[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/22507097/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/22541963/PAAD-TP.mergedcluster.txt"

nPatients in clinical file=185, in cluster file=185, common to both=185
[1]  10 185
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
26 74 46 38 
 1  2  3  4 
26 74 46 38 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
45 50 52 37 
 1  2  3  4 
45 50 52 37 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
40 25 20 15 23 
 1  2  3  4  5 
40 25 20 15 23 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
48 25 16 16 18 
 1  2  3  4  5 
48 25 16 16 18 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
39 26 43 40 30 
 1  2  3  4  5 
39 26 43 40 30 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
75 75 28 
 1  2  3 
75 75 28 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
52 47 26 31 22 
 1  2  3  4  5 
52 47 26 31 22 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
102  43  33 
  1   2   3 
102  43  33 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6  7 
28 11 27 13 51 27 17 
 1  2  3  4  5  6  7 
28 11 27 13 51 27 17 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
23 44 19 54 26  8 
 1  2  3  4  5  6 
23 44 19 54 26  8 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_PACK_YEARS_SMOKED"            
[15] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 185 columns.

[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=96,	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=84,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 185 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RESIDUAL_TUMOR"                "NUMBER_OF_LYMPH_NODES"        
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  7  24 148   4 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  7  24 148   4 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  7  24 148   4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  7  24 148   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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=31, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=30, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, 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  7 18
  subtype2 30 44
  subtype3 27 19
  subtype4 19 19
subtype1 subtype2 subtype3 subtype4 
      25       74       46       38 
subtype1 subtype2 subtype3 subtype4 
      18       44       19       19 
$subtype1
TCGA-LB-A7SX TCGA-2J-AAB1 TCGA-2J-AABA TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQI 
       12.92         2.17        19.96        15.22         9.11         3.39 
TCGA-3A-A9IC TCGA-3E-AAAY TCGA-FB-AAPQ TCGA-FB-AAPY TCGA-FZ-5921 TCGA-FZ-5922 
       24.26        75.12        37.15        34.82         5.10        36.20 
TCGA-H6-8124 TCGA-HV-A5A4 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-8315 TCGA-HZ-A49I 
       12.89         7.63        30.25        17.49         9.83        10.13 
TCGA-HZ-A77P TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7893 TCGA-LB-A9Q5 TCGA-RB-A7B8 
       10.85        41.33         3.62         3.85        10.29        15.32 
TCGA-US-A774 
       22.85 

$subtype2
TCGA-2J-AABT TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-HZ-7289 TCGA-HZ-A4BK 
       10.49        90.12         7.66         8.02        21.73        21.60 
TCGA-IB-7654 TCGA-IB-A5SS TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       15.65        15.12        16.37        23.97         9.63         2.63 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQE 
       22.22        22.72        42.31        14.47         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU 
       12.95         9.60        20.84         7.36        33.57        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A78T 
       36.26        10.13        24.43        10.98        17.00        12.33 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 
       12.53        23.54        15.55         5.03         1.02         2.01 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       17.79        22.06         4.21         9.50        66.94         8.28 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-8636 
       31.86        19.50         0.13        20.19         3.95        17.92 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 
        0.23        19.82        12.95         4.77        21.90        36.69 
TCGA-IB-7886 TCGA-IB-7890 TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
        4.04        19.66        17.16        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-OE-A75W 
       15.88         4.73         6.02         8.05         9.14         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A77G 
       15.45         3.12        24.23        23.08        39.98         0.39 
TCGA-XD-AAUI TCGA-XN-A8T3 
       12.03        31.27 

$subtype3
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-US-A77E TCGA-2J-AAB9 TCGA-2J-AABV 
       14.40        58.98        60.95        14.14        20.61        21.44 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 
       63.85        50.70         9.70        19.46         7.10         5.88 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPS TCGA-HV-A7OP TCGA-HZ-7920 TCGA-HZ-7923 
       16.37        11.61         7.50        32.15         7.76        10.32 
TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
       27.62        12.03        19.59        12.43        14.93         4.96 
TCGA-HZ-A49H TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       16.14        19.82        43.79        15.98        15.19        12.00 
TCGA-IB-A5ST TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
       20.88         0.26        14.17        11.11         7.40         9.44 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-RL-AAAS 
       13.28         7.56        12.46        13.68         9.40         0.30 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XN-A8T5 TCGA-Z5-AAPL 
       18.67        12.99        23.67        15.35 

$subtype4
TCGA-FZ-5924 TCGA-H6-A45N TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-2J-AABI TCGA-2J-AABK 
       15.78        13.84         1.08        17.26        31.86        15.91 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IN TCGA-3A-A9IS TCGA-3A-A9IX TCGA-3E-AAAZ 
       45.47        43.50        68.52        32.81        34.09        71.74 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A545 TCGA-FB-AAPP TCGA-FB-AAQ1 TCGA-FZ-5919 
       19.27         3.12        24.07        15.95         4.04        24.36 
TCGA-FZ-5923 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8637 TCGA-HZ-A49G TCGA-HZ-A4BH 
       20.35        17.03        23.21        17.00        21.70         6.38 
TCGA-HZ-A77O TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-A5SP 
        5.26        49.38        15.35        15.81        30.02        15.85 
TCGA-IB-A5SQ TCGA-IB-AAUO TCGA-M8-A5N4 TCGA-US-A779 TCGA-XD-AAUG TCGA-YB-A89D 
        7.20         7.86        19.20        16.80        13.81        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

subtype1 subtype2 subtype3 subtype4 
    2.17     0.13     0.26     1.08 
subtype1 subtype2 subtype3 subtype4 
   75.12    90.12    63.85    71.74 
subtype1 subtype2 subtype3 subtype4 
  12.920   15.090   14.155   17.015 
[1] "2.2 - 75.1 (12.9)" "0.1 - 90.1 (15.1)" "0.3 - 63.9 (14.2)"
[4] "1.1 - 71.7 (17.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        0        0         4        22         0        0
  subtype2       1        2        6        13        47         2        3
  subtype3       0        2        6         7        28         1        0
  subtype4       0        1        3         6        24         2        2
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        0        0
  STAGE IA         0        2        2        1
  STAGE IB         0        6        6        3
  STAGE IIA        4       13        7        6
  STAGE IIB       22       47       28       24
  STAGE III        0        2        1        2
  STAGE IV         0        3        0        2
[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  0  2 24  0
  subtype2  3  8 62  1
  subtype3  3  9 31  1
  subtype4  1  5 30  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        3        3        1
  T2        2        8        9        5
  T3       24       62       31       30
  T4        0        1        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1  4 22
  subtype2 22 50
  subtype3 15 29
  subtype4  9 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   22
  subtype2   22   50
  subtype3   15   29
  subtype4    9   28
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        4       22       15        9
  1       22       50       29       28
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 35  3
  subtype3 26  0
  subtype4 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   35    3
  subtype3   26    0
  subtype4   14    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       10       35       26       14
  1        0        3        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 13 13
  subtype2 26 48
  subtype3 23 23
  subtype4 21 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   13
  subtype2   26   48
  subtype3   23   23
  subtype4   21   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       13       26       23       21
  MALE         13       48       23       17
[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"
D1V8, binary
          cls
clus        0  1
  subtype1 18  6
  subtype2 57 11
  subtype3 32 12
  subtype4 18 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    6
  subtype2   57   11
  subtype3   32   12
  subtype4   18   15
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        18       57       32       18
  YES        6       11       12       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                                  22
  subtype2                                  64
  subtype3                                  36
  subtype4                                  31
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     3
  subtype2                                     9
  subtype3                                     7
  subtype4                                     6
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                3
  subtype4                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
D1V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    22       64       36
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   3        9        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        1        3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    31
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6
  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"
D1V10, continuous
D1V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 15  6  2  0
  subtype2 41 25  2  3
  subtype3 35 10  1  0
  subtype4 20 12  0  1
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       15       41       35       20
  R1        6       25       10       12
  R2        2        2        1        0
  RX        0        3        0        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"
D1V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    21
  subtype2     6                         1    66
  subtype3     2                         3    41
  subtype4     0                         2    33
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        6        2        0
  BLACK OR AFRICAN AMERICAN        1        1        3        2
  WHITE                           21       66       41       33
[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"
D1V15, binary
          cls
clus        0  1
  subtype1  0 17
  subtype2  2 53
  subtype3  1 39
  subtype4  2 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   17
  subtype2    2   53
  subtype3    1   39
  subtype4    2   27
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        1        2
  NOT HISPANIC OR LATINO       17       53       39       27
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16 28
  subtype2 29 21
  subtype3 18 34
  subtype4 21 16
subtype1 subtype2 subtype3 subtype4 
      44       50       52       37 
subtype1 subtype2 subtype3 subtype4 
      28       21       34       16 
$subtype1
TCGA-3A-A9I5 TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB1 
       58.98         7.66         8.02        17.26        14.14         2.17 
TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQJ 
        2.63        22.72        42.31        14.47         4.70        12.95 
TCGA-2L-AAQL TCGA-3A-A9IH TCGA-3E-AAAZ TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
        9.60        33.57        71.74        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HV-A5A4 
       37.15        15.55         4.04         5.03         2.01         7.63 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-A4BH TCGA-HZ-A77P 
        8.28        32.15        17.03         3.95         6.38        10.85 
TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7890 
        0.23         4.77        21.90        19.82         4.04        19.66 
TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUN TCGA-OE-A75W TCGA-S4-A8RM 
       17.16        21.90         1.35         4.73         8.78        24.23 
TCGA-US-A77G TCGA-YY-A8LH 
        0.39        66.28 

