[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"        "-oTLIHC-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/LIHC-TP/10006007/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/10667980/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=176, in cluster file=291, common to both=176
[1]   8 176
[1] "CN_CNMF"
[1] 3
 1  2  3 
45 61 54 
 1  2  3 
45 61 54 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
76 50 41 
 1  2  3 
76 50 41 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
34 25 45 28 30 
 1  2  3  4  5 
34 25 45 28 30 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
65 66 31 
 1  2  3 
65 66 31 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
37 70 64 
 1  2  3 
37 70 64 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
19 45 67 18 22 
 1  2  3  4  5 
19 45 67 18 22 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5 
21 29 32 54 35 
 1  2  3  4  5 
21 29 32 54 35 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
18 38 30 63 22 
 1  2  3  4  5 
18 38 30 63 22 
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 176 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
         216           NA          849           NA           NA           NA 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
          NA           NA         1351          421            8          680 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NQ TCGA-CC-5258 
         289          444          387          227           NA            2 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
           5           NA           12           NA           NA           NA 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
          NA           NA            3            2            3            4 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        2425           NA           NA           NA         3437           NA 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
          79           NA          662           NA           NA         2415 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
        2017          602         2301          204           NA           NA 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
        1495          183          887           NA           NA           NA 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
          NA         1008          989         2232           NA          428 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
         445          433          561          458           NA         1711 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
          NA         2245         2849           NA           NA           NA 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
        2018          334           NA          230          334           44 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
         843         3071          408          386          482          423 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
         406            7            6            6            6            6 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
           6            6            6            6            6          570 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
         608          357          334           NA          303          363 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
          NA           NA          987           NA           NA          848 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
          NA           NA            4            1           10         1836 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
          12           37         1553         1636          860          935 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
        1779           NA          655          673          780          180 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
         594          585          447          364          302          243 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
         133          236          182           NA           NA           NA 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
         122           NA          360          407           15          180 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
         130          291          155          433          391          265 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-YA-A8S7 TCGA-ZP-A9D4 
          52           NA          498          135           NA          395 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
        1066         2258 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=97,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=17,	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"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 176 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=53, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
71 44 50 10 
[1] "table(vv)"
vv
T1 T2 T3 T4 
71 44 50 10 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
71 44 50 10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
71 44 50 10 
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
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 23 21
  subtype2 40 21
  subtype3 28 24
subtype1 subtype2 subtype3 
      44       61       52 
subtype1 subtype2 subtype3 
      21       21       24 
$subtype1
TCGA-BC-4072 TCGA-BC-A10U TCGA-CC-5258 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 
       48.99        27.52         0.07         0.13        79.73         7.33 
TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39V 
       90.71         6.71        12.95        45.11        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A7 
       55.69         5.62        19.76         7.66        17.59        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A73A TCGA-DD-A73G 
        0.36        14.07        39.78        73.81        10.98       100.96 
TCGA-ED-A66X TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       13.35         0.20        18.74         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A7M7 
       14.40        60.36         0.39        19.53         7.99         5.98 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75H 
        2.66         4.01        11.84        13.38         9.57        12.85 
TCGA-MI-A75I TCGA-O8-A75V 
        8.71         4.44 

$subtype2
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A69I 
       27.91        37.32        46.78        25.32        69.57        12.72 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11D 
        2.86         3.39         3.32         0.10        37.78        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EK TCGA-DD-A3A2 
       79.40        66.31        19.79        75.65        18.35        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH 
       20.12       107.11        33.14        32.52        73.38        14.24 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       18.44        56.25        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       66.35         7.56         1.45        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A3RK 
       13.91         0.23         0.20         0.20        19.99        11.93 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U 
       19.10         8.12         0.13         0.33        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       28.27        30.74        22.13        25.64         5.92        19.23 
TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-KR-A7K0 TCGA-MI-A75E TCGA-MR-A8JO 
       11.97         7.76         1.02         2.14         5.10         1.71 
TCGA-NI-A4U2 
       58.88 

