[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"       "-oTACC-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/ACC-TP/10005775/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/10668128/ACC-TP.mergedcluster.txt"

nPatients in clinical file=82, in cluster file=92, common to both=82
[1]  8 82
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
27 21 14  9  9 
 1  2  3  4  5 
27 21 14  9  9 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
18 11 21 17 11 
 1  2  3  4  5 
18 11 21 17 11 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
24 14 17 22 
 1  2  3  4 
24 14 17 22 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
23 23  7 24 
 1  2  3  4 
23 23  7 24 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
38 15 25 
 1  2  3 
38 15 25 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
17 25 12 20  4 
 1  2  3  4  5 
17 25 12 20  4 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
39 17 22 
 1  2  3 
39 17 22 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
 9 23  9 18  9 10 
 1  2  3  4  5  6 
 9 23  9 18  9 10 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 82 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
          NA           NA         1942           NA           NA         2428 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
          NA           NA         1183           NA           NA           NA 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
        2782           NA         1259           NA         1227         1424 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
         309         1255          670           NA          889          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
         674         3688          383          488           NA         1541 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        1924          950           NA          211         1029         2723 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
          NA         2842          528          253         1130           NA 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
        1414         2673         4673         3659         1525         1091 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
          NA           NA         3897          724          840          628 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
         555          645          487           NA           NA           NA 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
          NA           NA         1589           NA           NA         2222 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
          NA         1858         1916         1949         1583          639 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OF TCGA-P6-A5OG TCGA-P6-A5OH 
         882          365          709           NA           NA           NA 
TCGA-PK-A5H8 TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
        3240          307          830         1293 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 82 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 8 39 11 19 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 8 39 11 19 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 8 39 11 19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 8 39 11 19 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 12 14
  subtype2 20  1
  subtype3  7  7
  subtype4  5  4
  subtype5  8  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      26       21       14        9        9 
subtype1 subtype2 subtype3 subtype4 subtype5 
      14        1        7        4        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JE 
       44.55        55.13        79.82        19.04        18.12        69.21 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JY 
       18.48        29.23         4.90         9.50        50.66        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV 
       33.83        32.68         8.32        37.15        87.88       120.30 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL 
      128.12         5.23        39.35        21.76        52.24        53.03 
TCGA-P6-A5OG TCGA-PK-A5H9 
       12.59        10.09 

$subtype2
TCGA-OR-A5J3 TCGA-OR-A5JF TCGA-OR-A5JK TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX 
       63.85        41.39        41.26       121.25        16.04        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KU TCGA-OR-A5KW 
        6.94        89.52        93.44        17.36       153.63        50.14 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LF 
       23.80        27.62        20.65        21.21        16.01        14.63 
TCGA-OR-A5LM TCGA-OR-A5LP TCGA-OR-A5LR 
       61.08        52.04        21.01 

$subtype3
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JG TCGA-OR-A5JJ 
       15.45        12.00        16.11        38.89        17.79        10.16 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LJ TCGA-OR-A5LO 
       35.87        12.85        18.25        39.58        36.33        64.08 
TCGA-OR-A5LS TCGA-OU-A5PI 
       29.00        23.31 

$subtype4
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JL TCGA-OR-A5JS TCGA-OR-A5JW TCGA-OR-A5K9 
       30.31        57.53        22.03        12.59        63.25        11.31 
TCGA-OR-A5KZ TCGA-PK-A5HA TCGA-PK-A5HB 
        4.11        27.29        42.51 

$subtype5
TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JQ TCGA-OR-A5KO TCGA-OR-A5LH 
       91.46        40.34        46.82        22.16        46.49        78.41 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LT 
       73.05        62.99        12.00 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.90     6.94    10.16     4.11    12.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
  128.12   153.63    64.08    63.25    91.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
  33.255   31.230   20.780   27.290   46.820 
[1] "4.9 - 128.1 (33.3)" "6.9 - 153.6 (31.2)" "10.2 - 64.1 (20.8)"
[4] "4.1 - 63.2 (27.3)"  "12.0 - 91.5 (46.8)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       4        8         7        7
  subtype2       2       12         6        1
  subtype3       0        4         3        7
  subtype4       1        4         0        1
  subtype5       1        6         1        1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          4        2        0        1        1
  STAGE II         8       12        4        4        6
  STAGE III        7        6        3        0        1
  STAGE IV         7        1        7        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  4  9  5  8
  subtype2  2 13  3  3
  subtype3  0  7  2  5
  subtype4  1  4  0  1
  subtype5  1  6  1  1
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4        2        0        1        1
  T2        9       13        7        4        6
  T3        5        3        2        0        1
  T4        8        3        5        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 24  2
  subtype2 20  1
  subtype3  7  7
  subtype4  7  0
  subtype5  9  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    2
  subtype2   20    1
  subtype3    7    7
  subtype4    7    0
  subtype5    9    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       24       20        7        7        9
  1        2        1        7        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 19  8
  subtype2 13  8
  subtype3 10  4
  subtype4  4  5
  subtype5  6  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    8
  subtype2   13    8
  subtype3   10    4
  subtype4    4    5
  subtype5    6    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       19       13       10        4        6
  MALE          8        8        4        5        3
[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"
D1V7, binary
          cls
clus        0  1
  subtype1  3 11
  subtype2  1  7
  subtype3  4  6
  subtype4  0  1
  subtype5  0  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   11
  subtype2    1    7
  subtype3    4    6
  subtype4    0    1
  subtype5    0    2
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        4        0        0
  NOT HISPANIC OR LATINO       11        7        6        1        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  6 12
  subtype2  8  3
  subtype3 14  7
  subtype4 14  3
  subtype5 10  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       11       21       17       11 
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        3        7        3        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JM 
       44.55        15.45        16.11        38.89        69.21        18.48 
TCGA-OR-A5JP TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 
        4.90        18.15        33.83        32.68         8.32        11.31 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
      120.30        35.87         4.11         5.23        39.35        21.76 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5JF TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KW 
       55.13        63.85        41.39        37.15        46.49        50.14 
TCGA-OR-A5L3 TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LT 
      128.12        52.24        36.33        53.03        12.00 

