[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/11541627/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/11588537/PAAD-TP.mergedcluster.txt"

nPatients in clinical file=133, in cluster file=185, common to both=133
[1]  10 133
[1] "CN_CNMF"
[1] 3
 1  2  3 
70 48 14 
 1  2  3 
70 48 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
52 31 28 
 1  2  3 
52 31 28 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
30 16 14 15 11 
 1  2  3  4  5 
30 16 14 15 11 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
17 16 26 13 14 
 1  2  3  4  5 
17 16 26 13 14 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
58 40 32 
 1  2  3 
58 40 32 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
59 53 18 
 1  2  3 
59 53 18 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
47 34 29 20 
 1  2  3  4 
47 34 29 20 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
75 35 20 
 1  2  3 
75 35 20 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
48 56 23 
 1  2  3 
48 56 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
60 42 25 
 1  2  3 
60 42 25 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 133 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
          NA          729           NA           80           NA           NA 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABK TCGA-2J-AABO 
         676           NA          677          969          484          440 
TCGA-2J-AABP TCGA-2J-AABR TCGA-2J-AABT TCGA-2J-AABU TCGA-2J-AABV TCGA-3E-AAAY 
         360          438          319           NA           NA         2172 
TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G 
          NA           NA          295          360           NA          153 
TCGA-F2-A44H TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
         586           NA          167            4          363          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-FZ-5920 
         449          378          166           NA           NA           NA 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
          NA           NA          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
          28           20           NA            4            8          840 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
         361            8           19           24           21           NA 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 
          28           16            3            5           NA           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
         660          491           NA          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P0 TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7645 
          13           33           NA            7          347           NA 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7654 
          NA           NA           NA           NA          724           NA 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
        1257           NA           NA           NA           NA           NA 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         648           NA           NA           75          522          329 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
         300           NA           NA          635          248           NA 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
          NA          181            8           NA           NA          290 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUV 
          NA          128          179          188          153          210 
TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 
         179          164          127           35          155          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
         110          247          416           95           36           42 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
         397          197           NA           NA          844           NA 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
          NA           NA           NA          161          164          160 
TCGA-YY-A8LH 
        1834 
Variable 1:'AGE':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=79,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[11] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 133 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=40, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  3  12 116   2 
[1] "table(vv)"
vv
T1+T2 T3+T4 
   15   118 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  3  12 116   2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 15

$Class1_nSamples
[1] 118

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
   15   118 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=26, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 41 12
  subtype2 30  4
  subtype3  6  2
subtype1 subtype2 subtype3 
      53       34        8 
subtype1 subtype2 subtype3 
      12        4        2 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABR TCGA-3E-AAAY TCGA-F2-6880 
        1962          484          360          438         2172          295 
TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR 
         360          153          586            4          449          166 
TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
         233            8          840          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          24           21           28           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P0 TCGA-IB-7649 
         660          491           13           33         1968         1951 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST 
        1989         1257          648           75          329          635 
TCGA-IB-AAUM TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
           8          290         1978          128          179          188 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-RB-A7B8 
         210          179           35          155          416           36 
TCGA-RB-AA9M TCGA-US-A774 TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
          42         1955          161          164          160 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABI TCGA-2J-AABO 
         729           80          676          677          969          440 
TCGA-2J-AABT TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 
         319          167          385          378          392          396 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          20            4            5          194           46           11 
TCGA-IB-7644 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF 
         347          724         1975          300         1991          248 
TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
         181          153          164          127          584          110 
TCGA-PZ-A5RE TCGA-S4-A8RM TCGA-S4-A8RO TCGA-YY-A8LH 
         247          397          197         1834 

$subtype3
TCGA-2J-AABF TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A8P1 TCGA-IB-8127 TCGA-IB-A6UG 
        1960          240           28            7          522         1968 
TCGA-Q3-AA2A TCGA-US-A776 
          95          844 