$subtype3
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       10.13        27.52         2.99        23.34         1.12         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        0.39         4.24         0.07         0.10        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EI 
      113.00         2.60         0.46        21.76        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NN 
       29.16        25.81       102.74        30.61        15.06        29.56 
TCGA-DD-A73B TCGA-DD-A73D TCGA-ED-A459 TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 
        9.30        10.98        13.41         0.20         0.20         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 
       11.74        10.98        32.45        27.88         6.38         0.03 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
        1.22        58.49        14.86        21.53        14.70         4.37 
TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF 
        1.84         0.49        14.24        16.37 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  100.96   107.11   113.00 
subtype1 subtype2 subtype3 
  13.150   19.230   12.575 
[1] "0.1 - 101.0 (13.1)" "0.1 - 107.1 (19.2)" "0.0 - 113.0 (12.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      22        9         0          8          1          0        1
  subtype2      27       10         0         13          3          4        0
  subtype3      16       18         2         10          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          22       27       16
  STAGE II          9       10       18
  STAGE III         0        0        2
  STAGE IIIA        8       13       10
  STAGE IIIB        1        3        1
  STAGE IIIC        0        4        1
  STAGE IV          1        0        0
  STAGE IVA         1        0        0
  STAGE IVB         0        1        1
[1] 9 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 23 11 10  0
  subtype2 28 12 17  4
  subtype3 17 18 15  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       23       28       17
  T2       11       12       18
  T3       10       17       15
  T4        0        4        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 26  1
  subtype2 47  1
  subtype3 29  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   47    1
  subtype3   29    1
   clus
vv  subtype1 subtype2 subtype3
  0       26       47       29
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 32  1 12
  subtype2 48  1 12
  subtype3 40  1 13
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       32       48       40
  M1        1        1        1
  MX       12       12       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"
D1V7, binary
          cls
clus        0  1
  subtype1  9 36
  subtype2 28 33
  subtype3 23 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   36
  subtype2   28   33
  subtype3   23   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       28       23
  MALE         36       33       31
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       44
  subtype2                       2                       59
  subtype3                       0                       53
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                1
D1V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        2        0
  HEPATOCELLULAR CARCINOMA               44       59       53
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        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"
          vv
clus       R0 R1 R2 RX
  subtype1 37  4  1  2
  subtype2 50  3  0  4
  subtype3 44  4  0  6
D1V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       37       50       44
  R1        4        3        4
  R2        1        0        0
  RX        2        4        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                         5
  subtype2                                0    13                         2
  subtype3                                0    16                         1
          vv
clus       WHITE
  subtype1    27
  subtype2    45
  subtype3    37
D1V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   7       13       16
  BLACK OR AFRICAN AMERICAN               5        2        1
  WHITE                                  27       45       37
[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, binary
          cls
clus        0  1
  subtype1  1 38
  subtype2  1 56
  subtype3  1 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   38
  subtype2    1   56
  subtype3    1   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        1
  NOT HISPANIC OR LATINO       38       56       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 42 32
  subtype2 29 20
  subtype3 24 16
subtype1 subtype2 subtype3 
      74       49       40 
subtype1 subtype2 subtype3 
      32       20       16 
$subtype1
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
        7.10        46.78        27.52        27.52        23.34         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I 
       44.42        13.84         0.26        22.36         9.50        12.72 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
        4.24         0.10        83.57         2.60        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK 
       79.40        66.31         6.71        45.11        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ 
      102.74         0.36        14.07        14.63        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       39.78        66.35        10.98        10.98         1.45        27.72 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74         0.62         9.96 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S 
       22.85        19.10         8.12         6.38         0.03         1.22 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       53.79        21.53        22.13        19.53        19.23        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-KR-A7K0 
        9.93         7.99         4.37         7.76         1.02         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       11.84        13.38         0.49        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-ZS-A9CF 
       58.88        74.24 

$subtype2
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5258 
       37.32        10.13         2.99         5.03        14.60         0.07 
TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 
        0.16         0.39         0.07         0.13        79.73        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
      113.00         7.33         0.46        12.95        49.15         6.02 
TCGA-DD-A39X TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE 
       55.69        17.59        20.12        13.78        30.61        21.70 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66X 
       29.56        73.81         9.30       100.96        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KB 
        0.23         0.20         0.20         0.20         0.20        10.98 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       32.45        27.88         0.13         0.33        60.36         0.39 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M7 TCGA-MI-A75C 
       58.49        14.86        25.64        14.70         5.98         9.57 
TCGA-O8-A75V 
        4.44 

$subtype3
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5260 TCGA-CC-5262 
       48.99        27.91        25.32        69.57         2.86         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED 
        3.32         0.10        37.78        90.71        19.79        75.65 
TCGA-DD-A1EL TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH 
       13.64       107.11        33.14        32.52        73.38        14.24 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73C 
       56.25        93.67        12.26         0.30        80.75         7.56 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7XO TCGA-ED-A97K TCGA-EP-A3RK 
       12.69        15.85        13.91         0.20         0.20        11.93 
TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI TCGA-G3-A7M9 
       14.40        51.06        28.27        30.74         5.92         1.84 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QD TCGA-MI-A75E 
        2.66         4.01         4.27         5.10 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  102.74   113.00   107.11 
subtype1 subtype2 subtype3 
  14.155   12.950   14.320 
[1] "0.0 - 102.7 (14.2)" "0.1 - 113.0 (12.9)" "0.1 - 107.1 (14.3)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      31       20         1         14          1          1        0
  subtype2      17       13         1         11          1          1        1
  subtype3      16        6         0         11          3          4        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         1
  subtype3         0         0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          31       17       16
  STAGE II         20       13        6
  STAGE III         1        1        0
  STAGE IIIA       14       11       11
  STAGE IIIB        1        1        3
  STAGE IIIC        1        1        4
  STAGE IV          0        1        0
  STAGE IVA         1        0        0
  STAGE IVB         1        1        0
[1] 9 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 33 22 17  3
  subtype2 17 14 16  3
  subtype3 17  7 14  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       33       17       17
  T2       22       14        7
  T3       17       16       14
  T4        3        3        3
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 40  2
  subtype2 34  0
  subtype3 32  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    2
  subtype2   34    0
  subtype3   32    1
   clus
vv  subtype1 subtype2 subtype3
  0       40       34       32
  1        2        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 54  1 21
  subtype2 40  2  8
  subtype3 33  0  8
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       54       40       33
  M1        1        2        0
  MX       21        8        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"
D2V7, binary
          cls
clus        0  1
  subtype1 23 53
  subtype2 24 26
  subtype3 15 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   53
  subtype2   24   26
  subtype3   15   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       24       15
  MALE         53       26       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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       75
  subtype2                       0                       49
  subtype3                       1                       39
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                1
  subtype3                                1
D2V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        0        1
  HEPATOCELLULAR CARCINOMA               75       49       39
  HEPATOCHOLANGIOCARCINOMA (MIXED)        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"
          vv
clus       R0 R1 R2 RX
  subtype1 64  5  0  5
  subtype2 41  4  1  4
  subtype3 33  2  0  3
D2V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       64       41       33
  R1        5        4        2
  R2        0        1        0
  RX        5        4        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     9                         4
  subtype2                                0    22                         0
  subtype3                                0     8                         4
          vv
clus       WHITE
  subtype1    59
  subtype2    26
  subtype3    28
D2V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   9       22        8
  BLACK OR AFRICAN AMERICAN               4        0        4
  WHITE                                  59       26       28
[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, binary
          cls
clus        0  1
  subtype1  0 65
  subtype2  3 46
  subtype3  2 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   65
  subtype2    3   46
  subtype3    2   38
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        3        2
  NOT HISPANIC OR LATINO       65       46       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 21 13
  subtype2 10 14
  subtype3 26 18
  subtype4 16 12
  subtype5 20  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      34       24       44       28       29 
subtype1 subtype2 subtype3 subtype4 subtype5 
      13       14       18       12        9 
$subtype1
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       48.99        37.32        10.13        25.32        69.57         5.03 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
        2.86         3.39         0.07         0.13        37.78         7.33 
TCGA-DD-A1EC TCGA-DD-A1EI TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       19.79         6.02       107.11        33.14        32.52        73.38 
TCGA-DD-A4NS TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A3JL 
       80.75        12.69        13.91         0.20         0.20         9.96 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X 
       27.88         0.13         0.03        51.06        28.27        58.49 
TCGA-HP-A5MZ TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V 
        2.66         5.10         1.71         4.44 

