[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/10006103/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/10667978/PAAD-TP.mergedcluster.txt"

nPatients in clinical file=93, in cluster file=147, common to both=93
[1]  8 93
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
23 43 14  6 
 1  2  3  4 
23 43 14  6 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
43 26 24 
 1  2  3 
43 26 24 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
43 24 22 
 1  2  3 
43 24 22 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
23 12 13 13 21  7 
 1  2  3  4  5  6 
23 12 13 13 21  7 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
29 23 13 19 
 1  2  3  4 
29 23 13 19 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
15 19 17  6 16 11 
 1  2  3  4  5  6 
15 19 17  6 16 11 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
33 21 30 
 1  2  3 
33 21 30 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
41 25 18 
 1  2  3 
41 25 18 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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 93 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
          NA          295          360           NA          153          586 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM 
          NA          167            4          363          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H6-8124 
           1          166           NA           NA           NA          392 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
         233          396          240           28           20           NA 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          24           21           NA           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
           5           NA           91           23           29           NA 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
         194           46           11           13           33            7 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 
         347           NA           NA           NA           NA           NA 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
         476          851           NA           NA           NA           NA 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
          NA          488           NA           NA           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         329          300           NA           NA            8           NA 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
          NA          181          164          127           35          155 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-S4-A8RM TCGA-S4-A8RO 
         584          110          247          416          397          197 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
          NA           NA          844           NA           NA           NA 
TCGA-US-A77J TCGA-YB-A89D TCGA-YY-A8LH 
          NA          160         1834 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	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=1,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=21,	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=13,	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=12,	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 93 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=37, 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 
 2  7 82  2 
[1] "table(vv)"
vv
T1+T2 T3+T4 
    9    84 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 2  7 82  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 9

$Class1_nSamples
[1] 84

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
    9    84 
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=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=20, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=13, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 13  3
  subtype2 26  6
  subtype3  7  2
  subtype4  4  0
subtype1 subtype2 subtype3 subtype4 
      16       32        9        4 
subtype1 subtype2 subtype3 subtype4 
       3        6        2        0 
$subtype1
TCGA-FB-A545 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-A4BH TCGA-HZ-A77O 
         385          240           28            4          194           11 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 
         476         1975          522         1991         1968          181 
TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-US-A776 TCGA-YY-A8LH 
         164          584          844         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR 
         295          360          586            4          449          166 
TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
         233            8          369          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-IB-7649 TCGA-IB-7651 
          23           29           13           33         1951         1989 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-LB-A8F3 
         851          488           17          329            8           35 
TCGA-Q3-A5QY TCGA-US-A774 
         416         1955 

$subtype3
TCGA-F2-A44G TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-8636 TCGA-HZ-A4BK 
         153            1          396           20            5           46 
TCGA-IB-7644 TCGA-OE-A75W TCGA-PZ-A5RE 
         347          110          247 