subtype1 subtype2 subtype3 
       3        4        7 
subtype1 subtype2 subtype3 
    2172     1991     1968 
subtype1 subtype2 subtype3 
   188.0    309.5    381.0 
[1] "3.0 - 2172.0 (188.0)" "4.0 - 1991.0 (309.5)" "7.0 - 1968.0 (381.0)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        2        3        10        51         2        2
  subtype2        0        1        11        34         0        2
  subtype3        0        3         1        10         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         2        0        0
  STAGE IB         3        1        3
  STAGE IIA       10       11        1
  STAGE IIB       51       34       10
  STAGE III        2        0        0
  STAGE IV         2        2        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     9    61
  subtype2     3    45
  subtype3     3    11
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        9        3        3
  T3+T4       61       45       11
[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"
D1V5, binary
          cls
clus        0  1
  subtype1 15 54
  subtype2 13 35
  subtype3  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   54
  subtype2   13   35
  subtype3    3   11
   clus
vv  subtype1 subtype2 subtype3
  0       15       13        3
  1       54       35       11
[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       M0 M1 MX
  subtype1 37  2 31
  subtype2 29  2 17
  subtype3  8  0  6
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       37       29        8
  M1        2        2        0
  MX       31       17        6
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 35 35
  subtype2 24 24
  subtype3  1 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   35
  subtype2   24   24
  subtype3    1   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       24        1
  MALE         35       24       13
[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                                  59
  subtype2                                  42
  subtype3                                  12
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     7
  subtype2                                     6
  subtype3                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                0
  subtype3                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D1V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    59       42       12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   7        6        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        0        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 47 18  1  1
  subtype2 27 18  1  0
  subtype3  6  6  0  2
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       47       27        6
  R1       18       18        6
  R2        1        1        0
  RX        1        0        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    63
  subtype2     1                         2    44
  subtype3     0                         0    13
D1V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        4        2        0
  WHITE                           63       44       13
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 29  6
  subtype2 20  6
  subtype3 17  3
subtype1 subtype2 subtype3 
      35       26       20 
subtype1 subtype2 subtype3 
       6        6        3 
$subtype1
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         167          385          378          392          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BK 
          20            4            8           28            5           46 
TCGA-HZ-A8P0 TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 
        1968            7          347         1989         1975          522 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUU 
         300         1991          248         1968          181          153 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 
         164          127          110          247           95           36 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         397          197          844          160         1834 

$subtype2
TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-H6-A45N 
        2172          295          360          586          363          233 
TCGA-HZ-7918 TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 
          28          840           24           21           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 
          91          660          491           11         1951          724 
TCGA-IB-8126 TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
          75            8          188          179           35          155 
TCGA-RB-AA9M TCGA-US-A774 
          42         1955 

$subtype3
TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7923 TCGA-HZ-7925 
         153            4          449          166            8          361 
TCGA-HZ-8001 TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7885 TCGA-IB-7891 
          19          194           13           33         1257          648 
TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
         329          635          290          128          179          210 
TCGA-M8-A5N4 TCGA-Q3-A5QY 
         584          416 

subtype1 subtype2 subtype3 
       4        3        4 
subtype1 subtype2 subtype3 
    1991     2172     1257 
subtype1 subtype2 subtype3 
   240.0    183.5    202.0 
[1] "4.0 - 1991.0 (240.0)" "3.0 - 2172.0 (183.5)" "4.0 - 1257.0 (202.0)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        4         8        38         0        2
  subtype2        2        1         4        22         1        1
  subtype3        0        2         4        21         1        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         0        2        0
  STAGE IB         4        1        2
  STAGE IIA        8        4        4
  STAGE IIB       38       22       21
  STAGE III        0        1        1
  STAGE IV         2        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     4    48
  subtype2     8    23
  subtype3     2    26
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        4        8        2
  T3+T4       48       23       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 12 40
  subtype2  7 24
  subtype3  6 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   40
  subtype2    7   24
  subtype3    6   21
   clus
vv  subtype1 subtype2 subtype3
  0       12        7        6
  1       40       24       21
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 24  2 26
  subtype2 13  1 17
  subtype3 18  0 10
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       24       13       18
  M1        2        1        0
  MX       26       17       10
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 21 31
  subtype2 16 15
  subtype3 15 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   31
  subtype2   16   15
  subtype3   15   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       16       15
  MALE         31       15       13
[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                                  45
  subtype2                                  27
  subtype3                                  25
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     2
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                2
  subtype3                                                1
D2V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    45       27       25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        2        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        2        1
[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"
D2V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 25 20  1  3
  subtype2 21  7  0  0
  subtype3 19  9  0  0
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       25       21       19
  R1       20        7        9
  R2        1        0        0
  RX        3        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"
D2V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    48
  subtype2     1                         2    27
  subtype3     1                         1    24
D2V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           48       27       24
[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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 17  2
  subtype2 10  5
  subtype3 10  2
  subtype4  7  2
  subtype5  6  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       15       12        9        7 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        5        2        2        1 
$subtype1
TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-HZ-7919 TCGA-HZ-7922 
         167            4          363          449           20            4 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-AAUP TCGA-IB-AAUU 
         724         1975          522          300          290          153 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-S4-A8RM TCGA-S4-A8RO TCGA-YB-A89D 
         127           35          110          397          197          160 
TCGA-YY-A8LH 
        1834 

$subtype2
TCGA-F2-A44G TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8638 TCGA-IB-7644 
         153          396          361           19           91          347 
TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A9Q5 
        1951         1257           75          635          181          155 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 
         584          247           36 

$subtype3
TCGA-F2-6880 TCGA-FB-A78T TCGA-H6-A45N TCGA-HZ-7924 TCGA-HZ-8003 TCGA-HZ-8519 
         295          378          233          840           21            3 
TCGA-HZ-A4BK TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-A6UF TCGA-IB-AAUM TCGA-US-A776 
          46         1989          648          248            8          844 