$subtype2
TCGA-2J-AABR TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-H6-A45N TCGA-IB-7654 TCGA-2J-AAB4 
       14.40        60.95        90.12        13.84        15.65        23.97 
TCGA-2J-AAB9 TCGA-2J-AABK TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9I9 
       20.61        15.91        21.44         3.39        45.47        20.84 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       68.52        63.85        50.70        32.81        36.26        34.09 
TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P6 
       75.12         9.70        19.46         7.10        19.27        25.22 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A5A5 TCGA-HZ-7918 TCGA-HZ-7924 
       36.20        20.35        17.79         9.50        31.86        27.62 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
       12.03        19.59        12.43        14.93         4.96        21.70 
TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 
       16.14         5.26        15.35        36.69        15.81        30.02 
TCGA-IB-8126 TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       15.19         0.26         9.44         7.56        12.46        10.29 
TCGA-RB-AA9M TCGA-XN-A8T3 
        9.40        31.27 

$subtype3
TCGA-FZ-5924 TCGA-HZ-7289 TCGA-HZ-A4BK TCGA-IB-A5SS TCGA-LB-A7SX TCGA-XD-AAUL 
       15.78        21.73        21.60        15.12        12.92        16.37 
TCGA-2J-AAB6 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABU TCGA-2L-AAQE 
        9.63        19.96        22.22        31.86         9.11        22.49 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-6879 
        7.36        24.26        15.06        10.13        24.43        10.98 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
        3.12        17.00        24.07        12.53        34.82        23.54 
TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HV-A5A3 TCGA-HV-A5A6 TCGA-HV-AA8X 
        1.02        12.89        22.06         4.21        66.94        17.49 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A9TJ 
       19.50         0.13         9.83        17.92        10.13        19.82 
TCGA-IB-7644 TCGA-IB-7893 TCGA-IB-A5SP TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO 
       12.95         3.85        15.85         8.22        15.88         7.86 
TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RP 
        8.05         9.14        15.45         3.12        15.32        23.08 
TCGA-US-A776 TCGA-US-A779 TCGA-YB-A89D TCGA-YH-A8SY 
       39.98        16.80        11.51        12.76 

$subtype4
TCGA-2J-AABT TCGA-HZ-A77Q TCGA-2J-AABP TCGA-3A-A9I7 TCGA-FB-A4P5 TCGA-FB-A7DR 
       10.49         1.08        15.22        43.50         5.88        11.61 
TCGA-FB-AAPS TCGA-FZ-5919 TCGA-HV-AA8V TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-7925 
        7.50        24.36        30.25         7.76        10.32        20.19 
TCGA-HZ-8001 TCGA-HZ-8637 TCGA-IB-7645 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 
       23.21        17.00        49.38        41.33         3.62        43.79 
TCGA-IB-7897 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.98        12.00         7.20        20.88        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-RL-AAAS 
       11.11         7.40        13.28        19.20        13.68         0.30 
TCGA-US-A774 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       22.85        18.67        13.81        12.99        12.03        23.67 
TCGA-Z5-AAPL 
       15.35 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.26     0.13     0.30 
subtype1 subtype2 subtype3 subtype4 
   71.74    90.12    66.94    49.38 
subtype1 subtype2 subtype3 subtype4 
  12.640   19.365   15.385   13.810 
[1] "0.2 - 71.7 (12.6)" "0.3 - 90.1 (19.4)" "0.1 - 66.9 (15.4)"
[4] "0.3 - 49.4 (13.8)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        4         6        31         1        0
  subtype2       1        3        6         6        30         2        1
  subtype3       0        0        1        13        34         1        3
  subtype4       0        0        4         5        26         1        1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        0        0
  STAGE IA         2        3        0        0
  STAGE IB         4        6        1        4
  STAGE IIA        6        6       13        5
  STAGE IIB       31       30       34       26
  STAGE III        1        2        1        1
  STAGE IV         0        1        3        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  2  4 37  1
  subtype2  5 12 30  2
  subtype3  0  3 49  0
  subtype4  0  5 31  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        5        0        0
  T2        4       12        3        5
  T3       37       30       49       31
  T4        1        2        0        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"
D2V5, binary
          cls
clus        0  1
  subtype1 14 31
  subtype2 14 33
  subtype3 13 38
  subtype4  9 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   31
  subtype2   14   33
  subtype3   13   38
  subtype4    9   27
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       14       14       13        9
  1       31       33       38       27
[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  0
  subtype2 23  1
  subtype3 20  3
  subtype4 21  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    0
  subtype2   23    1
  subtype3   20    3
  subtype4   21    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       20       23       20       21
  1        0        1        3        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"
D2V7, binary
          cls
clus        0  1
  subtype1 10 35
  subtype2 24 26
  subtype3 24 28
  subtype4 24 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   35
  subtype2   24   26
  subtype3   24   28
  subtype4   24   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       24       24       24
  MALE         35       26       28       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1 30  9
  subtype2 34 16
  subtype3 35 12
  subtype4 26  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    9
  subtype2   34   16
  subtype3   35   12
  subtype4   26    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        30       34       35       26
  YES        9       16       12        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  40
  subtype2                                  37
  subtype3                                  43
  subtype4                                  33
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     5
  subtype2                                    11
  subtype3                                     7
  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
D2V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    40       37       43
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   5       11        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        2        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        0
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    33
  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"
D2V10, continuous
D2V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 22 18  1  2
  subtype2 33 13  0  0
  subtype3 30 14  2  2
  subtype4 26  8  2  0
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       22       33       30       26
  R1       18       13       14        8
  R2        1        0        2        2
  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"
D2V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    39
  subtype2     2                         2    45
  subtype3     4                         1    47
  subtype4     2                         2    31
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        2        4        2
  BLACK OR AFRICAN AMERICAN        2        2        1        2
  WHITE                           39       45       47       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"
D2V15, binary
          cls
clus        0  1
  subtype1  1 31
  subtype2  1 39
  subtype3  1 38
  subtype4  2 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   31
  subtype2    1   39
  subtype3    1   38
  subtype4    2   29
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        1        2
  NOT HISPANIC OR LATINO       31       39       38       29
[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 18 22
  subtype2  9 16
  subtype3 10 10
  subtype4  7  8
  subtype5  8 15
subtype1 subtype2 subtype3 subtype4 subtype5 
      40       25       20       15       23 
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       16       10        8       15 
$subtype1
TCGA-IB-7654 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2L-AAQA 
       15.65        12.92        17.26        23.97         2.63         4.70 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9IH TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN 
        3.39         9.60        33.57        71.74        10.98        17.00 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAQ1 
        5.88        25.22        16.37        15.95        37.15         4.04 
TCGA-FZ-5920 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7890 
        2.01        31.86        19.50        36.69         4.04        19.66 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-AAUN TCGA-IB-AAUU 
        3.85        17.16        15.85         7.20         4.73         8.05 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 
       12.46         8.78        24.23        23.08        39.98        16.80 
TCGA-XD-AAUH TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.99        23.67        11.51        66.28 

$subtype2
TCGA-2J-AABR TCGA-F2-A44G TCGA-US-A77E TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2L-AAQJ 
       14.40         7.66        14.14        20.61        22.72        12.95 
TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HV-A5A6 TCGA-HZ-7924 TCGA-HZ-7925 
       24.36         5.10        22.06        66.94        27.62        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        15.19        20.88 
TCGA-IB-A7M4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 TCGA-XD-AAUI 
       15.88        10.29        19.20        15.45        15.32        12.03 
TCGA-YH-A8SY 
       12.76 

$subtype3
TCGA-3A-A9I5 TCGA-IB-A5SS TCGA-2J-AABA TCGA-2J-AABH TCGA-2J-AABO TCGA-3A-A9IB 
       58.98        15.12        19.96        42.31        14.47         7.36 
TCGA-3A-A9IN TCGA-3A-A9IU TCGA-3A-A9IX TCGA-FZ-5922 TCGA-HZ-7920 TCGA-HZ-7922 
       68.52        15.06        34.09        36.20         7.76         0.13 
TCGA-HZ-7923 TCGA-HZ-8002 TCGA-HZ-8315 TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUV 
       10.32        12.03         9.83         7.86        14.17        13.28 
TCGA-RB-AA9M TCGA-US-A774 
        9.40        22.85 

$subtype4
TCGA-H6-A45N TCGA-HZ-A4BK TCGA-2J-AABK TCGA-2L-AAQM TCGA-F2-6880 TCGA-FB-A78T 
       13.84        21.60        15.91        45.47         9.70        12.33 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-IB-7651 TCGA-IB-7891 
       20.35        17.79        19.59        14.93        19.82        30.02 
TCGA-IB-A6UF TCGA-IB-AAUM TCGA-US-A77G 
       21.90         0.26         0.39 