$subtype4
TCGA-H6-8124 TCGA-IB-A5SP TCGA-LB-A7SX TCGA-YB-A89D 
         392          300          127          160 

subtype1 subtype2 subtype3 subtype4 
       4        3        1      127 
subtype1 subtype2 subtype3 subtype4 
    1991     1989      396      392 
subtype1 subtype2 subtype3 subtype4 
   430.5     63.0    110.0    230.0 
[1] "4.0 - 1991.0 (430.5)"  "3.0 - 1989.0 (63.0)"   "1.0 - 396.0 (110.0)"  
[4] "127.0 - 392.0 (230.0)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         2        20         0        0
  subtype2        2        3         8        28         2        0
  subtype3        0        0         3         8         0        3
  subtype4        0        0         1         5         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE IA         0        2        0        0
  STAGE IB         1        3        0        0
  STAGE IIA        2        8        3        1
  STAGE IIB       20       28        8        5
  STAGE III        0        2        0        0
  STAGE IV         0        0        3        0
[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     2    21
  subtype2     6    37
  subtype3     0    14
  subtype4     0     6
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1+T2        2        6        0        0
  T3+T4       21       37       14        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1  3 20
  subtype2 13 29
  subtype3  4 10
  subtype4  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   20
  subtype2   13   29
  subtype3    4   10
  subtype4    1    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        3       13        4        1
  1       20       29       10        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 13  0 10
  subtype2 20  0 23
  subtype3  5  3  6
  subtype4  3  0  3
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       13       20        5        3
  M1        0        0        3        0
  MX       10       23        6        3
[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"
D1V7, binary
          cls
clus        0  1
  subtype1  9 14
  subtype2 25 18
  subtype3  7  7
  subtype4  3  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   14
  subtype2   25   18
  subtype3    7    7
  subtype4    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       25        7        3
  MALE         14       18        7        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  20
  subtype2                                  37
  subtype3                                  12
  subtype4                                   5
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     4
  subtype3                                     2
  subtype4                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                2
  subtype3                                                0
  subtype4                                                0
D1V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    20       37       12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1        4        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        2        0
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0
[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"
D1V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 12  8  1  1
  subtype2 34  7  0  1
  subtype3  7  6  0  0
  subtype4  2  4  0  0
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       12       34        7        2
  R1        8        7        6        4
  R2        1        0        0        0
  RX        1        1        0        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"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    19
  subtype2     1                         4    36
  subtype3     0                         0    14
  subtype4     0                         1     5
D1V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        0        0
  BLACK OR AFRICAN AMERICAN        1        4        0        1
  WHITE                           19       36       14        5
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 25  5
  subtype2 17  4
  subtype3 14  2
subtype1 subtype2 subtype3 
      30       21       16 
subtype1 subtype2 subtype3 
       5        4        2 
$subtype1
TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         167          385            1          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-A8P1 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
           7          347         1989         1975          522          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W 
        1991         1968          181          164          127          110 
TCGA-PZ-A5RE TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         247          397          197          844          160         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-H6-A45N TCGA-HZ-7918 
         295          360          586          363          233           28 
TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
         369           24           21           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-8126 
          23           29           11         1951          476           17 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-US-A774 
          35          155         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          851          488 
TCGA-IB-A5SO TCGA-IB-A5ST TCGA-M8-A5N4 TCGA-Q3-A5QY 
         329            8          584          416 

subtype1 subtype2 subtype3 
       1        3        4 
subtype1 subtype2 subtype3 
    1991     1955      851 
subtype1 subtype2 subtype3 
   218.5     91.0    180.0 
[1] "1.0 - 1991.0 (218.5)" "3.0 - 1955.0 (91.0)"  "4.0 - 851.0 (180.0)" 
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        2         7        32         0        2
  subtype2        2        1         4        17         1        1
  subtype3        0        2         4        17         1        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         0        2        0
  STAGE IB         2        1        2
  STAGE IIA        7        4        4
  STAGE IIB       32       17       17
  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     2    41
  subtype2     5    21
  subtype3     2    22
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        5        2
  T3+T4       41       21       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 10 33
  subtype2  7 19
  subtype3  6 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   33
  subtype2    7   19
  subtype3    6   17
   clus
vv  subtype1 subtype2 subtype3
  0       10        7        6
  1       33       19       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 19  2 22
  subtype2 10  1 15
  subtype3 14  0 10
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       19       10       14
  M1        2        1        0
  MX       22       15       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 17 26
  subtype2 15 11
  subtype3 14 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   26
  subtype2   15   11
  subtype3   14   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       15       14
  MALE         26       11       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                                  37
  subtype2                                  23
  subtype3                                  21
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                     2
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                1
  subtype3                                                1
D2V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    37       23       21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        2        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        1        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 21 17  1  2
  subtype2 18  6  0  0
  subtype3 19  5  0  0
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       21       18       19
  R1       17        6        5
  R2        1        0        0
  RX        2        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    39
  subtype2     1                         2    22
  subtype3     1                         1    20
D2V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           39       22       20
[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 = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 31  4
  subtype2 14  5
  subtype3 10  2
subtype1 subtype2 subtype3 
      35       19       12 
subtype1 subtype2 subtype3 
       4        5        2 
$subtype1
TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A7DR TCGA-H6-8124 TCGA-H8-A6C1 
         153          167          385          166          392          396 
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
         240           20            4          369          361            8 
TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A4BK TCGA-HZ-A77Q TCGA-HZ-A8P1 
          28            5           91           46           33            7 
TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A5ST 
         347          851         1975          522         1991            8 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         181          164          127          584          110          247 
TCGA-Q3-A5QY TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A776 TCGA-YY-A8LH 
         416          397          197          844         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 
         295          360          586          363            1           28 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7649 TCGA-IB-7651 
          16           23           11           13         1951         1989 
TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-LB-A8F3 
         476          488           17          300         1968           35 
TCGA-US-A774 
        1955 