$subtype4
TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-8002 TCGA-HZ-8315 TCGA-IB-A5SS TCGA-IB-AAUV 
          28            8           24           28         1991          210 
TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-US-A774 
         416           42         1955 

$subtype5
TCGA-FB-A545 TCGA-HZ-A4BH TCGA-IB-A5SO TCGA-IB-AAUS TCGA-IB-AAUW TCGA-L1-A7W4 
         385          194          329          179          179          164 
TCGA-Q3-AA2A 
          95 

subtype1 subtype2 subtype3 subtype4 subtype5 
       4       19        3        8       95 
subtype1 subtype2 subtype3 subtype4 subtype5 
    1975     1951     1989     1991      385 
subtype1 subtype2 subtype3 subtype4 subtype5 
   197.0    247.0    271.5     42.0    179.0 
[1] "4.0 - 1975.0 (197.0)"  "19.0 - 1951.0 (247.0)" "3.0 - 1989.0 (271.5)" 
[4] "8.0 - 1991.0 (42.0)"   "95.0 - 385.0 (179.0)" 
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        4         6        20         0        0
  subtype2        1        0         2        10         2        1
  subtype3        1        0         2        10         0        1
  subtype4        0        1         4        10         0        0
  subtype5        0        1         0        10         0        0
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE IA         0        1        1        0        0
  STAGE IB         4        0        0        1        1
  STAGE IIA        6        2        2        4        0
  STAGE IIB       20       10       10       10       10
  STAGE III        0        2        0        0        0
  STAGE IV         0        1        1        0        0
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     5    25
  subtype2     1    15
  subtype3     2    12
  subtype4     2    13
  subtype5     0    11
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T1+T2        5        1        2        2        0
  T3+T4       25       15       12       13       11
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 10 20
  subtype2  4 12
  subtype3  3 11
  subtype4  5 10
  subtype5  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   20
  subtype2    4   12
  subtype3    3   11
  subtype4    5   10
  subtype5    0   11
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       10        4        3        5        0
  1       20       12       11       10       11
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 18  0 12
  subtype2  7  1  8
  subtype3  6  1  7
  subtype4  6  0  9
  subtype5  7  0  4
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       18        7        6        6        7
  M1        0        1        1        0        0
  MX       12        8        7        9        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 13 17
  subtype2 11  5
  subtype3  6  8
  subtype4  6  9
  subtype5  6  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   17
  subtype2   11    5
  subtype3    6    8
  subtype4    6    9
  subtype5    6    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       11        6        6        6
  MALE         17        5        8        9        5
[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                                  29
  subtype2                                  13
  subtype3                                  10
  subtype4                                  14
  subtype5                                  11
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     2
  subtype3                                     3
  subtype4                                     1
  subtype5                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                1
  subtype4                                                0
  subtype5                                                0
D3V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    29       13       10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        2        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        1        1
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    14       11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        7        6        3        2 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype1" "subtype3" "subtype2" "subtype1" "subtype4" "subtype3"
[19] "subtype2" "subtype1" "subtype4" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype4" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1 18 10  0  0
  subtype2  9  6  0  0
  subtype3 11  2  0  0
  subtype4 11  4  0  0
  subtype5  3  5  1  1
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       18        9       11       11        3
  R1       10        6        2        4        5
  R2        0        0        0        0        1
  RX        0        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"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    25
  subtype2     0                         0    14
  subtype3     0                         0    14
  subtype4     0                         1    14
  subtype5     0                         0    11
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        3        0        0        1        0
  WHITE                           25       14       14       14       11
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 12  2
  subtype2 11  4
  subtype3 10  3
  subtype4 10  1
  subtype5  7  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       15       13       11        9 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        4        3        1        2 
$subtype1
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-HZ-7919 TCGA-HZ-8315 TCGA-IB-7652 
           4          363          449           20           28          724 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-AAUU TCGA-LB-A7SX TCGA-S4-A8RM 
        1975          522          300          153          127          397 
TCGA-S4-A8RO TCGA-YY-A8LH 
         197         1834 

$subtype2
TCGA-F2-A44G TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-A4BH TCGA-IB-7644 
         153          396          361           19          194          347 
TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A9Q5 
        1951         1257           75          635          181          155 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-RB-A7B8 
         584          247           36 

$subtype3
TCGA-F2-A8YN TCGA-FB-A545 TCGA-H6-A45N TCGA-HZ-7922 TCGA-HZ-8002 TCGA-IB-A5SO 
         167          385          233            4           24          329 
TCGA-IB-A5SS TCGA-IB-AAUP TCGA-IB-AAUS TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W 
        1991          290          179          164           35          110 
TCGA-RB-AA9M 
          42 

$subtype4
TCGA-F2-6880 TCGA-FB-A78T TCGA-HZ-7918 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A4BK 
         295          378           28           21            3           46 
TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-A6UF TCGA-IB-AAUM TCGA-US-A776 
        1989          648          248            8          844 

