.60        45.47        53.00        28.73        60.95        84.10 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3E-AAAY 
       68.52        63.85        50.70        30.64        31.79        75.12 
TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-AAPS TCGA-HZ-7920 
       19.46         7.10         5.88        14.76         7.50         7.76 
TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-7645 
        0.26        23.21        12.03        14.93         6.38        49.38 
TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-A5SQ TCGA-IB-AAUP TCGA-IB-AAUR 
       21.90        43.79        15.98         7.20        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A77J 
        7.40        13.28         7.56         9.40         0.30        18.67 
TCGA-XD-AAUH TCGA-XD-AAUI 
       12.99        12.03 

subtype1 subtype2 subtype3 
    0.23     0.13     0.26 
subtype1 subtype2 subtype3 
   71.74    34.09    84.10 
subtype1 subtype2 subtype3 
  12.950   15.060   14.845 
[1] "0.2 - 71.7 (12.9)" "0.1 - 34.1 (15.1)" "0.3 - 84.1 (14.8)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        3        16        54         2        2
  subtype2       0        1        1         7        35         1        1
  subtype3       1        3        9         2        22         1        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         2        1        3
  STAGE IB         3        1        9
  STAGE IIA       16        7        2
  STAGE IIB       54       35       22
  STAGE III        2        1        1
  STAGE IV         2        1        0
[1] 7 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  5 71  1
  subtype2  1  6 38  1
  subtype3  5 10 22  1
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        1        5
  T2        5        6       10
  T3       71       38       22
  T4        1        1        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"
D10V5, binary
          cls
clus        0  1
  subtype1 20 58
  subtype2 10 36
  subtype3 14 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   58
  subtype2   10   36
  subtype3   14   22
   clus
vv  subtype1 subtype2 subtype3
  0       20       10       14
  1       58       36       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 35  2
  subtype2 23  1
  subtype3 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    2
  subtype2   23    1
  subtype3   15    0
   clus
vv  subtype1 subtype2 subtype3
  0       35       23       15
  1        2        1        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"
D10V7, binary
          cls
clus        0  1
  subtype1 33 46
  subtype2 24 22
  subtype3 18 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   46
  subtype2   24   22
  subtype3   18   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       24       18
  MALE         46       22       21
[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       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  65
  subtype2                                  41
  subtype3                                  30
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                     4
  subtype3                                     9
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D10V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    65       41       30
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        4        9
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        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"
D10V9, continuous
D10V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 50 22  1  2
  subtype2 25 18  0  1
  subtype3 27  9  1  1
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       50       25       27
  R1       22       18        9
  R2        1        0        1
  RX        2        1        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"
D10V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    73
  subtype2     1                         2    42
  subtype3     0                         2    36
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        0
  BLACK OR AFRICAN AMERICAN        2        2        2
  WHITE                           73       42       36
[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"
D10V14, binary
          cls
clus        0  1
  subtype1  2 57
  subtype2  0 38
  subtype3  1 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   57
  subtype2    0   38
  subtype3    1   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        1
  NOT HISPANIC OR LATINO       57       38       34
[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"