$subtype3
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8002 
           4          449          233            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-A5SO TCGA-YB-A89D 
          21            3           29          194          329          160 

subtype1 subtype2 subtype3 
       4        1        3 
subtype1 subtype2 subtype3 
    1991     1989      449 
subtype1 subtype2 subtype3 
   197.0    300.0     26.5 
[1] "4.0 - 1991.0 (197.0)" "1.0 - 1989.0 (300.0)" "3.0 - 449.0 (26.5)"  
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         9        30         0        2
  subtype2        0        0         3        20         1        0
  subtype3        1        4         2        14         1        0
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        0        1
  STAGE IB         1        0        4
  STAGE IIA        9        3        2
  STAGE IIB       30       20       14
  STAGE III        0        1        1
  STAGE IV         2        0        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    41
  subtype2     2    22
  subtype3     5    17
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        2        5
  T3+T4       41       22       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 11 31
  subtype2  3 21
  subtype3  8 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   31
  subtype2    3   21
  subtype3    8   14
   clus
vv  subtype1 subtype2 subtype3
  0       11        3        8
  1       31       21       14
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 18  2 23
  subtype2 14  0 10
  subtype3  9  0 13
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       18       14        9
  M1        2        0        0
  MX       23       10       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"
D3V7, binary
          cls
clus        0  1
  subtype1 21 22
  subtype2 13 11
  subtype3 11 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   22
  subtype2   13   11
  subtype3   11   11
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       13       11
  MALE         22       11       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       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  34
  subtype2                                  23
  subtype3                                  20
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     5
  subtype2                                     1
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                3
  subtype2                                                0
  subtype3                                                0
D3V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    34       23       20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   5        1        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        0        0
[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"
D3V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 21 17  1  2
  subtype2 14  9  0  0
  subtype3 19  2  0  0
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       21       14       19
  R1       17        9        2
  R2        1        0        0
  RX        2        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"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    39
  subtype2     1                         2    20
  subtype3     0                         1    19
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        2        2        1
  WHITE                           39       20       19
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 13  2
  subtype2  5  4
  subtype3  4  1
  subtype4 11  1
  subtype5 15  3
  subtype6  7  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      15        9        5       12       18        7 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        4        1        1        3        0 
$subtype1
TCGA-F2-A44G TCGA-F2-A8YN TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-8636 TCGA-IB-7885 
         153          167          385          392            5          851 
TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
        1991          181          164          127          584          110 
TCGA-PZ-A5RE TCGA-S4-A8RO TCGA-YY-A8LH 
         247          197         1834 

$subtype2
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8315 TCGA-IB-7649 TCGA-IB-7651 
         233           20            4           28         1951         1989 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
        1975          522          300 

$subtype3
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 
           4          449            8           19            3 

$subtype4
TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8638 
         166          396          240          369            8           91 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7644 TCGA-S4-A8RM TCGA-US-A776 
          46           13            7          347          397          844 

$subtype5
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 
         295          360          586          363            1           28 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O 
          24           21           16           23           29           11 
TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-US-A774 
         476          488           17         1968           35         1955 