$subtype5
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-8638 TCGA-IB-AAUV TCGA-IB-AAUW TCGA-Q3-A5QY 
           8          840           91          210          179          416 
TCGA-Q3-AA2A TCGA-US-A774 TCGA-YB-A89D 
          95         1955          160 

subtype1 subtype2 subtype3 subtype4 subtype5 
       4       19        4        3        8 
subtype1 subtype2 subtype3 subtype4 subtype5 
    1975     1951     1991     1989     1955 
subtype1 subtype2 subtype3 subtype4 subtype5 
   331.5    247.0    167.0    248.0    179.0 
[1] "4.0 - 1975.0 (331.5)"  "19.0 - 1951.0 (247.0)" "4.0 - 1991.0 (167.0)" 
[4] "3.0 - 1989.0 (248.0)"  "8.0 - 1955.0 (179.0)" 
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        3         2        12         0        0
  subtype2        0        0         2        11         2        1
  subtype3        0        1         5        20         0        0
  subtype4        1        0         1        10         0        1
  subtype5        1        2         4         7         0        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE IA         0        0        0        1        1
  STAGE IB         3        0        1        0        2
  STAGE IIA        2        2        5        1        4
  STAGE IIB       12       11       20       10        7
  STAGE III        0        2        0        0        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    14
  subtype2     0    16
  subtype3     3    23
  subtype4     2    11
  subtype5     2    12
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T1+T2        3        0        3        2        2
  T3+T4       14       16       23       11       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"
D4V5, binary
          cls
clus        0  1
  subtype1  5 12
  subtype2  3 13
  subtype3  6 20
  subtype4  2 11
  subtype5  6  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   12
  subtype2    3   13
  subtype3    6   20
  subtype4    2   11
  subtype5    6    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        5        3        6        2        6
  1       12       13       20       11        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       M0 M1 MX
  subtype1  9  0  8
  subtype2  7  1  8
  subtype3 17  0  9
  subtype4  7  1  5
  subtype5  4  0 10
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0        9        7       17        7        4
  M1        0        1        0        1        0
  MX        8        8        9        5       10
[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"
D4V7, binary
          cls
clus        0  1
  subtype1 10  7
  subtype2 10  6
  subtype3 12 14
  subtype4  4  9
  subtype5  6  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    7
  subtype2   10    6
  subtype3   12   14
  subtype4    4    9
  subtype5    6    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       10       10       12        4        6
  MALE          7        6       14        9        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                                  17
  subtype2                                  14
  subtype3                                  24
  subtype4                                  10
  subtype5                                  12
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     0
  subtype2                                     2
  subtype3                                     2
  subtype4                                     2
  subtype5                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                0
  subtype4                                                1
  subtype5                                                1
D4V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    17       14       24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        2        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0        0
                                                  clus
vv                                                 subtype4 subtype5
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    10       12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   2        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1
[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"
D4V9, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      10        7        6        5        2 
 [1] "subtype4" "subtype3" "subtype1" "subtype1" "subtype1" "subtype4"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[13] "subtype1" "subtype3" "subtype4" "subtype2" "subtype1" "subtype3"
[19] "subtype4" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[25] "subtype3" "subtype1" "subtype1" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1  7  9  0  0
  subtype2  8  7  0  0
  subtype3 17  6  1  0
  subtype4 11  2  0  0
  subtype5  9  3  0  1
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7        8       17       11        9
  R1        9        7        6        2        3
  R2        0        0        1        0        0
  RX        0        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"
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    15
  subtype2     0                         0    14
  subtype3     0                         3    22
  subtype4     0                         0    13
  subtype5     0                         0    14
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        0
  BLACK OR AFRICAN AMERICAN        1        0        3        0        0
  WHITE                           15       14       22       13       14
[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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 37  7
  subtype2 24  7
  subtype3 17  4
subtype1 subtype2 subtype3 
      44       31       21 
subtype1 subtype2 subtype3 
       7        7        4 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABT TCGA-F2-A44G 
        1962           80          676          969          319          153 
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         167          385          166          392          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8315 
          20            4          840          361            8           28 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A77Q TCGA-HZ-A8P0 TCGA-HZ-A8P1 TCGA-IB-7644 
           5           91           33         1968            7          347 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 
        1257         1975          522         1991          635          181 
TCGA-IB-AAUP TCGA-IB-AAUS TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
         290          179          164          127          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
         247          416           95           36          397          197 
TCGA-US-A776 TCGA-YY-A8LH 
         844         1834 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-3E-AAAY 
         729         1960          677          484          438         2172 
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 
         295          360          586          363          378           28 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7649 
          16          660           46           11           13         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG 
        1989          724          648          300          248         1968 
TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
           8          188          153          179           35          155 
TCGA-US-A774 
        1955 