$subtype5
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-XD-AAUL TCGA-3A-A9IZ TCGA-FB-A545 TCGA-FB-AAPZ 
        8.02        15.78        16.37        10.13        24.07        23.54 
TCGA-HZ-8001 TCGA-HZ-8005 TCGA-HZ-A4BH TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7887 
       23.21         3.95         6.38         4.77        21.90         3.62 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-A5SO TCGA-IB-A7LX TCGA-IB-AAUS TCGA-IB-AAUW 
       43.79        15.81        12.00         8.22         7.40         7.56 
TCGA-L1-A7W4 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-US-A77J TCGA-Z5-AAPL 
        9.14        13.68         3.12        18.67        15.35 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.01     4.96     0.13     0.26     3.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
   71.74    66.94    68.52    45.47    43.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
   15.90    15.35    14.32    17.79    12.00 
[1] "2.0 - 71.7 (15.9)" "5.0 - 66.9 (15.3)" "0.1 - 68.5 (14.3)"
[4] "0.3 - 45.5 (17.8)" "3.1 - 43.8 (12.0)"
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        5         7        27         0        0
  subtype2        1        0         4        16         3        1
  subtype3        1        2         4        12         0        0
  subtype4        1        0         0        12         1        1
  subtype5        1        1         4        16         1        0
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE IA         1        1        1        1        1
  STAGE IB         5        0        2        0        1
  STAGE IIA        7        4        4        0        4
  STAGE IIB       27       16       12       12       16
  STAGE III        0        3        0        1        1
  STAGE IV         0        1        0        1        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  7 32  0
  subtype2  1  0 22  2
  subtype3  2  2 15  0
  subtype4  1  1 12  1
  subtype5  1  1 20  1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        2        1        1
  T2        7        0        2        1        1
  T3       32       22       15       12       20
  T4        0        2        0        1        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 13 27
  subtype2  6 19
  subtype3  7 12
  subtype4  1 14
  subtype5  5 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   27
  subtype2    6   19
  subtype3    7   12
  subtype4    1   14
  subtype5    5   18
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13        6        7        1        5
  1       27       19       12       14       18
[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 21  0
  subtype2 11  1
  subtype3  8  0
  subtype4  8  1
  subtype5 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    0
  subtype2   11    1
  subtype3    8    0
  subtype4    8    1
  subtype5   12    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       21       11        8        8       12
  1        0        1        0        1        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 26
  subtype2 20  5
  subtype3  7 13
  subtype4  6  9
  subtype5 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   26
  subtype2   20    5
  subtype3    7   13
  subtype4    6    9
  subtype5   10   13
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       14       20        7        6       10
  MALE         26        5       13        9       13
[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"
D3V8, binary
          cls
clus        0  1
  subtype1 24 11
  subtype2 17  8
  subtype3 12  6
  subtype4 12  3
  subtype5 20  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   11
  subtype2   17    8
  subtype3   12    6
  subtype4   12    3
  subtype5   20    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        24       17       12       12       20
  YES       11        8        6        3        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  36
  subtype2                                  20
  subtype3                                  18
  subtype4                                  11
  subtype5                                  23
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     3
  subtype2                                     3
  subtype3                                     2
  subtype4                                     4
  subtype5                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                1
  subtype3                                                0
  subtype4                                                0
  subtype5                                                0
D3V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    36       20       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   3        3        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1        0
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    11       23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        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"
D3V10, continuous
D3V11, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      11        9        6        4        2 
 [1] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [7] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype1" "subtype4"
[19] "subtype2" "subtype1" "subtype4" "subtype2" "subtype3" "subtype2"
[25] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1 22 14  1  1
  subtype2 12  9  0  0
  subtype3 15  5  0  0
  subtype4 10  4  0  0
  subtype5 13  7  1  1
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       22       12       15       10       13
  R1       14        9        5        4        7
  R2        1        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"
D3V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    35
  subtype2     1                         0    21
  subtype3     0                         0    20
  subtype4     0                         0    15
  subtype5     0                         1    22
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        0
  BLACK OR AFRICAN AMERICAN        3        0        0        0        1
  WHITE                           35       21       20       15       22
[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"
D3V15, binary
          cls
clus        0  1
  subtype1  2 29
  subtype2  0 17
  subtype3  0 17
  subtype4  0 12
  subtype5  1 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   29
  subtype2    0   17
  subtype3    0   17
  subtype4    0   12
  subtype5    1   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        0        0        0        1
  NOT HISPANIC OR LATINO       29       17       17       12       20
[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 19 29
  subtype2 10 15
  subtype3  9  7
  subtype4  9  7
  subtype5  5 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      48       25       16       16       18 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       15        7        7       13 
$subtype1
TCGA-H6-A45N TCGA-IB-7654 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB4 
       13.84        15.65        12.92        17.26        14.14        23.97 
TCGA-2J-AAB8 TCGA-2J-AABK TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9IH 
        2.63        15.91         4.70         3.39         9.60        33.57 
TCGA-3A-A9IX TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 
       34.09        71.74        10.98        17.00         5.88        25.22 
TCGA-FB-A5VM TCGA-FB-AAPQ TCGA-FB-AAQ1 TCGA-FZ-5920 TCGA-HZ-7919 TCGA-HZ-7924 
       16.37        37.15         4.04         2.01        19.50        27.62 
TCGA-HZ-8002 TCGA-HZ-8315 TCGA-HZ-8638 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 
       12.03         9.83         4.96        19.82        36.69         4.04 
TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       15.81         3.85        17.16        12.00        15.85         7.20 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RM 
        4.73         7.86         8.05        12.46         8.78        24.23 
TCGA-S4-A8RP TCGA-US-A779 TCGA-XD-AAUH TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       23.08        16.80        12.99        23.67        11.51        66.28 

$subtype2
TCGA-2J-AABR TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2L-AAQJ 
       14.40         7.66         8.02        20.61        22.72        12.95 
TCGA-FZ-5919 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HV-A5A6 TCGA-HZ-7925 TCGA-HZ-8001 
       24.36         5.10        22.06        66.94        20.19        23.21 
TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5ST 
       12.95         4.77        15.35        41.33        15.19        20.88 
TCGA-IB-A7M4 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 TCGA-YH-A8SY 
       15.88        10.29        19.20        15.45        15.32        12.76 
TCGA-Z5-AAPL 
       15.35 

$subtype3
TCGA-3A-A9I5 TCGA-XD-AAUL TCGA-2J-AABA TCGA-2J-AABH TCGA-2J-AABO TCGA-3A-A9IB 
       58.98        16.37        19.96        42.31        14.47         7.36 
TCGA-3A-A9IU TCGA-FZ-5922 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-A4BH TCGA-IB-AAUV 
       15.06        36.20         7.76        10.32         6.38        13.28 
TCGA-IB-AAUW TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-US-A774 
        7.56        13.68         3.12        22.85 

$subtype4
TCGA-HZ-A4BK TCGA-2L-AAQM TCGA-3A-A9IN TCGA-F2-6880 TCGA-FB-A78T TCGA-FB-AAPP 
       21.60        45.47        68.52         9.70        12.33        15.95 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HZ-7918 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-IB-7891 
       20.35        17.79        31.86        19.59        14.93        30.02 
TCGA-IB-A6UF TCGA-IB-AAUM TCGA-US-A776 TCGA-US-A77G 
       21.90         0.26        39.98         0.39 

$subtype5
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-3A-A9IZ TCGA-FB-A545 TCGA-FB-AAPZ TCGA-HZ-7922 
       15.78        15.12        10.13        24.07        23.54         0.13 
TCGA-HZ-8005 TCGA-IB-7647 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-A7LX 
        3.95        21.90         3.62        43.79        19.66         8.22 
TCGA-IB-AAUP TCGA-IB-AAUS TCGA-L1-A7W4 TCGA-RB-AA9M TCGA-US-A77J TCGA-XD-AAUI 
       14.17         7.40         9.14         9.40        18.67        12.03 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.01     4.77     3.12     0.26     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   71.74    66.94    58.98    68.52    43.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.990   15.350   14.075   19.970   13.100 
[1] "2.0 - 71.7 (14.0)" "4.8 - 66.9 (15.3)" "3.1 - 59.0 (14.1)"
[4] "0.3 - 68.5 (20.0)" "0.1 - 43.8 (13.1)"
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        3        4         8        33         0        0
  subtype2        1        0         4        15         4        1
  subtype3        0        2         4         9         0        0
  subtype4        1        1         1        11         1        1
  subtype5        0        1         2        15         0        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE IA         3        1        0        1        0
  STAGE IB         4        0        2        1        1
  STAGE IIA        8        4        4        1        2
  STAGE IIB       33       15        9       11       15
  STAGE III        0        4        0        1        0
  STAGE IV         0        1        0        1        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  3  6 39  0
  subtype2  1  0 21  3
  subtype3  0  1 14  0
  subtype4  1  2 12  1
  subtype5  1  2 15  0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        3        1        0        1        1
  T2        6        0        1        2        2
  T3       39       21       14       12       15
  T4        0        3        0        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 15 33
  subtype2  7 18
  subtype3  6 10
  subtype4  2 13
  subtype5  2 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   33
  subtype2    7   18
  subtype3    6   10
  subtype4    2   13
  subtype5    2   16
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       15        7        6        2        2
  1       33       18       10       13       16
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 24  0
  subtype2 13  1
  subtype3  6  0
  subtype4  7  1
  subtype5 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    0
  subtype2   13    1
  subtype3    6    0
  subtype4    7    1
  subtype5   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       24       13        6        7       10
  1        0        1        0        1        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"
D4V7, binary
          cls
clus        0  1
  subtype1 21 27
  subtype2 18  7
  subtype3  4 12
  subtype4  5 11
  subtype5  9  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   27
  subtype2   18    7
  subtype3    4   12
  subtype4    5   11
  subtype5    9    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       21       18        4        5        9
  MALE         27        7       12       11        9
[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"
D4V8, binary
          cls
clus        0  1
  subtype1 31 11
  subtype2 17  8
  subtype3 12  3
  subtype4 11  5
  subtype5 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   11
  subtype2   17    8
  subtype3   12    3
  subtype4   11    5
  subtype5   14    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        31       17       12       11       14
  YES       11        8        3        5        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  42
  subtype2                                  22
  subtype3                                  15
  subtype4                                  11
  subtype5                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     5
  subtype2                                     2
  subtype3                                     1
  subtype4                                     4
  subtype5                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
  subtype4                                                1
  subtype5                                                0
D4V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    42       22       15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   5        2        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        0        0
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    11       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        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"
D4V10, continuous
D4V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 25 18  1  1
  subtype2 13  8  0  0
  subtype3 13  2  0  1
  subtype4 12  4  0  0
  subtype5  9  7  1  0
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       25       13       13       12        9
  R1       18        8        2        4        7
  R2        1        0        0        0        1
  RX        1        0        1        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    44
  subtype2     1                         0    21
  subtype3     0                         0    16
  subtype4     0                         0    16
  subtype5     0                         1    16
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        0
  BLACK OR AFRICAN AMERICAN        3        0        0        0        1
  WHITE                           44       21       16       16       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"
D4V15, binary
          cls
clus        0  1
  subtype1  2 36
  subtype2  0 17
  subtype3  0 12
  subtype4  0 14
  subtype5  1 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   36
  subtype2    0   17
  subtype3    0   12
  subtype4    0   14
  subtype5    1   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        0        0        0        1
  NOT HISPANIC OR LATINO       36       17       12       14       16
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 14 25
  subtype2 20  6
  subtype3 15 28
  subtype4 16 23
  subtype5 19 11
subtype1 subtype2 subtype3 subtype4 subtype5 
      39       26       43       39       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
      25        6       28       23       11 
$subtype1
TCGA-FB-AAQ6 TCGA-HZ-7289 TCGA-HZ-A4BK TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB8 
        8.02        21.73        21.60        14.14         2.17         2.63 
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-F2-6879 TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
        4.70        12.95        10.98        15.95        37.15        12.53 
TCGA-FB-AAPY TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-H8-A6C1 TCGA-HV-A5A4 TCGA-HV-A7OP 
       34.82        15.55         1.02        22.06         7.63        32.15 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7924 TCGA-HZ-8638 TCGA-HZ-A49I TCGA-HZ-A8P1 
       17.49        19.50        27.62         4.96        10.13         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-AAUU TCGA-OE-A75W 
       19.82        12.95         4.04        15.85         8.05         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 
       15.45         3.12        15.32        24.23        23.08        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-YY-A8LH 
       16.80         0.39        66.28 