$subtype6
TCGA-HZ-7925 TCGA-HZ-A4BH TCGA-HZ-A77Q TCGA-IB-A5SO TCGA-IB-A5ST TCGA-Q3-A5QY 
         361          194           33          329            8          416 
TCGA-YB-A89D 
         160 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5        4        3        7        1        8 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1991     1989      449      844     1968      416 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     197      300        8      203       32      194 
[1] "5.0 - 1991.0 (197.0)" "4.0 - 1989.0 (300.0)" "3.0 - 449.0 (8.0)"   
[4] "7.0 - 844.0 (203.0)"  "1.0 - 1968.0 (32.0)"  "8.0 - 416.0 (194.0)" 
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         4        17         0        1
  subtype2        0        0         2        10         0        0
  subtype3        1        3         2         6         1        0
  subtype4        1        1         4         6         0        1
  subtype5        0        0         2        18         1        0
  subtype6        0        0         0         7         0        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE IA         0        0        1        1        0        0
  STAGE IB         1        0        3        1        0        0
  STAGE IIA        4        2        2        4        2        0
  STAGE IIB       17       10        6        6       18        7
  STAGE III        0        0        1        0        1        0
  STAGE IV         1        0        0        1        0        0
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     1    22
  subtype2     0    12
  subtype3     4     9
  subtype4     2    11
  subtype5     2    19
  subtype6     0     7
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1+T2        1        0        4        2        2        0
  T3+T4       22       12        9       11       19        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1  6 17
  subtype2  2 10
  subtype3  7  6
  subtype4  5  7
  subtype5  2 19
  subtype6  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   17
  subtype2    2   10
  subtype3    7    6
  subtype4    5    7
  subtype5    2   19
  subtype6    0    7
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        6        2        7        5        2        0
  1       17       10        6        7       19        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 14  1  8
  subtype2  6  0  6
  subtype3  6  0  7
  subtype4  1  1 11
  subtype5 12  0  9
  subtype6  2  0  5
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       14        6        6        1       12        2
  M1        1        0        0        1        0        0
  MX        8        6        7       11        9        5
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 13 10
  subtype2  8  4
  subtype3  8  5
  subtype4  3 10
  subtype5 11 10
  subtype6  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   10
  subtype2    8    4
  subtype3    8    5
  subtype4    3   10
  subtype5   11   10
  subtype6    2    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       13        8        8        3       11        2
  MALE         10        4        5       10       10        5
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  22
  subtype2                                  11
  subtype3                                  12
  subtype4                                   5
  subtype5                                  21
  subtype6                                   6
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     0
  subtype2                                     1
  subtype3                                     1
  subtype4                                     5
  subtype5                                     0
  subtype6                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                0
  subtype4                                                3
  subtype5                                                0
  subtype6                                                0
D4V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    22       11       12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        1        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        0        0
                                                  clus
vv                                                 subtype4 subtype5 subtype6
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     5       21        6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   5        0        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        3        0        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9        6        2        5        7        1 
 [1] "subtype5" "subtype1" "subtype5" "subtype5" "subtype4" "subtype1"
 [7] "subtype2" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype1" "subtype5" "subtype5" "subtype2"
[19] "subtype1" "subtype5" "subtype1" "subtype1" "subtype1" "subtype4"
[25] "subtype2" "subtype5" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1 10 10  1  0
  subtype2  5  6  0  0
  subtype3 12  1  0  0
  subtype4  8  3  0  2
  subtype5 13  7  0  0
  subtype6  6  1  0  0
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       10        5       12        8       13        6
  R1       10        6        1        3        7        1
  R2        1        0        0        0        0        0
  RX        0        0        0        2        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    20
  subtype2     0                         0    11
  subtype3     0                         1    11
  subtype4     1                         1    11
  subtype5     1                         2    18
  subtype6     0                         0     7
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        1
  BLACK OR AFRICAN AMERICAN        1        0        1        1        2
  WHITE                           20       11       11       11       18
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            7
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 18  4
  subtype2 16  5
  subtype3  5  1
  subtype4 12  1
subtype1 subtype2 subtype3 subtype4 
      22       21        6       13 
subtype1 subtype2 subtype3 subtype4 
       4        5        1        1 
$subtype1
TCGA-F2-A44G TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         153          385            1          392          396          240 
TCGA-HZ-7919 TCGA-HZ-7924 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7644 
          20          369           28            5           46          347 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 
        1975          522         1991          181          127          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-US-A776 TCGA-YY-A8LH 
         110          247          844         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-HZ-7918 TCGA-HZ-7922 
         295          360          586          363           28            4 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O 
          24           21           16           23           29           11 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SP 
        1951         1989          476          488           17          300 
TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-US-A774 
        1968           35         1955 

$subtype3
TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-A5SO TCGA-YB-A89D 
         233            8            3          194          329          160 