$subtype3
TCGA-2J-AABO TCGA-2J-AABP TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-H6-A45N TCGA-HZ-7923 
         440          360            4          449          233            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A4BH 
          19           24           21            3          491          194 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUV TCGA-RB-AA9M 
          75          329         1978          128          210           42 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
         161          164          160 

subtype1 subtype2 subtype3 
       4        8        3 
subtype1 subtype2 subtype3 
    1991     2172     1978 
subtype1 subtype2 subtype3 
   268.5    363.0    161.0 
[1] "4.0 - 1991.0 (268.5)" "8.0 - 2172.0 (363.0)" "3.0 - 1978.0 (161.0)"
D5V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        2        13        40         0        2
  subtype2        0        1         5        34         0        0
  subtype3        1        4         3        21         2        1
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        0        1
  STAGE IB         2        1        4
  STAGE IIA       13        5        3
  STAGE IIB       40       34       21
  STAGE III        0        0        2
  STAGE IV         2        0        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     2    56
  subtype2     7    33
  subtype3     6    26
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        7        6
  T3+T4       56       33       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 15 42
  subtype2  6 34
  subtype3  9 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   42
  subtype2    6   34
  subtype3    9   23
   clus
vv  subtype1 subtype2 subtype3
  0       15        6        9
  1       42       34       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 28  2 28
  subtype2 27  0 13
  subtype3 17  1 14
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       28       27       17
  M1        2        0        1
  MX       28       13       14
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 28 30
  subtype2 18 22
  subtype3 14 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   30
  subtype2   18   22
  subtype3   14   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       18       14
  MALE         30       22       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  47
  subtype2                                  35
  subtype3                                  29
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     8
  subtype2                                     4
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   1
D5V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    47       35       29
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   8        4        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 30 21  1  3
  subtype2 23 15  0  0
  subtype3 24  6  1  0
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       30       23       24
  R1       21       15        6
  R2        1        0        1
  RX        3        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"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    54
  subtype2     1                         2    36
  subtype3     0                         1    29
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        2        2        1
  WHITE                           54       36       29
[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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 36 12
  subtype2 33  5
  subtype3  9  1
subtype1 subtype2 subtype3 
      48       38       10 
subtype1 subtype2 subtype3 
      12        5        1 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
        1962          729         1960          677          484          440 
TCGA-2J-AABR TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H 
         438         2172          295          360          153          586 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A78T TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
           4          363          378          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
          20            4            8           24           21           28 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A8P0 
          16          660          491           46           11         1968 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          724         1975          648           75 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUS 
         522          300          248         1968            8          179 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-US-A774 
         188          153          179           35          155         1955 

$subtype2
TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABP TCGA-2J-AABT TCGA-F2-A8YN 
          80          676          969          360          319          167 
TCGA-FB-A545 TCGA-FB-A7DR TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7924 TCGA-HZ-7925 
         385          166          392          240          840          361 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 
           5           91           13           33            7          347 
TCGA-IB-7885 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUP TCGA-IB-AAUQ 
        1257         1991          635          181          290         1978 
TCGA-IB-AAUR TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         128          164          127          584          110          247 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 
         416           95           36          397          197          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

$subtype3
TCGA-FB-A5VM TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-A5SO 
         449            8           19            3          194          329 
TCGA-IB-AAUV TCGA-RB-AA9M TCGA-XD-AAUG TCGA-XD-AAUH 
         210           42          161          164 

subtype1 subtype2 subtype3 
       4        5        3 
subtype1 subtype2 subtype3 
    2172     1991      449 
subtype1 subtype2 subtype3 
   330.0    268.5    162.5 
[1] "4.0 - 2172.0 (330.0)" "5.0 - 1991.0 (268.5)" "3.0 - 449.0 (162.5)" 
D6V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         7        50         1        0
  subtype2        1        3        12        35         0        2
  subtype3        1        3         2        10         1        1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         0        1        1
  STAGE IB         1        3        3
  STAGE IIA        7       12        2
  STAGE IIB       50       35       10
  STAGE III        1        0        1
  STAGE IV         0        2        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     7    52
  subtype2     3    50
  subtype3     5    13
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        7        3        5
  T3+T4       52       50       13
[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"
D6V5, binary
          cls
clus        0  1
  subtype1  8 51
  subtype2 15 37
  subtype3  7 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   51
  subtype2   15   37
  subtype3    7   11
   clus
vv  subtype1 subtype2 subtype3
  0        8       15        7
  1       51       37       11
[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       M0 M1 MX
  subtype1 36  0 23
  subtype2 27  2 24
  subtype3  9  1  8
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       36       27        9
  M1        0        2        1
  MX       23       24        8
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 29 30
  subtype2 23 30
  subtype3  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   30
  subtype2   23   30
  subtype3    8   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       23        8
  MALE         30       30       10
[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                                  52
  subtype2                                  42
  subtype3                                  17
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     7
  subtype3                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                3
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   1
  subtype3                                   0
D6V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    52       42       17
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        7        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        3        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        1        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
      25       18        2 
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[43] "subtype2"
          vv
clus       R0 R1 R2 RX
  subtype1 33 22  0  1
  subtype2 30 17  1  2
  subtype3 14  3  1  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       33       30       14
  R1       22       17        3
  R2        0        1        1
  RX        1        2        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    54
  subtype2     1                         1    49
  subtype3     0                         1    16
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        3        1        1
  WHITE                           54       49       16
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 27  7
  subtype2 23  5
  subtype3 19  3
  subtype4  9  3
subtype1 subtype2 subtype3 subtype4 
      34       28       22       12 
subtype1 subtype2 subtype3 subtype4 
       7        5        3        3 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABI 
        1962          729           80          676         1960          969 
TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         153          167          385          392          396          240 
TCGA-HZ-7919 TCGA-HZ-7924 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-HZ-A8P0 TCGA-HZ-A8P1 
          20          840            5           46         1968            7 
TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-IB-AAUU 
         347         1975          522         1991          181          153 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 
         127          584          110          247           95           36 
TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-YY-A8LH 
         397          197          844         1834 