$subtype2
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-H6-A45N TCGA-2J-AAB4 TCGA-2J-AABF 
       58.98        60.95        90.12        13.84        23.97        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IH TCGA-3A-A9IN 
       42.31        15.91         9.60        45.47        33.57        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-HV-A5A5 TCGA-HZ-7920 
       63.85        50.70        32.81        36.26         9.50         7.76 
TCGA-HZ-8001 TCGA-HZ-8519 TCGA-IB-A5SQ TCGA-IB-AAUQ TCGA-RB-AA9M TCGA-XD-AAUG 
       23.21        14.93         7.20         6.02         9.40        13.81 
TCGA-XD-AAUH TCGA-YB-A89D 
       12.99        11.51 

$subtype3
TCGA-F2-A44G TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB6 
        7.66        15.12        12.92        17.26        16.37         9.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABU TCGA-2L-AAQE 
       19.96        22.22        31.86        14.47         9.11        22.49 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-A7TX 
        7.36        24.26        15.06        10.13        24.43         3.12 
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-H6-8124 
       17.00        24.07        16.37        23.54         5.03        12.89 
TCGA-HV-A5A3 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7925 TCGA-HZ-8005 
        4.21        66.94         8.28        30.25        20.19         3.95 
TCGA-HZ-8315 TCGA-HZ-8636 TCGA-IB-7646 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
        9.83        17.92         4.77         3.62        19.66         3.85 
TCGA-IB-8127 TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-L1-A7W4 TCGA-M8-A5N4 
       17.16         8.22        15.88         7.86         9.14        19.20 
TCGA-YH-A8SY 
       12.76 

$subtype4
TCGA-2J-AABR TCGA-IB-7654 TCGA-2J-AAB9 TCGA-2J-AABV TCGA-2L-AAQI TCGA-3A-A9I9 
       14.40        15.65        20.61        21.44         3.39        20.84 
TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H 
       34.09        75.12         9.70        19.46         7.10        19.27 
TCGA-FB-A4P6 TCGA-FB-A78T TCGA-FB-AAQ1 TCGA-HZ-7918 TCGA-HZ-7926 TCGA-HZ-8002 
       25.22        12.33         4.04        31.86        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 
       19.59        12.43        21.70         5.26        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A6UF TCGA-IB-A6UG 
       36.69        15.81        30.02        15.19        21.90         1.35 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUT TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        0.26         4.73         9.44         7.56        12.46        10.29 
TCGA-RL-AAAS TCGA-US-A774 TCGA-XN-A8T3 
        0.30        22.85        31.27 

$subtype5
TCGA-2J-AABT TCGA-HZ-A77Q TCGA-2J-AABP TCGA-3A-A9I7 TCGA-3E-AAAZ TCGA-FB-A4P5 
       10.49         1.08        15.22        43.50        71.74         5.88 
TCGA-FB-A7DR TCGA-FB-AAPS TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-8637 TCGA-HZ-A49H 
       11.61         7.50         0.13        10.32        17.00        16.14 
TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7888 
        6.38        10.85        49.38        21.90        41.33        43.79 
TCGA-IB-7897 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
       15.98        12.00        20.88        14.17        11.11         7.40 
TCGA-IB-AAUV TCGA-Q3-A5QY TCGA-US-A77J TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-Z5-AAPL 
       13.28        13.68        18.67        12.03        23.67        15.35 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     6.02     3.12     0.26     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   66.28    90.12    66.94    75.12    71.74 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.320   22.965   15.060   15.650   13.925 
[1] "0.2 - 66.3 (15.3)" "6.0 - 90.1 (23.0)" "3.1 - 66.9 (15.1)"
[4] "0.3 - 75.1 (15.7)" "0.1 - 71.7 (13.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        2         8        24         1        2
  subtype2       1        2        7         1        11         1        1
  subtype3       0        0        2        10        29         1        1
  subtype4       0        1        3         4        31         1        0
  subtype5       0        0        1         5        24         0        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        0        0        0
  STAGE IA         2        2        0        1        0
  STAGE IB         2        7        2        3        1
  STAGE IIA        8        1       10        4        5
  STAGE IIB       24       11       29       31       24
  STAGE III        1        1        1        1        0
  STAGE IV         2        1        1        0        0
[1] 7 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  2  3 33  1
  subtype2  4  8 11  1
  subtype3  0  3 40  0
  subtype4  1  8 30  1
  subtype5  0  2 28  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        4        0        1        0
  T2        3        8        3        8        2
  T3       33       11       40       30       28
  T4        1        1        0        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 13 26
  subtype2 11 12
  subtype3 12 30
  subtype4  8 32
  subtype5  5 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   26
  subtype2   11   12
  subtype3   12   30
  subtype4    8   32
  subtype5    5   24
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       11       12        8        5
  1       26       12       30       32       24
[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"
D5V6, binary
          cls
clus        0  1
  subtype1  9  2
  subtype2  8  1
  subtype3 23  1
  subtype4 24  0
  subtype5 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    2
  subtype2    8    1
  subtype3   23    1
  subtype4   24    0
  subtype5   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        9        8       23       24       16
  1        2        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"
D5V7, binary
          cls
clus        0  1
  subtype1 15 24
  subtype2 10 16
  subtype3 18 25
  subtype4 19 21
  subtype5 18 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   24
  subtype2   10   16
  subtype3   18   25
  subtype4   19   21
  subtype5   18   12
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       15       10       18       19       18
  MALE         24       16       25       21       12
[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"
D5V8, binary
          cls
clus        0  1
  subtype1 26  9
  subtype2 17  9
  subtype3 31 10
  subtype4 26 12
  subtype5 19  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    9
  subtype2   17    9
  subtype3   31   10
  subtype4   26   12
  subtype5   19    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        26       17       31       26       19
  YES        9        9       10       12        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  28
  subtype2                                  14
  subtype3                                  41
  subtype4                                  39
  subtype5                                  25
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                    12
  subtype3                                     1
  subtype4                                     0
  subtype5                                     3
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                2
  subtype2                                                0
  subtype3                                                0
  subtype4                                                1
  subtype5                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   0
  subtype4                                   0
  subtype5                                   1
D5V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    28       14       41
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9       12        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2        0        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        0
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    39       25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     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"
D5V10, continuous
D5V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 23 11  1  2
  subtype2 17  5  1  1
  subtype3 21 16  3  0
  subtype4 23 14  0  1
  subtype5 22  7  0  0
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       23       17       21       23       22
  R1       11        5       16       14        7
  R2        1        1        3        0        0
  RX        2        1        0        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         0    35
  subtype2     1                         0    25
  subtype3     4                         1    36
  subtype4     1                         3    35
  subtype5     1                         2    26
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            4        1        4        1        1
  BLACK OR AFRICAN AMERICAN        0        0        1        3        2
  WHITE                           35       25       36       35       26
[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"
D5V15, binary
          cls
clus        0  1
  subtype1  0 29
  subtype2  0 19
  subtype3  1 28
  subtype4  1 33
  subtype5  3 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   29
  subtype2    0   19
  subtype3    1   28
  subtype4    1   33
  subtype5    3   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        1        1        3
  NOT HISPANIC OR LATINO       29       19       28       33       22
[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(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 32 42
  subtype2 34 41
  subtype3 18 10
subtype1 subtype2 subtype3 
      74       75       28 
subtype1 subtype2 subtype3 
      42       41       10 
$subtype1
TCGA-2J-AABR TCGA-F2-A44G TCGA-H6-A45N TCGA-HZ-A4BK TCGA-IB-7654 TCGA-XD-AAUL 
       14.40         7.66        13.84        21.60        15.65        16.37 
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        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IB 
       14.47        21.44         3.39         9.60        20.84         7.36 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 
       15.06        34.09        10.13        75.12         9.70        19.46 
TCGA-F2-7276 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A78T 
        7.10        19.27         3.12         5.88        25.22        12.33 
TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-H8-A6C1 
        7.50        34.82        23.54         4.04         1.02        22.06 
TCGA-HV-A5A5 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8002 
        9.50        31.86        19.50         0.13        17.03        12.03 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O 
       19.59         9.83        12.43        21.70        16.14         5.26 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7891 
       15.35        19.82        36.69         4.04        15.81        30.02 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
       15.19        17.16        15.85        21.90         1.35         0.26 
TCGA-IB-AAUN TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 
        4.73         7.40         9.44         8.05         7.56        12.46 
TCGA-LB-A9Q5 TCGA-RL-AAAS TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G 
       10.29         0.30        23.08        22.85        16.80         0.39 
TCGA-XD-AAUI TCGA-XN-A8T3 
       12.03        31.27 