$subtype2
TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       27.91        27.52         2.99        44.42        13.84        22.36 
TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A1EG TCGA-DD-A39Y 
        0.16         4.24         3.32         0.10        45.11         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-ED-A459 TCGA-EP-A2KA 
        7.66        13.78        12.26         0.30        13.41        11.74 
TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75I 
        8.12         1.22        11.97         1.02         0.49         8.71 

$subtype3
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 
       46.78        27.52        23.34         1.12         0.26         9.50 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        0.10        83.57         2.60         0.46        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI 
       66.31        18.35        70.06       102.74        21.70        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A 
       15.06        39.78        56.25        73.81        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        9.30         7.56        27.72        22.85        14.40        19.10 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
        6.38         0.33        53.79        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-K7-A6G5 
        5.92        14.70         9.93         4.37         5.98         4.01 
TCGA-MI-A75G TCGA-NI-A4U2 
       14.24        58.88 

$subtype4
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EF 
       14.60         0.07         0.39        79.73       113.00        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A9 
       49.15        29.16        55.69        19.76        17.59        30.61 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       14.24        29.56       100.96        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B 
        0.20         0.20         0.20         0.20        10.98        32.45 
TCGA-FV-A4ZP TCGA-G3-A25Y TCGA-G3-A7M9 TCGA-KR-A7K2 
       60.36        14.86         1.84        11.84 

$subtype5
TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       12.72        53.33        79.40        75.65         6.71        13.64 
TCGA-DD-A39V TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP 
       21.14        20.12         0.36        14.07        14.63        93.67 
TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       10.98         1.45         0.20        18.74        19.99         0.62 
TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       11.93         0.39        19.53        19.23         7.99         7.76 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75H TCGA-NI-A8LF 
        2.14        13.38         9.57        12.85        16.37 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.10     0.07     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11    45.11   102.74   113.00    93.67 
subtype1 subtype2 subtype3 subtype4 subtype5 
  11.410    8.415   18.770   14.730   13.380 
[1] "0.0 - 107.1 (11.4)" "0.1 - 45.1 (8.4)"   "0.1 - 102.7 (18.8)"
[4] "0.1 - 113.0 (14.7)" "0.2 - 93.7 (13.4)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      12        7         0          6          0          4        1
  subtype2       5        7         0          8          1          1        0
  subtype3      25        5         1          9          0          0        0
  subtype4       8       10         1          5          2          1        0
  subtype5      14        8         0          6          1          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         0
  subtype3         1         1
  subtype4         0         1
  subtype5         0         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          12        5       25        8       14
  STAGE II          7        7        5       10        8
  STAGE III         0        0        1        1        0
  STAGE IIIA        6        8        9        5        6
  STAGE IIIB        0        1        0        2        1
  STAGE IIIC        4        1        0        1        0
  STAGE IV          1        0        0        0        0
  STAGE IVA         0        0        1        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 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 13  9  9  3
  subtype2  5  9  9  2
  subtype3 26  5 11  3
  subtype4  9 10  8  1
  subtype5 14  8  7  0
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       13        5       26        9       14
  T2        9        9        5       10        8
  T3        9        9       11        8        7
  T4        3        2        3        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 20  1
  subtype2 15  0
  subtype3 30  1
  subtype4 19  1
  subtype5 19  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   15    0
  subtype3   30    1
  subtype4   19    1
  subtype5   19    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       20       15       30       19       19
  1        1        0        1        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 24  1  9
  subtype2 18  0  7
  subtype3 33  1 11
  subtype4 25  1  2
  subtype5 22  0  8
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       24       18       33       25       22
  M1        1        0        1        1        0
  MX        9        7       11        2        8
[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 17 17
  subtype2  9 16
  subtype3 15 30
  subtype4 18 10
  subtype5  3 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   17
  subtype2    9   16
  subtype3   15   30
  subtype4   18   10
  subtype5    3   27
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17        9       15       18        3
  MALE         17       16       30       10       27
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       2                       31
  subtype2                       0                       25
  subtype3                       0                       45
  subtype4                       0                       27
  subtype5                       0                       30
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                0
  subtype4                                1
  subtype5                                0
D3V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 2        0        0        0        0
  HEPATOCELLULAR CARCINOMA               31       25       45       27       30
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        0        0        1        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 26  3  1  2
  subtype2 17  4  0  3
  subtype3 38  3  0  4
  subtype4 25  1  0  2
  subtype5 27  0  0  1
D3V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       26       17       38       25       27
  R1        3        4        3        1        0
  R2        1        0        0        0        0
  RX        2        3        4        2        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                         2
  subtype2                                0     8                         1
  subtype3                                0     5                         2
  subtype4                                0    11                         0
  subtype5                                1     4                         3
          vv
clus       WHITE
  subtype1    20
  subtype2    14
  subtype3    37
  subtype4    16
  subtype5    22
D3V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  10        8        5       11        4
  BLACK OR AFRICAN AMERICAN               2        1        2        0        3
  WHITE                                  20       14       37       16       22
[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, binary
          cls
clus        0  1
  subtype1  1 31
  subtype2  1 20
  subtype3  2 40
  subtype4  0 26
  subtype5  0 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   31
  subtype2    1   20
  subtype3    2   40
  subtype4    0   26
  subtype5    0   27
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        1        2        0        0
  NOT HISPANIC OR LATINO       31       20       40       26       27
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 36 28
  subtype2 36 29
  subtype3 21  9
subtype1 subtype2 subtype3 
      64       65       30 
subtype1 subtype2 subtype3 
      28       29        9 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 
       48.99        27.91        37.32        10.13         2.99         5.03 
TCGA-BC-A216 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       44.42        14.60         0.07         0.16         2.86         0.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH 
       37.78       113.00         7.33        19.79        12.95        49.15 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       55.69         5.62        19.76        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH 
       13.78        30.61        33.14        32.52        73.38        14.24 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73G TCGA-ED-A459 
       15.06        29.56        12.26         0.30       100.96        13.41 
TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E 
       15.85        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 
        0.20         0.20        11.74        10.98        32.45        27.88 
TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        0.13        60.36        51.06        58.49        14.86        25.64 
TCGA-G3-A5SJ TCGA-G3-A7M9 TCGA-MI-A75C TCGA-MR-A8JO 
       11.97         1.84         9.57         1.71 