$subtype2
TCGA-2J-AABH TCGA-2J-AABR TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H 
         677          438         2172          295          360          586 
TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8003 TCGA-HZ-8315 
         363          378           28            4           21           28 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
         660          491           11         1951         1989          724 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
         648           75          300          248         1968            8 
TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-US-A774 
         188           35          155         1955 

$subtype3
TCGA-2J-AABP TCGA-2J-AABT TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7925 
         360          319            4          449          166          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8317 TCGA-HZ-8638 TCGA-HZ-A4BH 
           8           19           24           16           91          194 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7885 TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUR 
          13           33         1257          635          290          128 
TCGA-IB-AAUS TCGA-IB-AAUW TCGA-L1-A7W4 TCGA-Q3-A5QY 
         179          179          164          416 

$subtype4
TCGA-2J-AABK TCGA-2J-AABO TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8519 TCGA-IB-A5SO 
         484          440          233            8            3          329 
TCGA-IB-AAUQ TCGA-IB-AAUV TCGA-RB-AA9M TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D 
        1978          210           42          161          164          160 

subtype1 subtype2 subtype3 subtype4 
       5        4        4        3 
subtype1 subtype2 subtype3 subtype4 
    1991     2172     1257     1978 
subtype1 subtype2 subtype3 subtype4 
   366.0    361.5    172.5    187.0 
[1] "5.0 - 1991.0 (366.0)" "4.0 - 2172.0 (361.5)" "4.0 - 1257.0 (172.5)"
[4] "3.0 - 1978.0 (187.0)"
D7V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        3        10        32         0        2
  subtype2        0        0         6        27         1        0
  subtype3        1        1         3        23         1        0
  subtype4        1        3         2        13         0        1
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE IA         0        0        1        1
  STAGE IB         3        0        1        3
  STAGE IIA       10        6        3        2
  STAGE IIB       32       27       23       13
  STAGE III        0        1        1        0
  STAGE IV         2        0        0        1
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     3    44
  subtype2     5    29
  subtype3     2    27
  subtype4     5    15
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1+T2        3        5        2        5
  T3+T4       44       29       27       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"
D7V5, binary
          cls
clus        0  1
  subtype1 13 34
  subtype2  6 28
  subtype3  5 23
  subtype4  6 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   34
  subtype2    6   28
  subtype3    5   23
  subtype4    6   14
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       13        6        5        6
  1       34       28       23       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 23  2 22
  subtype2 22  0 12
  subtype3 15  0 14
  subtype4 12  1  7
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       23       22       15       12
  M1        2        0        0        1
  MX       22       12       14        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 22 25
  subtype2 18 16
  subtype3 13 16
  subtype4  7 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   25
  subtype2   18   16
  subtype3   13   16
  subtype4    7   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       22       18       13        7
  MALE         25       16       16       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"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  37
  subtype2                                  32
  subtype3                                  24
  subtype4                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                     1
  subtype3                                     2
  subtype4                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                1
  subtype3                                                2
  subtype4                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   0
  subtype2                                   0
  subtype3                                   1
  subtype4                                   0
D7V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    37       32       24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        1        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1        2
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0        0        1
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 25 18  0  2
  subtype2 20 12  0  0
  subtype3 18  8  1  1
  subtype4 14  4  1  0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       25       20       18       14
  R1       18       12        8        4
  R2        0        0        1        1
  RX        2        0        1        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    45
  subtype2     1                         2    30
  subtype3     1                         1    26
  subtype4     0                         1    18
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        1        0
  BLACK OR AFRICAN AMERICAN        1        2        1        1
  WHITE                           45       30       26       18
[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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 46 11
  subtype2 22  5
  subtype3 10  2
subtype1 subtype2 subtype3 
      57       27       12 
subtype1 subtype2 subtype3 
      11        5        2 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABI 
        1962          729           80          676         1960          969 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABT TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 
         440          360          319          153          167          385 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 
         166          392          396          240           20            4 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 
         840          361            8           28            5           91 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P0 TCGA-HZ-A8P1 TCGA-IB-7644 
          46           13           33         1968            7          347 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1989         1257         1975          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUP TCGA-IB-AAUQ 
        1991          635          248          181          290         1978 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
         179          153          164          127          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO 
         247          416           95           36          397          197 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