$subtype2
TCGA-2J-AABT TCGA-FB-AAQ6 TCGA-HZ-7289 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX 
       10.49         8.02        21.73         1.08        15.12        12.92 
TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
       17.26        14.14         9.63         2.63        19.96        22.22 
TCGA-2J-AABI TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       31.86        15.22         9.11         4.70        22.49        12.95 
TCGA-3A-A9I7 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 
       43.50        24.26        33.57        24.43        71.74        10.98 
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-AAQ0 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 
       15.55         5.03        12.89         4.21         7.63        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7924 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        27.62        20.19 
TCGA-HZ-8005 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
        3.95        17.92         4.96        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7890 
       19.82        12.95         4.77        41.33         3.62        19.66 
TCGA-IB-7893 TCGA-IB-A5ST TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUP 
        3.85        20.88         8.22        15.88         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        6.02        11.11         9.14        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-YB-A89D 
       13.68         3.12        15.32        24.23        39.98        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

$subtype3
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO 
       58.98        60.95        90.12        45.47        68.52        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-A5VM TCGA-HZ-7920 TCGA-HZ-7923 
       50.70        32.81        36.26        16.37         7.76        10.32 
TCGA-HZ-8001 TCGA-HZ-8519 TCGA-HZ-8637 TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 
       23.21        14.93        17.00         6.38        49.38        21.90 
TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-AAUV TCGA-RB-AA9M 
       43.79        15.98        12.00         7.20        13.28         9.40 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T5 
       18.67        13.81        12.99        23.67 

subtype1 subtype2 subtype3 
    0.13     0.23     6.38 
subtype1 subtype2 subtype3 
   75.12    71.74    90.12 
subtype1 subtype2 subtype3 
  15.125   14.170   20.285 
[1] "0.1 - 75.1 (15.1)" "0.2 - 71.7 (14.2)" "6.4 - 90.1 (20.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        3         9        61         1        0
  subtype2       0        3        3        17        47         2        3
  subtype3       1        1        9         2        11         1        1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         1        3        1
  STAGE IB         3        3        9
  STAGE IIA        9       17        2
  STAGE IIB       61       47       11
  STAGE III        1        2        1
  STAGE IV         0        3        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 12 61  1
  subtype2  3  3 68  1
  subtype3  3  9 13  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        3        3
  T2       12        3        9
  T3       61       68       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 13 62
  subtype2 23 50
  subtype3 13 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   62
  subtype2   23   50
  subtype3   13   12
   clus
vv  subtype1 subtype2 subtype3
  0       13       23       13
  1       62       50       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 39  0
  subtype2 31  3
  subtype3 10  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   31    3
  subtype3   10    1
   clus
vv  subtype1 subtype2 subtype3
  0       39       31       10
  1        0        3        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 34 41
  subtype2 33 42
  subtype3 13 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   41
  subtype2   33   42
  subtype3   13   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       33       13
  MALE         41       42       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"
D6V8, binary
          cls
clus        0  1
  subtype1 48 20
  subtype2 53 16
  subtype3 18  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   20
  subtype2   53   16
  subtype3   18    8
     clus
vv    subtype1 subtype2 subtype3
  NO        48       53       18
  YES       20       16        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  68
  subtype2                                  61
  subtype3                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     9
  subtype3                                    10
          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
D6V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    68       61       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        9       10
  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"
D6V10, continuous
D6V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 42 27  0  2
  subtype2 42 21  4  2
  subtype3 22  5  1  0
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       42       42       22
  R1       27       21        5
  R2        0        4        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"
D6V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    69
  subtype2     9                         2    62
  subtype3     0                         1    26
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        9        0
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           69       62       26
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
          cls
clus        0  1
  subtype1  2 56
  subtype2  1 53
  subtype3  2 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   56
  subtype2    1   53
  subtype3    2   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        2
  NOT HISPANIC OR LATINO       56       53       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 22 29
  subtype2 22 25
  subtype3 13 13
  subtype4 16 15
  subtype5 11 11
subtype1 subtype2 subtype3 subtype4 subtype5 
      51       47       26       31       22 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       25       13       15       11 
$subtype1
TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-HZ-A4BK TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        7.66         8.02        21.60        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABE 
       14.14        16.37         2.17        23.97         9.63        22.22 
TCGA-2J-AABI TCGA-2J-AABO TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-3A-A9IU TCGA-F2-6879 
       31.86        14.47         4.70        12.95        15.06        10.98 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       17.00        12.33        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ3 TCGA-H8-A6C1 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A7OL TCGA-HV-AA8X 
        1.02        22.06         4.21         7.63         8.28        17.49 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-IB-7887 
       19.50         0.13        17.92        10.13         0.23         3.62 
TCGA-IB-8127 TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUU TCGA-M8-A5N4 TCGA-OE-A75W 
       17.16         8.22         4.73         8.05        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A779 
       15.45         3.12        15.32        24.23        23.08        16.80 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

$subtype2
TCGA-2J-AABT TCGA-HZ-A77Q TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABP TCGA-2J-AABU 
       10.49         1.08         2.63        19.96        15.22         9.11 
TCGA-2L-AAQE TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3E-AAAZ TCGA-F2-7276 TCGA-FB-A4P5 
       22.49        43.50         7.36        71.74         7.10         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-FB-AAPS TCGA-HZ-7925 TCGA-HZ-7926 
       24.07        16.37        11.61         7.50        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P 
       23.21        12.03         3.95        16.14         6.38        10.85 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-7897 
       49.38         4.77        41.33        15.81         3.85        15.98 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUP 
       15.19        12.00        20.88        15.88         7.86        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-Q3-A5QY 
       11.11         7.40        13.28         7.56         9.14        13.68 
TCGA-RL-AAAS TCGA-US-A77J TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-Z5-AAPL 
        0.30        18.67        12.03        23.67        15.35 

$subtype3
TCGA-2J-AABR TCGA-IB-7654 TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2L-AAQI TCGA-3A-A9I9 
       14.40        15.65        20.61        42.31         3.39        20.84 
TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 
       34.09        75.12        19.46        19.27         3.12        25.22 
TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7891 
        9.83        21.70         5.26        15.35        36.69        30.02 
TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT TCGA-LB-A9Q5 
       15.85        21.90         1.35         0.26         9.44        10.29 
TCGA-US-A774 TCGA-XN-A8T3 
       22.85        31.27 

$subtype4
TCGA-3A-A9IL TCGA-HZ-7289 TCGA-2J-AABF TCGA-2J-AABV TCGA-2L-AAQM TCGA-3A-A9IC 
       90.12        21.73        22.72        21.44        45.47        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 
       63.85        50.70        32.81        36.26        10.13        24.43 
TCGA-F2-6880 TCGA-FB-AAPP TCGA-FB-AAQ1 TCGA-H6-8124 TCGA-HV-A5A6 TCGA-HV-A7OP 
        9.70        15.95         4.04        12.89        66.94        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7924 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8638 
       30.25        31.86        27.62        19.59        12.43         4.96 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7886 TCGA-LB-A8F3 TCGA-US-A776 
       19.82        12.95        19.82         4.04        12.46        39.98 
TCGA-US-A77G 
        0.39 