$subtype2
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5262 
       69.57        13.84         0.26        22.36         9.50         3.39 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        0.10        83.57         2.60         0.46        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A3A1 TCGA-DD-A3A2 
       66.31        45.11         6.02        18.35         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NS 
      102.74        21.70        18.44        39.78        73.81        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A4XI 
       66.35        10.98         9.30         7.56        27.72        12.69 
TCGA-ED-A627 TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 
       13.91         9.96        22.85        14.40        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        6.38         0.03         0.33         1.22        53.79        28.27 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM 
       21.53        22.13         5.92        14.70         9.93         4.37 
TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-LG-A6GG 
        5.98         1.02         2.66         4.01        11.84         0.49 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24         8.71        58.88         4.44 

$subtype3
TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EJ 
       12.72        53.33        79.40        75.65         6.71        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NL 
       13.64        21.14         0.36        14.07        14.63        56.25 
TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J 
       93.67        10.98         1.45         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK 
       19.99         0.62        11.93         0.39        19.53        19.23 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-NI-A8LF 
        7.99         7.76         2.14        13.38        12.85        16.37 

subtype1 subtype2 subtype3 
    0.07     0.03     0.20 
subtype1 subtype2 subtype3 
  113.00   102.74    93.67 
subtype1 subtype2 subtype3 
  13.595   13.910   13.510 
[1] "0.1 - 113.0 (13.6)" "0.0 - 102.7 (13.9)" "0.2 - 93.7 (13.5)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      16       17         1         19          3          3        1
  subtype2      34       11         1         10          0          2        0
  subtype3      14        9         0          5          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         1
  subtype3         0         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          16       34       14
  STAGE II         17       11        9
  STAGE III         1        1        0
  STAGE IIIA       19       10        5
  STAGE IIIB        3        0        1
  STAGE IIIC        3        2        1
  STAGE IV          1        0        0
  STAGE IVA         0        1        0
  STAGE IVB         1        1        0
[1] 9 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 16 19 26  4
  subtype2 36 13 12  5
  subtype3 15  9  6  0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       16       36       15
  T2       19       13        9
  T3       26       12        6
  T4        4        5        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"
D4V5, binary
          cls
clus        0  1
  subtype1 45  1
  subtype2 40  1
  subtype3 18  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    1
  subtype2   40    1
  subtype3   18    1
   clus
vv  subtype1 subtype2 subtype3
  0       45       40       18
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 53  2 10
  subtype2 46  1 19
  subtype3 23  0  8
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       53       46       23
  M1        2        1        0
  MX       10       19        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"
D4V7, binary
          cls
clus        0  1
  subtype1 35 30
  subtype2 23 43
  subtype3  4 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   30
  subtype2   23   43
  subtype3    4   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       23        4
  MALE         30       43       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       2                       62
  subtype2                       0                       65
  subtype3                       0                       31
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                1
  subtype3                                0
D4V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 2        0        0
  HEPATOCELLULAR CARCINOMA               62       65       31
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        1        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"
          vv
clus       R0 R1 R2 RX
  subtype1 52  5  1  6
  subtype2 53  6  0  5
  subtype3 28  0  0  1
D4V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       52       53       28
  R1        5        6        0
  R2        1        0        0
  RX        6        5        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    26                         1
  subtype2                                0     7                         4
  subtype3                                1     5                         3
          vv
clus       WHITE
  subtype1    36
  subtype2    51
  subtype3    22
D4V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  26        7        5
  BLACK OR AFRICAN AMERICAN               1        4        3
  WHITE                                  36       51       22
[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"
D4V11, binary
          cls
clus        0  1
  subtype1  1 60
  subtype2  3 56
  subtype3  0 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   60
  subtype2    3   56
  subtype3    0   28
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       60       56       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 17 18
  subtype2 46 23
  subtype3 38 25
subtype1 subtype2 subtype3 
      35       69       63 
subtype1 subtype2 subtype3 
      18       23       25 
$subtype1
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT 
       27.91        10.13        23.34         1.12         3.39         3.32 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EG 
        0.10        83.57        21.76        51.29        66.31        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 
       18.35        13.64         5.62        70.06       102.74        13.78 
TCGA-DD-A73F TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-EP-A3RK 
       27.72         0.20         0.20         0.20         9.96        11.93 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25Z 
       19.10         8.12         0.03         1.22        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A7M9 TCGA-MI-A75I TCGA-ZS-A9CF 
       22.13         5.92         1.84         8.71        74.24 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 
        7.10        46.78        27.52         2.99        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-CC-5263 
        0.26        22.36         9.50        12.72         7.46         4.24 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EA 
       79.73        53.33       113.00         2.60         0.46        79.40 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 
       19.79         6.71        12.95        21.14        19.76         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NF 
       17.59        20.12       107.11         0.36        33.14        14.07 
TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B 
       14.63        93.67        12.26         0.30        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y 
        7.56        10.98         1.45        13.41        15.85         0.23 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
        0.20         0.20         0.20        18.74        19.99        10.98 
TCGA-ES-A2HS TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK 
       22.85         0.33        60.36        53.79        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-KR-A7K2 
       14.70         9.93         7.99         7.76         1.02        11.84 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 
        0.49         5.92         9.57        14.24        12.85        58.88 
TCGA-NI-A8LF TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       16.37        12.99        35.05 