$subtype2
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-3E-AAAY TCGA-F2-6880 TCGA-F2-7273 
         677          484          438         2172          295          360 
TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 TCGA-HZ-8002 TCGA-HZ-8003 
         586          363          378           28           24           21 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 
          16          660          491           11         1951          724 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUT TCGA-IB-AAUW 
         648           75         1968            8          188          179 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-US-A774 
          35          155         1955 

$subtype3
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 
           4          449          233            8           19            3 
TCGA-HZ-A4BH TCGA-IB-AAUR TCGA-IB-AAUV TCGA-RB-AA9M TCGA-XD-AAUG TCGA-XD-AAUH 
         194          128          210           42          161          164 

subtype1 subtype2 subtype3 
       4        8        3 
subtype1 subtype2 subtype3 
    1991     2172      449 
subtype1 subtype2 subtype3 
   300.0    363.0    144.5 
[1] "4.0 - 1991.0 (300.0)" "8.0 - 2172.0 (363.0)" "3.0 - 449.0 (144.5)" 
D8V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        4        15        53         0        2
  subtype2        0        0         4        30         1        0
  subtype3        1        3         2        12         1        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        0        1
  STAGE IB         4        0        3
  STAGE IIA       15        4        2
  STAGE IIB       53       30       12
  STAGE III        0        1        1
  STAGE IV         2        0        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     5    70
  subtype2     5    30
  subtype3     5    15
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        5        5        5
  T3+T4       70       30       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"
D8V5, binary
          cls
clus        0  1
  subtype1 19 55
  subtype2  4 31
  subtype3  7 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   55
  subtype2    4   31
  subtype3    7   13
   clus
vv  subtype1 subtype2 subtype3
  0       19        4        7
  1       55       31       13
[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       M0 M1 MX
  subtype1 41  2 32
  subtype2 22  0 13
  subtype3  9  1 10
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       41       22        9
  M1        2        0        1
  MX       32       13       10
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 32 43
  subtype2 18 17
  subtype3 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   43
  subtype2   18   17
  subtype3   10   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       18       10
  MALE         43       17       10
[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                                  60
  subtype2                                  33
  subtype3                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                    11
  subtype2                                     1
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D8V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    60       33       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                  11        1        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 41 27  1  3
  subtype2 22 11  0  0
  subtype3 14  4  1  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       41       22       14
  R1       27       11        4
  R2        1        0        1
  RX        3        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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    70
  subtype2     1                         2    31
  subtype3     0                         1    18
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        2        2        1
  WHITE                           70       31       18
[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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 29  7
  subtype2 32  8
  subtype3 16  3
subtype1 subtype2 subtype3 
      36       40       19 
subtype1 subtype2 subtype3 
       7        8        3 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABP TCGA-F2-A44G 
        1962           80          676          969          360          153 
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7919 
         167          385          378          392          396           20 
TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A8P0 
           4          840           28            5           11         1968 
TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS 
         347         1989         1257         1975          522         1991 
TCGA-IB-A6UF TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         248          164          127          584          110          247 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-US-A776 TCGA-YY-A8LH 
         416           95           36          397          844         1834 

$subtype2
TCGA-2J-AAB4 TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABT TCGA-3E-AAAY 
         729          484          440          438          319         2172 
TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-A45N 
         360            4          363          449          166          233 
TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
          28            8          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A4BH 
          21           16            3           91          660          194 
TCGA-HZ-A77P TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
          13         1951          724          648           75          329 
TCGA-IB-A5ST TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
         635          290         1978          128          179          210 
TCGA-IB-AAUW TCGA-RB-AA9M TCGA-XD-AAUG TCGA-XD-AAUH 
         179           42          161          164 

$subtype3
TCGA-2J-AABF TCGA-2J-AABH TCGA-F2-A44H TCGA-HZ-7289 TCGA-HZ-A49H TCGA-HZ-A4BK 
        1960          677          586          240          491           46 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
          33            7          300         1968          181            8 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-S4-A8RO TCGA-US-A774 
         188          153           35          155          197         1955 
TCGA-YB-A89D 
         160 