$subtype4
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4          449          166          361            8           19 
TCGA-HZ-8638 TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7885 TCGA-IB-A5ST TCGA-L1-A7W4 
          91           13           33          851            8          164 
TCGA-Q3-A5QY 
         416 

subtype1 subtype2 subtype3 subtype4 
       1        4        3        4 
subtype1 subtype2 subtype3 subtype4 
    1991     1989      329      851 
subtype1 subtype2 subtype3 subtype4 
     297      295      177       91 
[1] "1.0 - 1991.0 (297.0)" "4.0 - 1989.0 (295.0)" "3.0 - 329.0 (177.0)" 
[4] "4.0 - 851.0 (91.0)"  
D5V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        0         6        21         0        2
  subtype2        0        0         3        19         1        0
  subtype3        1        2         2         8         0        0
  subtype4        1        2         2        13         1        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE IA         0        0        1        1
  STAGE IB         0        0        2        2
  STAGE IIA        6        3        2        2
  STAGE IIB       21       19        8       13
  STAGE III        0        1        0        1
  STAGE IV         2        0        0        0
[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     0    29
  subtype2     2    21
  subtype3     3    10
  subtype4     3    16
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1+T2        0        2        3        3
  T3+T4       29       21       10       16
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1  7 22
  subtype2  3 20
  subtype3  5  8
  subtype4  5 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   22
  subtype2    3   20
  subtype3    5    8
  subtype4    5   13
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7        3        5        5
  1       22       20        8       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       M0 M1 MX
  subtype1 12  2 15
  subtype2 12  0 11
  subtype3  6  0  7
  subtype4  9  0 10
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       12       12        6        9
  M1        2        0        0        0
  MX       15       11        7       10
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 17 12
  subtype2 13 10
  subtype3  5  8
  subtype4  9 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   12
  subtype2   13   10
  subtype3    5    8
  subtype4    9   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       13        5        9
  MALE         12       10        8       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  23
  subtype2                                  23
  subtype3                                  11
  subtype4                                  15
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                     0
  subtype3                                     2
  subtype4                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
  subtype4                                                2
D5V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    23       23       11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        0        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        1        0        0
                                                  clus
vv                                                 subtype4
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2
[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"
D5V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      13        8        1        5 
 [1] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype4"
 [7] "subtype1" "subtype1" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype4" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype2" "subtype1"
          vv
clus       R0 R1 R2 RX
  subtype1 13 13  0  1
  subtype2 14  8  0  0
  subtype3 10  2  0  0
  subtype4 15  2  1  1
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       13       14       10       15
  R1       13        8        2        2
  R2        0        0        0        1
  RX        1        0        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    27
  subtype2     1                         2    19
  subtype3     0                         1    11
  subtype4     1                         1    16
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        1
  BLACK OR AFRICAN AMERICAN        1        2        1        1
  WHITE                           27       19       11       16
[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(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  7  2
  subtype2 14  2
  subtype3  7  2
  subtype4  4  2
  subtype5 11  2
  subtype6  8  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       16        9        6       13        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        2        2        2        1 
$subtype1
TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-L1-A7W4 
         153          385          392         1991          181          164 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-YY-A8LH 
         127          110         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A7DR TCGA-HZ-7918 
         295          360          586          363          166           28 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A49H 
           8           24           21           16           23           29 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 
        1951          476          488           17 

$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-HZ-A77P TCGA-IB-A5SO 
         194           13          329 

$subtype4
TCGA-FB-A78T TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-US-A774 
           1            4           11         1968           35         1955 

$subtype5
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8638 TCGA-HZ-A77Q 
         396          240          369          361           91           33 
TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-A5ST TCGA-M8-A5N4 TCGA-Q3-A5QY 
         347          851         1975            8          584          416 
TCGA-US-A776 
         844 