$subtype3
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       48.99        37.32        27.52        25.32        69.57         5.03 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 
       14.60         0.07         0.16         2.86         0.39         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1ED TCGA-DD-A1EH 
        0.07         0.13        37.78         7.33        75.65        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NB 
        6.02        29.16        55.69        25.81        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        21.70        14.24        18.44        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A627 
       73.81        80.75        66.35       100.96        12.69        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KC 
       13.35         0.20         0.20         0.20        11.74         0.62 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
       14.40        32.45        27.88         0.39        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M7 
       58.49        14.86        25.64        11.97         4.37         5.98 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75E 
        2.66         4.01         2.14        13.38         4.27         5.10 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-YA-A8S7 
        1.71         4.44        13.55 

subtype1 subtype2 subtype3 
    0.03     0.20     0.07 
subtype1 subtype2 subtype3 
  102.74   113.00   100.96 
subtype1 subtype2 subtype3 
   13.64    12.95    14.24 
[1] "0.0 - 102.7 (13.6)" "0.2 - 113.0 (12.9)" "0.1 - 101.0 (14.2)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      15        5         1          7          3          1        0
  subtype2      25       22         0         15          1          2        0
  subtype3      24       12         1         16          1          4        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         0
  subtype3         0         1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          15       25       24
  STAGE II          5       22       12
  STAGE III         1        0        1
  STAGE IIIA        7       15       16
  STAGE IIIB        3        1        1
  STAGE IIIC        1        2        4
  STAGE IV          0        0        1
  STAGE IVA         1        0        0
  STAGE IVB         1        0        1
[1] 9 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 16  6 12  3
  subtype2 26 24 17  2
  subtype3 26 13 20  5
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       16       26       26
  T2        6       24       13
  T3       12       17       20
  T4        3        2        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 25  1
  subtype2 41  1
  subtype3 42  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    1
  subtype2   41    1
  subtype3   42    1
   clus
vv  subtype1 subtype2 subtype3
  0       25       41       42
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 24  1 12
  subtype2 55  0 15
  subtype3 49  2 13
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       24       55       49
  M1        1        0        2
  MX       12       15       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"
D5V7, binary
          cls
clus        0  1
  subtype1 12 25
  subtype2 28 42
  subtype3 24 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   25
  subtype2   28   42
  subtype3   24   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       28       24
  MALE         25       42       40
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       37
  subtype2                       0                       69
  subtype3                       2                       60
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                1
  subtype3                                2
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        0        2
  HEPATOCELLULAR CARCINOMA               37       69       60
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        1        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 27  3  0  3
  subtype2 61  4  0  4
  subtype3 53  4  1  6
D5V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       27       61       53
  R1        3        4        4
  R2        0        0        1
  RX        3        4        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     8                         2
  subtype2                                1    15                         2
  subtype3                                0    18                         4
          vv
clus       WHITE
  subtype1    25
  subtype2    50
  subtype3    40
D5V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   8       15       18
  BLACK OR AFRICAN AMERICAN               2        2        4
  WHITE                                  25       50       40
[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, binary
          cls
clus        0  1
  subtype1  0 34
  subtype2  2 61
  subtype3  4 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    2   61
  subtype3    4   56
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        4
  NOT HISPANIC OR LATINO       34       61       56
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  7 11
  subtype2 28 16
  subtype3 38 29
  subtype4 10  6
  subtype5 18  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       44       67       16       22 
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       16       29        6        4 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       48.99        27.91         1.12         3.39         4.24         3.32 
TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-ED-A7PZ 
       83.57        45.11        18.35        13.64        27.72         0.20 
TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M9 TCGA-MI-A75I 
        0.20         9.96         0.03         1.22         1.84         8.71 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
        7.10        10.13        46.78        27.52        27.52        23.34 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-CC-A3MB TCGA-DD-A113 
       13.84        22.36         9.50         7.46         0.10        79.73 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A3A1 TCGA-DD-A3A2 
        2.60        21.76        51.29        66.31         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73A 
      102.74        13.78        14.63        12.26        66.35        10.98 
TCGA-DD-A73C TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25U 
        7.56        11.93        19.10         8.12         0.33        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SJ 
       28.27        30.74        21.53        22.13         5.92        11.97 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-NI-A4U2 
        9.93         4.37         1.02        11.84         0.49        58.88 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5260 
       37.32         2.99        25.32        69.57         5.03         2.86 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        0.39         0.07         0.13        37.78       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X 
        0.46        19.79        12.95        49.15         6.02        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 
       19.76        25.81        17.59        20.12       107.11        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        21.70        14.24        18.44 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73G 
       56.25        29.56        73.81        80.75         9.30       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-ES-A2HT 
        0.20        11.74        10.98         0.62        22.85        14.40 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI 
       27.88        51.06        58.49        14.86        25.64        14.70 
TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO 
        5.98         2.66         4.01         4.27         5.10         1.71 
TCGA-O8-A75V 
        4.44 