subtype1 subtype2 subtype3 
       4        3        7 
subtype1 subtype2 subtype3 
    1991     2172     1968 
subtype1 subtype2 subtype3 
   381.5    202.0    188.0 
[1] "4.0 - 1991.0 (381.5)" "3.0 - 2172.0 (202.0)" "7.0 - 1968.0 (188.0)"
D9V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        2        11        33         0        2
  subtype2        2        4         6        41         2        1
  subtype3        0        1         4        18         0        0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         0        2        0
  STAGE IB         2        4        1
  STAGE IIA       11        6        4
  STAGE IIB       33       41       18
  STAGE III        0        2        0
  STAGE IV         2        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     2    46
  subtype2    10    46
  subtype3     3    20
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2       10        3
  T3+T4       46       46       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 13 35
  subtype2 12 43
  subtype3  5 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   35
  subtype2   12   43
  subtype3    5   18
   clus
vv  subtype1 subtype2 subtype3
  0       13       12        5
  1       35       43       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 27  2 19
  subtype2 34  1 21
  subtype3  9  0 14
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       27       34        9
  M1        2        1        0
  MX       19       21       14
[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"
D9V7, binary
          cls
clus        0  1
  subtype1 27 21
  subtype2 25 31
  subtype3  8 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   21
  subtype2   25   31
  subtype3    8   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       25        8
  MALE         21       31       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  40
  subtype2                                  50
  subtype3                                  18
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     6
  subtype2                                     4
  subtype3                                     4
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                2
  subtype3                                                1
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D9V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    40       50       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   6        4        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        2        1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 26 18  1  1
  subtype2 35 15  1  1
  subtype3 15  7  0  1
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       26       35       15
  R1       18       15        7
  R2        1        1        0
  RX        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"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    46
  subtype2     2                         3    48
  subtype3     0                         1    22
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        1        3        1
  WHITE                           46       48       22
[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"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 36  9
  subtype2 27  7
  subtype3 14  2
subtype1 subtype2 subtype3 
      45       34       16 
subtype1 subtype2 subtype3 
       9        7        2 
$subtype1
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2J-AABI TCGA-2J-AABO 
        1962          729           80          676          969          440 
TCGA-2J-AABP TCGA-2J-AABT TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR 
         360          319          153          167          385          166 
TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8638 
         392          240           20          840          361           91 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 
          13           33            7          347         1257         1975 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUQ 
         329          300         1991          635          181         1978 
TCGA-IB-AAUU TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         153          164          127          584          110          247 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 
         416           95           36          397          197          844 
TCGA-XD-AAUG TCGA-YB-A89D TCGA-YY-A8LH 
         161          160         1834 

$subtype2
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABR TCGA-F2-A44H TCGA-FB-A4P6 
        1960          677          484          438          586          363 
TCGA-FB-A78T TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7926 
         378          233          396           28            4            8 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
          21           28           16            5          660          491 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A8P0 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          46           11         1968         1951         1989          724 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM 
         648           75          522          248         1968            8 
TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-US-A774 
         188           35          155         1955 

$subtype3
TCGA-3E-AAAY TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-HZ-7923 TCGA-HZ-8001 
        2172          360            4          449            8           19 
TCGA-HZ-8002 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
          24            3          194          290          128          179 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-RB-AA9M TCGA-XD-AAUH 
         210          179           42          164 

subtype1 subtype2 subtype3 
       7        4        3 
subtype1 subtype2 subtype3 
    1991     1989     2172 
subtype1 subtype2 subtype3 
   319.0    370.5    171.5 
[1] "7.0 - 1991.0 (319.0)" "4.0 - 1989.0 (370.5)" "3.0 - 2172.0 (171.5)"
D10V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        3        13        41         0        2
  subtype2        0        1         6        33         1        1
  subtype3        1        3         2        18         1        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        0        1
  STAGE IB         3        1        3
  STAGE IIA       13        6        2
  STAGE IIB       41       33       18
  STAGE III        0        1        1
  STAGE IV         2        1        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     4    56
  subtype2     6    36
  subtype3     5    20
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        4        6        5
  T3+T4       56       36       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 15 44
  subtype2  8 34
  subtype3  7 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   44
  subtype2    8   34
  subtype3    7   18
   clus
vv  subtype1 subtype2 subtype3
  0       15        8        7
  1       44       34       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 33  2 25
  subtype2 23  1 18
  subtype3 14  0 11
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       33       23       14
  M1        2        1        0
  MX       25       18       11
[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"
D10V7, binary
          cls
clus        0  1
  subtype1 26 34
  subtype2 24 18
  subtype3 10 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   34
  subtype2   24   18
  subtype3   10   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26       24       10
  MALE         34       18       15
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  47
  subtype2                                  37
  subtype3                                  24
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     9
  subtype2                                     4
  subtype3                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                1
  subtype3                                                0
          vv
clus       PANCREAS-UNDIFFERENTIATED CARCINOMA
  subtype1                                   1
  subtype2                                   0
  subtype3                                   0
D10V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    47       37       24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   9        4        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        1        0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                     1        0        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 38 16  1  2
  subtype2 22 17  0  1
  subtype3 16  7  1  0
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       38       22       16
  R1       16       17        7
  R2        1        0        1
  RX        2        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"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    56
  subtype2     1                         2    38
  subtype3     0                         2    22
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        1        2        2
  WHITE                           56       38       22
[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"