$subtype5
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-H6-A45N TCGA-2J-AABK TCGA-2L-AAQL TCGA-3A-A9IH 
       58.98        60.95        13.84        15.91         9.60        33.57 
TCGA-3A-A9IN TCGA-FB-AAPQ TCGA-FB-AAQ2 TCGA-HV-A5A5 TCGA-HZ-7920 TCGA-HZ-7923 
       68.52        37.15         5.03         9.50         7.76        10.32 
TCGA-HZ-8519 TCGA-HZ-8637 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-A5SQ 
       14.93        17.00        21.90        43.79        19.66         7.20 
TCGA-IB-AAUQ TCGA-RB-AA9M TCGA-XD-AAUG TCGA-XD-AAUH 
        6.02         9.40        13.81        12.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.30     0.26     0.39     5.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
   66.28    71.74    75.12    90.12    68.52 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.140   13.280   19.365   21.730   14.385 
[1] "0.1 - 66.3 (14.1)" "0.3 - 71.7 (13.3)" "0.3 - 75.1 (19.4)"
[4] "0.4 - 90.1 (21.7)" "5.0 - 68.5 (14.4)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        3        13        32         2        1
  subtype2       0        0        3         4        38         2        0
  subtype3       0        1        1         6        18         0        0
  subtype4       1        1        3         3        20         0        2
  subtype5       0        2        5         2        11         0        1
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        0        0        1        0
  STAGE IA         1        0        1        1        2
  STAGE IB         3        3        1        3        5
  STAGE IIA       13        4        6        3        2
  STAGE IIB       32       38       18       20       11
  STAGE III        2        2        0        0        0
  STAGE IV         1        0        0        2        1
[1] 7 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  6 44  1
  subtype2  0  4 41  2
  subtype3  1  6 19  0
  subtype4  2  3 25  0
  subtype5  3  5 13  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        0        1        2        3
  T2        6        4        6        3        5
  T3       44       41       19       25       13
  T4        1        2        0        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 17 34
  subtype2  7 39
  subtype3  8 18
  subtype4  8 21
  subtype5  9 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   34
  subtype2    7   39
  subtype3    8   18
  subtype4    8   21
  subtype5    9   12
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       17        7        8        8        9
  1       34       39       18       21       12
[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"
D7V6, binary
          cls
clus        0  1
  subtype1 18  1
  subtype2 29  0
  subtype3 16  0
  subtype4  9  2
  subtype5  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   29    0
  subtype3   16    0
  subtype4    9    2
  subtype5    8    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       18       29       16        9        8
  1        1        0        0        2        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 24 28
  subtype2 23 24
  subtype3 10 16
  subtype4 13 18
  subtype5 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   28
  subtype2   23   24
  subtype3   10   16
  subtype4   13   18
  subtype5   10   12
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       23       10       13       10
  MALE         28       24       16       18       12
[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"
D7V8, binary
          cls
clus        0  1
  subtype1 31 15
  subtype2 35  4
  subtype3 16  9
  subtype4 23  8
  subtype5 14  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   15
  subtype2   35    4
  subtype3   16    9
  subtype4   23    8
  subtype5   14    8
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        31       35       16       23       14
  YES       15        4        9        8        8
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  43
  subtype2                                  42
  subtype3                                  24
  subtype4                                  20
  subtype5                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     8
  subtype2                                     3
  subtype3                                     1
  subtype4                                     9
  subtype5                                     4
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                1
  subtype4                                                2
  subtype5                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
  subtype4                                   0
  subtype5                                   0
D7V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    43       42       24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   8        3        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        1        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        1        0
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    20       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 29 16  2  1
  subtype2 31 12  1  1
  subtype3 12 12  0  0
  subtype4 21  8  1  1
  subtype5 13  5  1  1
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       29       31       12       21       13
  R1       16       12       12        8        5
  R2        2        1        0        1        1
  RX        1        1        0        1        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"
D7V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         1    45
  subtype2     1                         2    43
  subtype3     1                         1    23
  subtype4     3                         1    27
  subtype5     1                         1    19
D7V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        1        1        3        1
  BLACK OR AFRICAN AMERICAN        1        2        1        1        1
  WHITE                           45       43       23       27       19
[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"
D7V15, binary
          cls
clus        0  1
  subtype1  0 37
  subtype2  2 36
  subtype3  1 18
  subtype4  1 23
  subtype5  1 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   37
  subtype2    2   36
  subtype3    1   18
  subtype4    1   23
  subtype5    1   17
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        1        1        1
  NOT HISPANIC OR LATINO       37       36       18       23       17
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 44 57
  subtype2 21 22
  subtype3 19 14
subtype1 subtype2 subtype3 
     101       43       33 
subtype1 subtype2 subtype3 
      57       22       14 
$subtype1
TCGA-2J-AABT TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-HZ-7289 TCGA-HZ-A4BK TCGA-HZ-A77Q 
       10.49         7.66         8.02        21.73        21.60         1.08 
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.12        12.92        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
       23.97         9.63         2.63        19.96        22.22        22.72 
TCGA-2J-AABI TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE 
       31.86        14.47        15.22         9.11         4.70        22.49 
TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ 
       12.95        43.50         7.36        24.26        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR 
       24.43        71.74        10.98        17.00        24.07        11.61 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 
        4.04        12.89        22.06         4.21         7.63        66.94 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
        8.28        32.15        30.25        17.49        19.50         0.13 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 
       27.62        20.19        17.03         3.95         9.83        17.92 
TCGA-HZ-8638 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        4.96        10.13        10.85         0.23        19.82        12.95 
TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 
        4.77        19.82        41.33         4.04         3.62        19.66 
TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
        3.85        17.16        12.00        15.85        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-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        7.40         8.05         9.14        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 
       13.68         3.12        15.32        24.23        23.08        39.98 
TCGA-US-A779 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.80        11.51        12.76        66.28        15.35 

$subtype2
TCGA-2J-AABR TCGA-3A-A9IJ TCGA-IB-7654 TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2J-AABK 
       14.40        60.95        15.65        20.61        42.31        15.91 
TCGA-2J-AABV TCGA-2L-AAQI TCGA-3A-A9I9 TCGA-3A-A9IX TCGA-3E-AAAY TCGA-F2-6880 
       21.44         3.39        20.84        34.09        75.12         9.70 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 TCGA-FB-A78T 
       19.46         7.10        19.27         3.12        25.22        12.33 
TCGA-FB-AAPS TCGA-FB-AAQ3 TCGA-HV-A5A5 TCGA-HZ-7918 TCGA-HZ-8002 TCGA-HZ-8003 
        7.50         1.02         9.50        31.86        12.03        19.59 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 
       12.43        21.70        16.14         5.26        15.35        36.69 
TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT 
       15.81        30.02        15.19         1.35         0.26         9.44 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A77G 
        7.56        12.46        10.29         0.30        22.85         0.39 
TCGA-XN-A8T3 
       31.27 

$subtype3
TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-H6-A45N TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IH 
       58.98        90.12        13.84         9.60        45.47        33.57 
TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-A4P5 
       68.52        63.85        50.70        32.81        36.26         5.88 
TCGA-FB-A5VM TCGA-FB-AAQ2 TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 
       16.37         5.03         7.76        10.32        23.21        14.93 
TCGA-HZ-8637 TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 
       17.00         6.38        49.38        21.90        43.79        15.98 
TCGA-IB-A5SQ TCGA-IB-AAUR TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A77J TCGA-XD-AAUG 
        7.20        11.11        13.28         9.40        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       12.99        12.03        23.67 

subtype1 subtype2 subtype3 
    0.13     0.26     5.03 
subtype1 subtype2 subtype3 
   71.74    75.12    90.12 
subtype1 subtype2 subtype3 
   15.12    15.35    16.37 
[1] "0.1 - 71.7 (15.1)" "0.3 - 75.1 (15.3)" "5.0 - 90.1 (16.4)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        2        4        21        70         2        3
  subtype2       0        1        3         5        33         1        0
  subtype3       1        2        8         2        16         1        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        0        1
  STAGE IA         2        1        2
  STAGE IB         4        3        8
  STAGE IIA       21        5        2
  STAGE IIB       70       33       16
  STAGE III        2        1        1
  STAGE IV         3        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  7 92  1
  subtype2  1  9 32  1
  subtype3  4  8 18  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        1        4
  T2        7        9        8
  T3       92       32       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 27 73
  subtype2  9 34
  subtype3 13 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   73
  subtype2    9   34
  subtype3   13   17
   clus
vv  subtype1 subtype2 subtype3
  0       27        9       13
  1       73       34       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 45  3
  subtype2 25  0
  subtype3 10  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    3
  subtype2   25    0
  subtype3   10    1
   clus
vv  subtype1 subtype2 subtype3
  0       45       25       10
  1        3        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 41 61
  subtype2 21 22
  subtype3 18 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   61
  subtype2   21   22
  subtype3   18   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       41       21       18
  MALE         61       22       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"
D8V8, binary
          cls
clus        0  1
  subtype1 68 22
  subtype2 29 14
  subtype3 22  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   22
  subtype2   29   14
  subtype3   22    8
     clus
vv    subtype1 subtype2 subtype3
  NO        68       29       22
  YES       22       14        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  84
  subtype2                                  40
  subtype3                                  23
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                    13
  subtype2                                     2
  subtype3                                    10
          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
D8V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    84       40       23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                  13        2       10
  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"
D8V10, continuous
D8V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 57 32  4  3
  subtype2 27 13  0  0
  subtype3 22  8  1  1
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       57       27       22
  R1       32       13        8
  R2        4        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"
D8V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     9                         3    88
  subtype2     2                         2    38
  subtype3     0                         1    31
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            9        2        0
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           88       38       31
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
          cls
clus        0  1
  subtype1  2 72
  subtype2  1 32
  subtype3  2 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   72
  subtype2    1   32
  subtype3    2   27
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        2
  NOT HISPANIC OR LATINO       72       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 14 14
  subtype2  5  6
  subtype3 10 17
  subtype4  8  5
  subtype5 18 33
  subtype6 16 10
  subtype7 11  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      28       11       27       13       51       26       17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      14        6       17        5       33       10        6 
$subtype1
TCGA-2J-AABR TCGA-H6-A45N TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABF 
       14.40        13.84         2.17        23.97        20.61        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-3A-A9IX TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P5 
       42.31        15.91        34.09        19.27         3.12         5.88 
TCGA-FB-A4P6 TCGA-FB-AAPQ TCGA-FB-AAPY TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-HV-A5A5 
       25.22        37.15        34.82         4.04         1.02         9.50 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT TCGA-LB-A8F3 
       21.70        16.14         1.35         0.26         9.44        12.46 
TCGA-LB-A9Q5 TCGA-US-A774 TCGA-US-A77G TCGA-XN-A8T3 
       10.29        22.85         0.39        31.27 

$subtype2
TCGA-US-A77E TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABI 
       14.14         9.63         2.63        19.96        22.22        31.86 
TCGA-2J-AABU TCGA-H6-8124 TCGA-HV-AA8V TCGA-IB-7893 TCGA-IB-AAUQ 
        9.11        12.89        30.25         3.85         6.02 