$subtype4
TCGA-BC-A216 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 TCGA-DD-A1EJ 
       44.42        14.60         0.07         0.16         0.10        29.16 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A4NR TCGA-FV-A23B TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       21.14         5.62         0.30        32.45        60.36         0.39 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75G TCGA-YA-A8S7 
       13.38         9.57        14.24        13.55 

$subtype5
TCGA-BC-A3KF TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE 
        0.26        12.72        53.33        79.40        75.65         6.71 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-EP-A12J 
        0.36        14.07        93.67        10.98         1.45        18.74 
TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K0 
       19.99        19.53        19.23         7.99         7.76         2.14 
TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF TCGA-ZP-A9D4 
        5.92        12.85        16.37        12.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.07     0.07     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   83.57   102.74   113.00    60.36    93.67 
subtype1 subtype2 subtype3 subtype4 subtype5 
   6.475   14.235   14.240   13.465   12.920 
[1] "0.0 - 83.6 (6.5)"   "0.1 - 102.7 (14.2)" "0.1 - 113.0 (14.2)"
[4] "0.1 - 60.4 (13.5)"  "0.3 - 93.7 (12.9)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       6        3         0          6          1          1        0
  subtype2      16       11         1          8          2          1        0
  subtype3      26       15         1         15          1          3        1
  subtype4       4        6         0          6          0          2        0
  subtype5      12        4         0          3          1          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         1
  subtype4         0         0
  subtype5         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       16       26        4       12
  STAGE II          3       11       15        6        4
  STAGE III         0        1        1        0        0
  STAGE IIIA        6        8       15        6        3
  STAGE IIIB        1        2        1        0        1
  STAGE IIIC        1        1        3        2        0
  STAGE IV          0        0        1        0        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         1        0        1        0        0
[1] 9 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  6  4  7  2
  subtype2 17 12 13  3
  subtype3 27 17 19  4
  subtype4  5  6  6  1
  subtype5 13  4  4  0
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6       17       27        5       13
  T2        4       12       17        6        4
  T3        7       13       19        6        4
  T4        2        3        4        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 13  0
  subtype2 25  1
  subtype3 45  1
  subtype4 11  1
  subtype5 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    0
  subtype2   25    1
  subtype3   45    1
  subtype4   11    1
  subtype5   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       25       45       11       14
  1        0        1        1        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 12  1  6
  subtype2 32  0 13
  subtype3 51  2 14
  subtype4 17  0  1
  subtype5 16  0  6
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       12       32       51       17       16
  M1        1        0        2        0        0
  MX        6       13       14        1        6
[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"
D6V7, binary
          cls
clus        0  1
  subtype1  6 13
  subtype2 17 28
  subtype3 31 36
  subtype4  7 11
  subtype5  3 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   13
  subtype2   17   28
  subtype3   31   36
  subtype4    7   11
  subtype5    3   19
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        6       17       31        7        3
  MALE         13       28       36       11       19
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       19
  subtype2                       0                       44
  subtype3                       2                       63
  subtype4                       0                       18
  subtype5                       0                       22
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                1
  subtype3                                2
  subtype4                                0
  subtype5                                0
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        2        0        0
  HEPATOCELLULAR CARCINOMA               19       44       63       18       22
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        1        2        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"
          vv
clus       R0 R1 R2 RX
  subtype1 11  3  0  2
  subtype2 37  4  0  3
  subtype3 58  3  1  5
  subtype4 14  1  0  3
  subtype5 21  0  0  0
D6V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       11       37       58       14       21
  R1        3        4        3        1        0
  R2        0        0        1        0        0
  RX        2        3        5        3        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         2
  subtype2                                0     3                         1
  subtype3                                0    24                         4
  subtype4                                0     6                         0
  subtype5                                1     3                         1
          vv
clus       WHITE
  subtype1    12
  subtype2    38
  subtype3    36
  subtype4    12
  subtype5    17
D6V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   5        3       24        6        3
  BLACK OR AFRICAN AMERICAN               2        1        4        0        1
  WHITE                                  12       38       36       12       17
[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"
D6V11, binary
          cls
clus        0  1
  subtype1  0 18
  subtype2  1 39
  subtype3  4 60
  subtype4  1 15
  subtype5  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   18
  subtype2    1   39
  subtype3    4   60
  subtype4    1   15
  subtype5    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        4        1        0
  NOT HISPANIC OR LATINO       18       39       60       15       19
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 14  5
  subtype2 19 10
  subtype3 14 17
  subtype4 36 18
  subtype5 18 16
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       29       31       54       34 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       10       17       18       16 
$subtype1
TCGA-BC-4072 TCGA-BC-A10X TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 
       48.99        25.32        14.60         0.07         0.16         0.10 
TCGA-CC-A3MB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-ED-A459 TCGA-ED-A627 
        0.10        75.65        49.15        29.16        13.41        13.91 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A7M9 
       13.35         0.20        32.45        27.88         0.39         1.84 
TCGA-KR-A7K7 
       13.38 

$subtype2
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A110 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
       10.13        27.52        69.57         0.07         0.13        37.78 
TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4ND 
        7.33         6.02        55.69        25.81        32.52        73.38 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-ED-A4XI TCGA-ED-A7PX TCGA-ED-A7XO 
       73.81        80.75        66.35        12.69         0.20         0.20 
TCGA-ES-A2HT TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M7 
       14.40        28.27        58.49        25.64         4.37         5.98 
TCGA-HP-A5MZ TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V 
        2.66         4.27         5.10         1.71         4.44 