$subtype6
TCGA-HZ-7919 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7651 TCGA-IB-8127 
          20           28            5           46         1989          522 
TCGA-IB-A5SP TCGA-PZ-A5RE TCGA-YB-A89D 
         300          247          160 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     110        8        3        1        8        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1991     1951      449     1968     1975     1989 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   181.0     97.5     19.0     23.0    369.0    160.0 
[1] "110.0 - 1991.0 (181.0)" "8.0 - 1951.0 (97.5)"    "3.0 - 449.0 (19.0)"    
[4] "1.0 - 1968.0 (23.0)"    "8.0 - 1975.0 (369.0)"   "5.0 - 1989.0 (160.0)"  
D6V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         2        12         0        0
  subtype2        0        0         2        16         1        0
  subtype3        1        3         2        10         1        0
  subtype4        0        0         1         5         0        0
  subtype5        1        0         4        10         0        1
  subtype6        0        0         2         8         0        1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE IA         0        0        1        0        1        0
  STAGE IB         1        0        3        0        0        0
  STAGE IIA        2        2        2        1        4        2
  STAGE IIB       12       16       10        5       10        8
  STAGE III        0        1        1        0        0        0
  STAGE IV         0        0        0        0        1        1
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     1    14
  subtype2     1    18
  subtype3     4    13
  subtype4     1     5
  subtype5     1    15
  subtype6     0    11
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1+T2        1        1        4        1        1        0
  T3+T4       14       18       13        5       15       11
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1  3 12
  subtype2  1 17
  subtype3  7 10
  subtype4  1  5
  subtype5  5 11
  subtype6  3  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   12
  subtype2    1   17
  subtype3    7   10
  subtype4    1    5
  subtype5    5   11
  subtype6    3    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        3        1        7        1        5        3
  1       12       17       10        5       11        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 10  0  5
  subtype2 11  0  8
  subtype3  7  0 10
  subtype4  2  0  4
  subtype5  4  1 11
  subtype6  5  1  5
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       10       11        7        2        4        5
  M1        0        0        0        0        1        1
  MX        5        8       10        4       11        5
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1  7  8
  subtype2  8 11
  subtype3  9  8
  subtype4  5  1
  subtype5  8  8
  subtype6  7  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    8
  subtype2    8   11
  subtype3    9    8
  subtype4    5    1
  subtype5    8    8
  subtype6    7    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        7        8        9        5        8        7
  MALE          8       11        8        1        8        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  14
  subtype2                                  18
  subtype3                                  14
  subtype4                                   6
  subtype5                                  10
  subtype6                                  10
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     0
  subtype2                                     0
  subtype3                                     3
  subtype4                                     0
  subtype5                                     4
  subtype6                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                0
  subtype4                                                0
  subtype5                                                2
  subtype6                                                0
D6V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    14       18       14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        0        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        1        0
                                                  clus
vv                                                 subtype4 subtype5 subtype6
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                     6       10       10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   0        4        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        0        2        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1  9  4  1  0
  subtype2 11  6  0  1
  subtype3 14  2  0  0
  subtype4  5  1  0  0
  subtype5 10  5  0  1
  subtype6  3  7  0  0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        9       11       14        5       10        3
  R1        4        6        2        1        5        7
  R2        1        0        0        0        0        0
  RX        0        1        0        0        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    13
  subtype2     2                         2    14
  subtype3     0                         1    15
  subtype4     0                         1     5
  subtype5     0                         0    15
  subtype6     0                         0    11
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        0        0        0
  BLACK OR AFRICAN AMERICAN        1        2        1        1        0
  WHITE                           13       14       15        5       15
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           11
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 20  5
  subtype2 15  5
  subtype3 16  1
subtype1 subtype2 subtype3 
      25       20       17 
subtype1 subtype2 subtype3 
       5        5        1 
$subtype1
TCGA-F2-A44G TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         153          385            1          392          396          240 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A4BK TCGA-HZ-A77O 
         369          361            5           91           46           11 
TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 
         347         1975          522         1991         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-US-A776 
         164          127          584          110          247          844 
TCGA-YY-A8LH 
        1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-H6-A45N TCGA-HZ-7918 
         295          360          586          363          233           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          20            4           21           28           16            3 
TCGA-HZ-A49G TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-A5SP 
          23         1951         1989          476          488          300 
TCGA-LB-A8F3 TCGA-US-A774 
          35         1955 

$subtype3
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7923 TCGA-HZ-7926 TCGA-HZ-8001 
           4          449          166            8            8           19 
TCGA-HZ-8002 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7885 
          24           29          194           13           33          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-Q3-A5QY TCGA-YB-A89D 
          17          329            8          416          160 