$subtype3
TCGA-2J-AABT TCGA-IB-7654 TCGA-2J-AABO TCGA-F2-7273 TCGA-F2-7276 TCGA-HZ-7918 
       10.49        15.65        14.47        19.46         7.10        31.86 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8315 
        0.13        10.32        20.19        17.03        12.03         9.83 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7651 
       14.93        17.92        19.82        49.38        15.35        19.82 
TCGA-IB-7652 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 
       36.69        43.79        15.81        19.66        30.02        15.98 
TCGA-IB-8127 TCGA-RL-AAAS TCGA-XD-AAUI 
       17.16         0.30        12.03 

$subtype4
TCGA-2J-AABP TCGA-FB-A7DR TCGA-HZ-7924 TCGA-HZ-8317 TCGA-HZ-8637 TCGA-HZ-8638 
       15.22        11.61        27.62        12.43        17.00         4.96 
TCGA-HZ-A77P TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5ST TCGA-Q3-A5QY 
       10.85        21.90        41.33        15.19        20.88        13.68 
TCGA-Z5-AAPL 
       15.35 

$subtype5
TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
       90.12         7.66         8.02        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2L-AAQA TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IZ 
       16.37         4.70        20.84        24.26        15.06        10.13 
TCGA-3A-A9J0 TCGA-F2-6879 TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPP 
       24.43        10.98        17.00        24.07        12.33        15.95 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 
       12.53        23.54        15.55         4.21         7.63        66.94 
TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
        8.28        17.49        19.50        10.13         5.26         0.23 
TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-A5SP TCGA-IB-A6UF 
       12.95         4.77         4.04         3.62        15.85        21.90 
TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W 
        8.22         4.73         8.05         9.14        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 
       15.45         3.12        15.32        24.23        23.08        39.98 
TCGA-US-A779 TCGA-YH-A8SY TCGA-YY-A8LH 
       16.80        12.76        66.28 

$subtype6
TCGA-HZ-A4BK TCGA-HZ-A77Q TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 
       21.60         1.08        22.49        12.95         9.60        43.50 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-FB-A5VM TCGA-FB-AAPS 
        7.36        33.57        75.12        71.74        16.37         7.50 
TCGA-H8-A6C1 TCGA-HZ-A4BH TCGA-IB-A5SQ TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUP 
       22.06         6.38         7.20        15.88         7.86        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-RB-AA9M TCGA-US-A77J 
       11.11         7.40        13.28         7.56         9.40        18.67 
TCGA-XN-A8T5 TCGA-YB-A89D 
       23.67        11.51 

$subtype7
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-HZ-7289 TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9IN 
       58.98        60.95        21.73         3.39        45.47        68.52 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-FB-AAQ2 TCGA-HZ-7920 
       63.85        50.70        32.81        36.26         5.03         7.76 
TCGA-HZ-8001 TCGA-HZ-8003 TCGA-IB-A5SO TCGA-XD-AAUG TCGA-XD-AAUH 
       23.21        19.59        12.00        13.81        12.99 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.26     2.63     0.13     4.96     0.23     1.08     3.39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   42.31    31.86    49.38    41.33    90.12    75.12    68.52 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  15.155   12.890   15.980   15.220   15.060   13.115   23.210 
[1] "0.3 - 42.3 (15.2)" "2.6 - 31.9 (12.9)" "0.1 - 49.4 (16.0)"
[4] "5.0 - 41.3 (15.2)" "0.2 - 90.1 (15.1)" "1.1 - 75.1 (13.1)"
[7] "3.4 - 68.5 (23.2)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        1         4        22         0        0
  subtype2       0        0        0         4         7         0        0
  subtype3       0        1        2         3        19         0        2
  subtype4       0        1        0         3         8         1        0
  subtype5       1        1        3        12        32         1        1
  subtype6       0        1        3         2        20         1        0
  subtype7       0        0        6         0         7         1        1
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          0        0        0        0        1        0        0
  STAGE IA         1        0        1        1        1        1        0
  STAGE IB         1        0        2        0        3        3        6
  STAGE IIA        4        4        3        3       12        2        0
  STAGE IIB       22        7       19        8       32       20        7
  STAGE III        0        0        0        1        1        1        1
  STAGE IV         0        0        2        0        1        0        1
[1] 7 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  6 21  0
  subtype2  0  0 11  0
  subtype3  1  3 23  0
  subtype4  1  0 11  1
  subtype5  2  5 44  0
  subtype6  2  4 20  1
  subtype7  0  6  8  1
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        1        0        1        1        2        2        0
  T2        6        0        3        0        5        4        6
  T3       21       11       23       11       44       20        8
  T4        0        0        0        1        0        1        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1  6 22
  subtype2  4  7
  subtype3  8 19
  subtype4  3  9
  subtype5 14 35
  subtype6  7 20
  subtype7  7  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   22
  subtype2    4    7
  subtype3    8   19
  subtype4    3    9
  subtype5   14   35
  subtype6    7   20
  subtype7    7    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        6        4        8        3       14        7        7
  1       22        7       19        9       35       20        8
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 14  0
  subtype2  9  0
  subtype3 17  2
  subtype4  7  0
  subtype5 18  1
  subtype6 10  0
  subtype7  2  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    0
  subtype2    9    0
  subtype3   17    2
  subtype4    7    0
  subtype5   18    1
  subtype6   10    0
  subtype7    2    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       14        9       17        7       18       10        2
  1        0        0        2        0        1        0        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 11 17
  subtype2  2  9
  subtype3 14 13
  subtype4  9  4
  subtype5 26 25
  subtype6 11 16
  subtype7  7 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   17
  subtype2    2    9
  subtype3   14   13
  subtype4    9    4
  subtype5   26   25
  subtype6   11   16
  subtype7    7   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       11        2       14        9       26       11        7
  MALE         17        9       13        4       25       16       10
[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"
D9V8, binary
          cls
clus        0  1
  subtype1 16 11
  subtype2  7  3
  subtype3 18  4
  subtype4 11  2
  subtype5 35 13
  subtype6 16  6
  subtype7 13  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   11
  subtype2    7    3
  subtype3   18    4
  subtype4   11    2
  subtype5   35   13
  subtype6   16    6
  subtype7   13    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        16        7       18       11       35       16       13
  YES       11        3        4        2       13        6        4
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  23
  subtype2                                   9
  subtype3                                  25
  subtype4                                   9
  subtype5                                  46
  subtype6                                  23
  subtype7                                   9
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                     2
  subtype3                                     2
  subtype4                                     1
  subtype5                                     3
  subtype6                                     4
  subtype7                                     8
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
  subtype4                                                2
  subtype5                                                1
  subtype6                                                0
  subtype7                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   0
  subtype4                                   1
  subtype5                                   0
  subtype6                                   0
  subtype7                                   0
D9V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    23        9       25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        2        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        0        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        0
                                                  clus
vv                                                 subtype4 subtype5 subtype6
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     9       46       23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        3        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
                                                  clus
vv                                                 subtype7
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     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"
D9V10, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      12        6        5        3       17       11        1 
 [1] "subtype1" "subtype6" "subtype6" "subtype5" "subtype5" "subtype5"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[13] "subtype5" "subtype6" "subtype5" "subtype6" "subtype1" "subtype5"
[19] "subtype1" "subtype1" "subtype6" "subtype5" "subtype4" "subtype1"
[25] "subtype6" "subtype1" "subtype2" "subtype6" "subtype2" "subtype5"
[31] "subtype5" "subtype3" "subtype3" "subtype4" "subtype5" "subtype5"
[37] "subtype3" "subtype4" "subtype3" "subtype5" "subtype1" "subtype6"
[43] "subtype2" "subtype6" "subtype1" "subtype5" "subtype6" "subtype1"
[49] "subtype5" "subtype5" "subtype5" "subtype1" "subtype6" "subtype5"
D9V11, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      11        4        6        3       11       10        2 
 [1] "subtype6" "subtype6" "subtype5" "subtype5" "subtype5" "subtype1"
 [7] "subtype2" "subtype1" "subtype2" "subtype3" "subtype6" "subtype1"
[13] "subtype1" "subtype1" "subtype6" "subtype5" "subtype4" "subtype1"
[19] "subtype6" "subtype1" "subtype2" "subtype6" "subtype5" "subtype5"
[25] "subtype3" "subtype3" "subtype4" "subtype5" "subtype3" "subtype4"
[31] "subtype3" "subtype5" "subtype1" "subtype6" "subtype2" "subtype6"
[37] "subtype1" "subtype6" "subtype1" "subtype5" "subtype5" "subtype1"
[43] "subtype3" "subtype6" "subtype5"
          vv
clus       R0 R1 R2 RX
  subtype1 17  8  0  0
  subtype2  6  4  1  0
  subtype3 19  7  0  1
  subtype4 10  3  0  0
  subtype5 25 17  3  1
  subtype6 16  8  0  1
  subtype7 11  4  1  1
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       17        6       19       10       25       16       11
  R1        8        4        7        3       17        8        4
  R2        0        1        0        0        3        0        1
  RX        0        0        1        0        1        1        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    26
  subtype2     1                         0    10
  subtype3     1                         3    20
  subtype4     1                         0    12
  subtype5     6                         1    43
  subtype6     0                         1    26
  subtype7     0                         0    17
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        1        1        6
  BLACK OR AFRICAN AMERICAN        1        0        3        0        1
  WHITE                           26       10       20       12       43
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                           26       17
[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"
D9V15, binary
          cls
clus        0  1
  subtype1  1 18
  subtype2  0  4
  subtype3  0 22
  subtype4  1 11
  subtype5  1 40
  subtype6  2 21
  subtype7  0 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   18
  subtype2    0    4
  subtype3    0   22
  subtype4    1   11
  subtype5    1   40
  subtype6    2   21
  subtype7    0   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        0        1        1        2
  NOT HISPANIC OR LATINO       18        4       22       11       40       21
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       14
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 12 11
  subtype2 15 29
  subtype3 12  7
  subtype4 21 32
  subtype5 14 12
  subtype6  8  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      23       44       19       53       26        8 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      11       29        7       32       12        0 
$subtype1
TCGA-FB-AAQ6 TCGA-HZ-A4BK TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABA TCGA-2J-AABE 
        8.02        21.60         2.17        23.97        19.96        22.22 
TCGA-2J-AABO TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPY TCGA-HV-A5A4 TCGA-HV-AA8V 
       14.47        37.15        12.53        34.82         7.63        30.25 
TCGA-HZ-7919 TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-AAUQ 
       19.50         0.23        19.82        12.00        15.85         6.02 
TCGA-IB-AAUU TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A779 TCGA-XD-AAUG 
        8.05        24.23        23.08        16.80        13.81 