$subtype3
TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A8YO 
       27.91        27.52        23.34         1.12        13.84         7.46 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EG 
        3.39         3.32        83.57        21.76        51.29        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A73F 
       18.35        13.64         7.66       102.74        13.78        27.72 
TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 
        0.20         9.96        11.93        19.10         8.12         0.03 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-GJ-A6C0 TCGA-LG-A6GG 
        1.22        30.74        21.53        22.13         1.02         0.49 
TCGA-MI-A75I 
        8.71 

$subtype4
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        7.10        46.78         2.99        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        9.50        12.72        53.33       113.00         2.60         0.46 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A2 
       79.40        66.31         6.71        21.14        19.76        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI 
       20.12       107.11         0.36        14.07        14.63        18.44 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       56.25        93.67         9.30         7.56        10.98         1.45 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
        0.20        18.74        19.99        10.98         0.62        22.85 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK 
        0.33        53.79         5.92        19.53        19.23         9.93 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75G 
        7.99         7.76         2.14         5.92         9.57        14.24 
TCGA-MI-A75H TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       12.85        58.88        16.37        12.99        35.05        74.24 

$subtype5
TCGA-BC-A10Q TCGA-BC-A112 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 
       37.32         5.03         2.86         0.39         4.24        79.73 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A9 TCGA-DD-A4NA 
       19.79        12.95         5.62        17.59        30.61        33.14 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A 
       21.70        14.24        29.56        12.26         0.30        10.98 
TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 
      100.96        15.85         0.23         0.20         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A5SI 
        0.20        11.74        60.36        51.06        14.86        14.70 
TCGA-G3-A5SJ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-YA-A8S7 
       11.97         4.01        11.84        13.55 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.07     0.03     0.20     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
   75.65    80.75   102.74   113.00   100.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.410   12.690   13.780   14.155   12.605 
[1] "0.1 - 75.7 (13.4)"  "0.1 - 80.8 (12.7)"  "0.0 - 102.7 (13.8)"
[4] "0.2 - 113.0 (14.2)" "0.2 - 101.0 (12.6)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       4        7         1          6          1          2        0
  subtype2      13        5         0          6          0          1        1
  subtype3      10        6         1          6          2          2        0
  subtype4      25       15         0          9          1          0        0
  subtype5      12        6         0         11          1          2        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         0
  subtype3         1         1
  subtype4         0         0
  subtype5         0         1
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           4       13       10       25       12
  STAGE II          7        5        6       15        6
  STAGE III         1        0        1        0        0
  STAGE IIIA        6        6        6        9       11
  STAGE IIIB        1        0        2        1        1
  STAGE IIIC        2        1        2        0        2
  STAGE IV          0        1        0        0        0
  STAGE IVA         0        0        1        0        0
  STAGE IVB         0        0        1        0        1
[1] 9 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  7  8  1
  subtype2 14  5  8  2
  subtype3 11  8  9  4
  subtype4 26 15 11  1
  subtype5 12  8 13  2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        5       14       11       26       12
  T2        7        5        8       15        8
  T3        8        8        9       11       13
  T4        1        2        4        1        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 13  1
  subtype2 17  0
  subtype3 22  1
  subtype4 29  0
  subtype5 27  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   17    0
  subtype3   22    1
  subtype4   29    0
  subtype5   27    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       17       22       29       27
  1        1        0        1        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 18  0  3
  subtype2 21  1  7
  subtype3 21  1 10
  subtype4 39  0 15
  subtype5 29  1  5
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       18       21       21       39       29
  M1        0        1        1        0        1
  MX        3        7       10       15        5
[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"
D7V7, binary
          cls
clus        0  1
  subtype1  8 13
  subtype2  6 23
  subtype3 13 19
  subtype4 17 37
  subtype5 20 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   13
  subtype2    6   23
  subtype3   13   19
  subtype4   17   37
  subtype5   20   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        8        6       13       17       20
  MALE         13       23       19       37       15
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       20
  subtype2                       2                       27
  subtype3                       0                       32
  subtype4                       0                       54
  subtype5                       0                       33
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                0
  subtype4                                0
  subtype5                                2
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        2        0        0        0
  HEPATOCELLULAR CARCINOMA               20       27       32       54       33
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        0        0        0        2
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 17  1  0  3
  subtype2 25  2  1  1
  subtype3 21  4  0  3
  subtype4 50  2  0  1
  subtype5 28  2  0  5
D7V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       17       25       21       50       28
  R1        1        2        4        2        2
  R2        0        1        0        0        0
  RX        3        1        3        1        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     8                         0
  subtype2                                0     9                         3
  subtype3                                0     4                         2
  subtype4                                1     6                         3
  subtype5                                0    14                         0
          vv
clus       WHITE
  subtype1    13
  subtype2    15
  subtype3    24
  subtype4    42
  subtype5    21
D7V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   8        9        4        6       14
  BLACK OR AFRICAN AMERICAN               0        3        2        3        0
  WHITE                                  13       15       24       42       21
[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"
D7V11, binary
          cls
clus        0  1
  subtype1  0 20
  subtype2  2 25
  subtype3  0 28
  subtype4  1 47
  subtype5  3 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   20
  subtype2    2   25
  subtype3    0   28
  subtype4    1   47
  subtype5    3   31
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        0        1        3
  NOT HISPANIC OR LATINO       20       25       28       47       31
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  7 10
  subtype2 23 14
  subtype3 15 14
  subtype4 39 23
  subtype5 17  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       37       29       62       22 
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       14       14       23        5 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 
       48.99        27.91         1.12         3.39         3.32        83.57 
TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-ED-A7PZ TCGA-ED-A8O5 
       45.11        18.35        13.64        27.72         0.20         0.20 
TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M9 TCGA-MI-A75I 
        9.96         0.03         1.22         1.84         8.71 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A217 
        7.10        46.78        27.52        27.52        23.34        13.84 
TCGA-BC-A3KG TCGA-BC-A8YO TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
       22.36         7.46         2.60        21.76        51.29        66.31 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NV 
        7.66        70.06       102.74        13.78        14.63        66.35 
TCGA-DD-A73A TCGA-DD-A73C TCGA-ED-A7XO TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 
       10.98         7.56         0.20        11.93        19.10         8.12 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       53.79        28.27        30.74        21.53        22.13         5.92 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-NI-A4U2 TCGA-ZS-A9CE 
        9.93         4.37         1.02         0.49        58.88        35.05 
TCGA-ZS-A9CF 
       74.24 