$subtype3
TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ 
       12.00        30.31        57.53        17.79        46.82        10.16 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K3 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L6 
       63.25        31.23        93.44       153.63        12.85        20.65 
TCGA-OR-A5LB TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF 
       39.58        61.08        64.08        29.00        23.31         6.81 
TCGA-PK-A5H8 TCGA-PK-A5HA TCGA-PK-A5HB 
      106.52        27.29        42.51 

$subtype4
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JR 
       79.82        19.04        18.12        41.26        29.23       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5KT 
       16.04        50.66         6.94        89.52        17.36        87.88 
TCGA-OR-A5L4 TCGA-OR-A5L9 TCGA-OR-A5LK TCGA-P6-A5OG TCGA-PK-A5H9 
       23.80        21.21        73.05        12.59        10.09 

$subtype5
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5L5 TCGA-OR-A5L8 
       91.46        22.03        22.16        12.59        27.62        18.25 
TCGA-OR-A5LA TCGA-OR-A5LH TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       16.01        78.41        62.99        52.04        21.01 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.11    12.00     6.81     6.94    12.59 
subtype1 subtype2 subtype3 subtype4 subtype5 
  120.30   128.12   153.63   121.25    91.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
   20.12    50.14    31.23    23.80    22.16 
[1] "4.1 - 120.3 (20.1)"  "12.0 - 128.1 (50.1)" "6.8 - 153.6 (31.2)" 
[4] "6.9 - 121.2 (23.8)"  "12.6 - 91.5 (22.2)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        7         6        4
  subtype2       1        3         4        3
  subtype3       1        7         3        6
  subtype4       3        7         3        3
  subtype5       2        9         0        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        1        1        3        2
  STAGE II         7        3        7        7        9
  STAGE III        6        4        3        3        0
  STAGE IV         4        3        6        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       T1 T2 T3 T4
  subtype1  1  9  3  5
  subtype2  1  5  4  1
  subtype3  1  8  1  7
  subtype4  3  7  1  5
  subtype5  2  9  0  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1        1        1        3        2
  T2        9        5        8        7        9
  T3        3        4        1        1        0
  T4        5        1        7        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"
D2V5, binary
          cls
clus        0  1
  subtype1 14  4
  subtype2  9  2
  subtype3 14  4
  subtype4 16  0
  subtype5 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    4
  subtype2    9    2
  subtype3   14    4
  subtype4   16    0
  subtype5   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       14        9       14       16       11
  1        4        2        4        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 13  5
  subtype2  9  2
  subtype3  7 14
  subtype4  9  8
  subtype5 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    5
  subtype2    9    2
  subtype3    7   14
  subtype4    9    8
  subtype5   11    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13        9        7        9       11
  MALE          5        2       14        8        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"
D2V7, binary
          cls
clus       0 1
  subtype1 3 6
  subtype2 2 6
  subtype3 1 7
  subtype4 2 5
  subtype5 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    2    6
  subtype3    1    7
  subtype4    2    5
  subtype5    0    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        1        2        0
  NOT HISPANIC OR LATINO        6        6        7        5        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 10 14
  subtype2  9  5
  subtype3 12  5
  subtype4 21  1
subtype1 subtype2 subtype3 subtype4 
      24       14       17       22 
subtype1 subtype2 subtype3 subtype4 
      14        5        5        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JM 
       44.55        16.11        19.04        18.12        69.21        18.48 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
        4.90        12.59        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ 
       37.15        11.31        87.88       120.30        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-P6-A5OG 
      128.12         5.23        39.35        21.76        52.24        12.59 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JX TCGA-OR-A5KU 
       55.13        38.89        41.39        10.16        31.23       153.63 
TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LS 
       12.85        18.25        39.58        36.33        64.08        29.00 
TCGA-OU-A5PI TCGA-P6-A5OF 
       23.31         6.81 