$subtype2
TCGA-F2-A44G TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        7.66        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB6 TCGA-2J-AABI TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
        9.63        31.86         9.11         4.70        22.49        12.95 
TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IZ TCGA-F2-6879 TCGA-F2-A8YN 
       43.50         7.36        24.26        10.13        10.98        17.00 
TCGA-FB-A545 TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HV-A5A3 
       24.07        23.54        15.55        12.89        22.06         4.21 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A49I TCGA-IB-7646 
       66.94         8.28        17.49        20.19        10.13         4.77 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-L1-A7W4 
       19.66         3.85         8.22        15.88         7.86         9.14 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-YB-A89D 
       19.20         8.78        15.45         3.12        15.32        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

$subtype3
TCGA-2J-AABT TCGA-HZ-7289 TCGA-HZ-A77Q TCGA-2J-AAB8 TCGA-2J-AABP TCGA-3A-A9J0 
       10.49        21.73         1.08         2.63        15.22        24.43 
TCGA-3E-AAAZ TCGA-FB-A7DR TCGA-FB-AAPP TCGA-HZ-7924 TCGA-HZ-8638 TCGA-HZ-A77P 
       71.74        11.61        15.95        27.62         4.96        10.85 
TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-A5ST TCGA-Q3-A5QY TCGA-US-A776 
       12.95        41.33         4.04        20.88        13.68        39.98 
TCGA-Z5-AAPL 
       15.35 

$subtype4
TCGA-2J-AABR TCGA-H6-A45N TCGA-IB-7654 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH 
       14.40        13.84        15.65        20.61        22.72        42.31 
TCGA-2J-AABK TCGA-2L-AAQI TCGA-3A-A9I9 TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3E-AAAY 
       15.91         3.39        20.84        15.06        34.09        75.12 
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-F2-A7TX TCGA-FB-A4P6 TCGA-FB-A78T 
       19.46         7.10        19.27         3.12        25.22        12.33 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-HV-A5A5 TCGA-HZ-7918 TCGA-HZ-7922 
        4.04         5.03         1.02         9.50        31.86         0.13 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8636 
       17.03        12.03        19.59         9.83        12.43        17.92 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
       21.70        16.14         5.26        15.35        19.82        36.69 
TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A6UF 
        3.62        15.81        30.02        15.19        17.16        21.90 
TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUT TCGA-IB-AAUW TCGA-LB-A8F3 
        1.35         0.26         4.73         9.44         7.56        12.46 
TCGA-LB-A9Q5 TCGA-RL-AAAS TCGA-US-A774 TCGA-US-A77G TCGA-XN-A8T3 
       10.29         0.30        22.85         0.39        31.27 

$subtype5
TCGA-3A-A9I5 TCGA-2L-AAQL TCGA-3A-A9IH TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-AAPS 
       58.98         9.60        33.57         5.88        16.37         7.50 
TCGA-HZ-7920 TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 TCGA-HZ-8637 TCGA-HZ-A4BH 
        7.76        10.32        23.21        14.93        17.00         6.38 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-A5SQ TCGA-IB-AAUP 
       49.38        21.90        43.79        15.98         7.20        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-RB-AA9M TCGA-US-A77J TCGA-XD-AAUH 
       11.11         7.40        13.28         9.40        18.67        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 
       12.03        23.67 

$subtype6
TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-2L-AAQM TCGA-3A-A9IN TCGA-3A-A9IO TCGA-3A-A9IR 
       60.95        90.12        45.47        68.52        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV 
       32.81        36.26 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.23     3.12     1.08     0.13     5.88    32.81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   37.15    66.94    71.74    75.12    58.98    90.12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  16.800   13.545   15.220   15.190   13.725   55.825 
[1] "0.2 - 37.1 (16.8)"  "3.1 - 66.9 (13.5)"  "1.1 - 71.7 (15.2)" 
[4] "0.1 - 75.1 (15.2)"  "5.9 - 59.0 (13.7)"  "32.8 - 90.1 (55.8)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1       0        1        1         4        15         0        2
  subtype2       0        0        2        11        29         2        0
  subtype3       0        1        0         5        12         0        1
  subtype4       0        1        3         6        42         1        1
  subtype5       0        2        4         2        16         1        0
  subtype6       1        0        5         0         1         0        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          0        0        0        0        0        1
  STAGE IA         1        0        1        1        2        0
  STAGE IB         1        2        0        3        4        5
  STAGE IIA        4       11        5        6        2        0
  STAGE IIB       15       29       12       42       16        1
  STAGE III        0        2        0        1        1        0
  STAGE IV         2        0        1        1        0        0
[1] 7 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  3 19  0
  subtype2  0  3 40  1
  subtype3  1  0 18  0
  subtype4  1  8 44  1
  subtype5  3  5 16  1
  subtype6  1  5  1  0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        1        0        1        1        3        1
  T2        3        3        0        8        5        5
  T3       19       40       18       44       16        1
  T4        0        1        0        1        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  7 16
  subtype2 12 31
  subtype3  5 13
  subtype4 11 43
  subtype5 10 16
  subtype6  4  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   16
  subtype2   12   31
  subtype3    5   13
  subtype4   11   43
  subtype5   10   16
  subtype6    4    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        7       12        5       11       10        4
  1       16       31       13       43       16        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2 18  0
  subtype3  8  1
  subtype4 29  1
  subtype5 12  0
  subtype6  0  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2   18    0
  subtype3    8    1
  subtype4   29    1
  subtype5   12    0
  subtype6    0    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       10       18        8       29       12
  1        2        0        1        1        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"
D10V7, binary
          cls
clus        0  1
  subtype1  6 17
  subtype2 20 24
  subtype3  9 10
  subtype4 28 26
  subtype5 13 13
  subtype6  4  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   17
  subtype2   20   24
  subtype3    9   10
  subtype4   28   26
  subtype5   13   13
  subtype6    4    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        6       20        9       28       13        4
  MALE         17       24       10       26       13        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1 15  5
  subtype2 30 14
  subtype3 14  1
  subtype4 35 14
  subtype5 15  8
  subtype6  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    5
  subtype2   30   14
  subtype3   14    1
  subtype4   35   14
  subtype5   15    8
  subtype6    7    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        15       30       14       35       15        7
  YES        5       14        1       14        8        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  19
  subtype2                                  38
  subtype3                                  12
  subtype4                                  51
  subtype5                                  24
  subtype6                                   0
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                     5
  subtype3                                     3
  subtype4                                     2
  subtype5                                     2
  subtype6                                     8
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                3
  subtype4                                                1
  subtype5                                                0
  subtype6                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
  subtype5                                   0
  subtype6                                   0
D10V9, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    19       38       12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        5        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0        3
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        1
                                                  clus
vv                                                 subtype4 subtype5 subtype6
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    51       24        0
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   2        2        8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        0        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12       13        5       18        6        1 
 [1] "subtype4" "subtype3" "subtype4" "subtype2" "subtype2" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype2"
[19] "subtype5" "subtype4" "subtype5" "subtype4" "subtype3" "subtype1"
[25] "subtype5" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[31] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype4"
[37] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
[43] "subtype1" "subtype5" "subtype4" "subtype1" "subtype5" "subtype4"
[49] "subtype2" "subtype1" "subtype1" "subtype4" "subtype5" "subtype2"
D10V11, continuous
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8       10        5       15        7        2 
 [1] "subtype3" "subtype4" "subtype2" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
[13] "subtype5" "subtype4" "subtype5" "subtype4" "subtype3" "subtype1"
[19] "subtype5" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype2" "subtype1" "subtype5"
[37] "subtype4" "subtype5" "subtype4" "subtype2" "subtype1" "subtype4"
[43] "subtype5" "subtype5" "subtype2"
          vv
clus       R0 R1 R2 RX
  subtype1 15  6  1  0
  subtype2 24 12  3  1
  subtype3 14  3  0  1
  subtype4 28 21  0  1
  subtype5 17  7  1  1
  subtype6  6  2  0  0
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       15       24       14       28       17        6
  R1        6       12        3       21        7        2
  R2        1        3        0        0        1        0
  RX        0        1        1        1        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0    20
  subtype2     4                         2    36
  subtype3     1                         0    18
  subtype4     2                         3    48
  subtype5     0                         1    24
  subtype6     0                         0     8
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        4        1        2        0
  BLACK OR AFRICAN AMERICAN        0        2        0        3        1
  WHITE                           20       36       18       48       24
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            8
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
          cls
clus        0  1
  subtype1  0 13
  subtype2  1 30
  subtype3  1 15
  subtype4  1 44
  subtype5  2 21
  subtype6  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   13
  subtype2    1   30
  subtype3    1   15
  subtype4    1   44
  subtype5    2   21
  subtype6    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        1        1        2        0
  NOT HISPANIC OR LATINO       13       30       15       44       21        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