$subtype3
TCGA-BC-A216 TCGA-BC-A5W4 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A118 
       44.42         9.50         0.16         0.39         4.24       113.00 
TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 
        0.46        12.95        21.14         5.62        19.76        17.59 
TCGA-DD-A3A9 TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73B TCGA-DD-A73G 
       30.61        29.56        12.26         0.30         9.30       100.96 
TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A2KB 
       15.85         0.23         0.20         0.20         0.20        10.98 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A5SI TCGA-MI-A75C TCGA-MI-A75G 
        0.33        60.36        14.70         9.57        14.24 

$subtype4
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       37.32        10.13         2.99        25.32        69.57         5.03 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
       14.60         0.07         2.86         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1ED 
        0.13        79.73        37.78         7.33        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A4 
       49.15         6.02        29.16        55.69        25.81        20.12 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        21.70        14.24        18.44 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NS TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 
       56.25        73.81        80.75        13.41        12.69        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KC 
       13.35         0.20         0.20         0.20        11.74         0.62 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
       22.85        14.40        32.45        27.88         0.39        51.06 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-HP-A5MZ 
       58.49        14.86        25.64        11.97         5.98         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO 
        4.01        11.84        13.38         4.27         5.10         1.71 
TCGA-O8-A75V TCGA-YA-A8S7 
        4.44        13.55 

$subtype5
TCGA-BC-A3KF TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A3A6 
        0.26        12.72        53.33        79.40         6.71       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-EP-A12J 
        0.36        14.07        93.67        10.98         1.45        18.74 
TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-KR-A7K0 
       19.99        19.53        19.23         7.99         7.76         2.14 
TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF TCGA-ZP-A9D4 
        5.92        12.85        16.37        12.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.20     0.16     0.07     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   83.57   102.74   113.00    80.75   107.11 
subtype1 subtype2 subtype3 subtype4 subtype5 
    8.71    21.53    10.98    13.73    12.92 
[1] "0.0 - 83.6 (8.7)"   "0.2 - 102.7 (21.5)" "0.2 - 113.0 (11.0)"
[4] "0.1 - 80.8 (13.7)"  "0.3 - 107.1 (12.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       6        3         0          5          1          1        0
  subtype2      13        9         1          7          2          1        0
  subtype3      11       10         0          7          0          1        0
  subtype4      23       12         1         16          1          4        1
  subtype5      11        5         0          3          1          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         1
  subtype4         0         0
  subtype5         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       13       11       23       11
  STAGE II          3        9       10       12        5
  STAGE III         0        1        0        1        0
  STAGE IIIA        5        7        7       16        3
  STAGE IIIB        1        2        0        1        1
  STAGE IIIC        1        1        1        4        0
  STAGE IV          0        0        0        1        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         1        0        1        0        0
[1] 9 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  6  4  6  2
  subtype2 14 10 11  3
  subtype3 11 10  7  2
  subtype4 25 14 21  3
  subtype5 12  5  4  0
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6       14       11       25       12
  T2        4       10       10       14        5
  T3        6       11        7       21        4
  T4        2        3        2        3        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2 22  1
  subtype3 21  0
  subtype4 39  2
  subtype5 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2   22    1
  subtype3   21    0
  subtype4   39    2
  subtype5   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12       22       21       39       14
  1        0        1        0        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 11  1  6
  subtype2 26  0 12
  subtype3 28  1  1
  subtype4 47  1 15
  subtype5 16  0  6
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       11       26       28       47       16
  M1        1        0        1        1        0
  MX        6       12        1       15        6
[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"
D8V7, binary
          cls
clus        0  1
  subtype1  6 12
  subtype2 14 24
  subtype3 17 13
  subtype4 23 40
  subtype5  4 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   12
  subtype2   14   24
  subtype3   17   13
  subtype4   23   40
  subtype5    4   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        6       14       17       23        4
  MALE         12       24       13       40       18
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       18
  subtype2                       0                       38
  subtype3                       0                       30
  subtype4                       2                       58
  subtype5                       0                       22
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                0
  subtype3                                0
  subtype4                                3
  subtype5                                0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        2        0
  HEPATOCELLULAR CARCINOMA               18       38       30       58       22
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        0        0        3        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"
          vv
clus       R0 R1 R2 RX
  subtype1 11  3  0  1
  subtype2 31  3  0  3
  subtype3 24  2  0  4
  subtype4 54  3  1  5
  subtype5 21  0  0  0
D8V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       11       31       24       54       21
  R1        3        3        2        3        0
  R2        0        0        0        1        0
  RX        1        3        4        5        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         2
  subtype2                                0     3                         1
  subtype3                                0    12                         0
  subtype4                                0    19                         4
  subtype5                                1     3                         1
          vv
clus       WHITE
  subtype1    12
  subtype2    31
  subtype3    17
  subtype4    38
  subtype5    17
D8V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   4        3       12       19        3
  BLACK OR AFRICAN AMERICAN               2        1        0        4        1
  WHITE                                  12       31       17       38       17
[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"
D8V11, binary
          cls
clus        0  1
  subtype1  0 17
  subtype2  0 34
  subtype3  2 26
  subtype4  4 55
  subtype5  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   17
  subtype2    0   34
  subtype3    2   26
  subtype4    4   55
  subtype5    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        2        4        0
  NOT HISPANIC OR LATINO       17       34       26       55       19
[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"