subtype1 subtype2 subtype3 
       1        3        4 
subtype1 subtype2 subtype3 
    1991     1989      851 
subtype1 subtype2 subtype3 
     347      264       29 
[1] "1.0 - 1991.0 (347.0)" "3.0 - 1989.0 (264.0)" "4.0 - 851.0 (29.0)"  
D7V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        0         5        25         0        2
  subtype2        1        0         4        16         0        0
  subtype3        0        4         4        20         2        0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        1        0
  STAGE IB         0        0        4
  STAGE IIA        5        4        4
  STAGE IIB       25       16       20
  STAGE III        0        0        2
  STAGE IV         2        0        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    31
  subtype2     2    19
  subtype3     4    26
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        2        4
  T3+T4       31       19       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"
D7V5, binary
          cls
clus        0  1
  subtype1  7 26
  subtype2  5 16
  subtype3  8 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   26
  subtype2    5   16
  subtype3    8   21
   clus
vv  subtype1 subtype2 subtype3
  0        7        5        8
  1       26       16       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 13  2 18
  subtype2 10  0 11
  subtype3 16  0 14
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       13       10       16
  M1        2        0        0
  MX       18       11       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"
D7V7, binary
          cls
clus        0  1
  subtype1 18 15
  subtype2 12  9
  subtype3 14 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   15
  subtype2   12    9
  subtype3   14   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       12       14
  MALE         15        9       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  26
  subtype2                                  19
  subtype3                                  27
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     4
  subtype2                                     2
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                2
  subtype2                                                0
  subtype3                                                1
D7V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    26       19       27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   4        2        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2        0        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"
D7V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 16 13  1  1
  subtype2 11  8  0  0
  subtype3 25  4  0  1
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       16       11       25
  R1       13        8        4
  R2        1        0        0
  RX        1        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"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    31
  subtype2     1                         2    17
  subtype3     1                         2    25
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        1        2        2
  WHITE                           31       17       25
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 26  4
  subtype2 17  5
  subtype3  8  2
subtype1 subtype2 subtype3 
      30       22       10 
subtype1 subtype2 subtype3 
       4        5        2 
$subtype1
TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
         153          385          392          396          240           20 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A4BK 
         369          361           28            5           91           46 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
          33          347          851         1975          522          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 
        1991            8          181          164          127          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416          844          160         1834 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-FB-A78T TCGA-HZ-7918 
         295          360          586          363            1           28 
TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G 
           4            8           24           21           16           23 
TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 
          29           11         1951         1989          476          488 
TCGA-IB-8126 TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-US-A774 
          17         1968           35         1955 

$subtype3
TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8001 
           4          449          166          233            8           19 
TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-IB-A5SO 
           3          194           13          329 

subtype1 subtype2 subtype3 
       5        1        3 
subtype1 subtype2 subtype3 
    1991     1989      449 
subtype1 subtype2 subtype3 
   273.5     32.0     92.5 
[1] "5.0 - 1991.0 (273.5)" "1.0 - 1989.0 (32.0)"  "3.0 - 449.0 (92.5)"  
D8V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         8        29         0        2
  subtype2        0        0         2        22         1        0
  subtype3        1        3         3        10         1        0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IA         1        0        1
  STAGE IB         1        0        3
  STAGE IIA        8        2        3
  STAGE IIB       29       22       10
  STAGE III        0        1        1
  STAGE IV         2        0        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    39
  subtype2     2    23
  subtype3     4    14
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        2        4
  T3+T4       39       23       14
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 11 30
  subtype2  2 23
  subtype3  7 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   30
  subtype2    2   23
  subtype3    7   10
   clus
vv  subtype1 subtype2 subtype3
  0       11        2        7
  1       30       23       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       M0 M1 MX
  subtype1 18  2 21
  subtype2 13  0 12
  subtype3  8  0 10
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       18       13        8
  M1        2        0        0
  MX       21       12       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 21 20
  subtype2 14 11
  subtype3  9  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   20
  subtype2   14   11
  subtype3    9    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       14        9
  MALE         20       11        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  33
  subtype2                                  25
  subtype3                                  14
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     5
  subtype2                                     0
  subtype3                                     3
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                2
  subtype2                                                0
  subtype3                                                1
D8V8, multiclass
                                                  clus
vv                                                 subtype1 subtype2 subtype3
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                    33       25       14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                   5        0        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA        2        0        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"
D8V9, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 21 16  1  1
  subtype2 16  7  0  1
  subtype3 15  2  0  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       21       16       15
  R1       16        7        2
  R2        1        0        0
  RX        1        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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    38
  subtype2     1                         3    20
  subtype3     1                         1    15
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        1        3        1
  WHITE                           38       20       15
[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"