$subtype3
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JL 
       63.85        12.00        30.31        57.53        17.79        22.03 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KW 
       50.66        63.25        93.44        17.36        46.49        50.14 
TCGA-OR-A5L4 TCGA-OR-A5LH TCGA-OR-A5LM TCGA-PK-A5H8 TCGA-PK-A5HB 
       23.80        78.41        61.08       106.52        42.51 

$subtype4
TCGA-OR-A5J6 TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JQ 
       79.82        91.46        46.82        41.26        29.23        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5L5 TCGA-OR-A5L6 
      121.25        16.04         6.94        89.52        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP 
       21.21        16.01        73.05        53.03        62.99        52.04 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.01        12.00        10.09        27.29 

subtype1 subtype2 subtype3 subtype4 
    4.11     6.81    12.00     6.94 
subtype1 subtype2 subtype3 subtype4 
  128.12   153.63   106.52   121.25 
subtype1 subtype2 subtype3 subtype4 
  20.400   33.780   50.140   28.425 
[1] "4.1 - 128.1 (20.4)"  "6.8 - 153.6 (33.8)"  "12.0 - 106.5 (50.1)"
[4] "6.9 - 121.2 (28.4)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3        8         8        5
  subtype2       0        6         2        6
  subtype3       1        5         5        3
  subtype4       4       14         1        1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          3        0        1        4
  STAGE II         8        6        5       14
  STAGE III        8        2        5        1
  STAGE IV         5        6        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 10  4  7
  subtype2  0  8  2  4
  subtype3  1  6  1  6
  subtype4  4 14  1  1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        0        1        4
  T2       10        8        6       14
  T3        4        2        1        1
  T4        7        4        6        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 21  3
  subtype2 10  4
  subtype3 12  2
  subtype4 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    3
  subtype2   10    4
  subtype3   12    2
  subtype4   21    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       21       10       12       21
  1        3        4        2        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 16  8
  subtype2 11  3
  subtype3  8  9
  subtype4 13  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    8
  subtype2   11    3
  subtype3    8    9
  subtype4   13    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       16       11        8       13
  MALE          8        3        9        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1  2 11
  subtype2  2  7
  subtype3  2  5
  subtype4  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   11
  subtype2    2    7
  subtype3    2    5
  subtype4    1    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        2        1
  NOT HISPANIC OR LATINO       11        7        5        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  9 14
  subtype2 16  7
  subtype3  4  3
  subtype4 23  1
subtype1 subtype2 subtype3 subtype4 
      23       23        7       24 
subtype1 subtype2 subtype3 subtype4 
      14        7        3        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JP 
       44.55        55.13        16.11        69.21        18.48         4.90 
TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 
       12.59        18.15        33.83        32.68         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LC 
       11.31       120.30        35.87         4.11       128.12         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LL 
       39.35        21.76        52.24        36.33        53.03 

$subtype2
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF 
       63.85        12.00        38.89        30.31        57.53        41.39 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5KO 
       17.79        10.16        41.26        63.25        31.23        46.49 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LM 
      153.63        50.14        12.85        18.25        39.58        61.08 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF TCGA-PK-A5HB 
       64.08        29.00        23.31         6.81        42.51 

$subtype3
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5KT TCGA-P6-A5OG 
       79.82        19.04        18.12        29.23        87.88        12.59 
TCGA-PK-A5H9 
       10.09 

$subtype4
TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       91.46        46.82        22.03        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5L4 
       50.66         6.94        89.52        93.44        17.36        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LH TCGA-OR-A5LK 
       27.62        20.65        21.21        16.01        78.41        73.05 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H8 TCGA-PK-A5HA 
       62.99        52.04        21.01        12.00       106.52        27.29 

subtype1 subtype2 subtype3 subtype4 
    4.11     6.81    10.09     6.94 
subtype1 subtype2 subtype3 subtype4 
  128.12   153.63    87.88   121.25 
subtype1 subtype2 subtype3 subtype4 
  33.830   39.580   19.040   27.455 
[1] "4.1 - 128.1 (33.8)" "6.8 - 153.6 (39.6)" "10.1 - 87.9 (19.0)"
[4] "6.9 - 121.2 (27.5)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2        9         7        5
  subtype2       0        8         5        8
  subtype3       2        1         1        2
  subtype4       4       15         3        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        2        4
  STAGE II         9        8        1       15
  STAGE III        7        5        1        3
  STAGE IV         5        8        2        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 12  4  5
  subtype2  0 10  2  9
  subtype3  2  1  1  2
  subtype4  4 15  1  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        0        2        4
  T2       12       10        1       15
  T3        4        2        1        1
  T4        5        9        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 19  4
  subtype2 16  5
  subtype3  6  0
  subtype4 23  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    4
  subtype2   16    5
  subtype3    6    0
  subtype4   23    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       19       16        6       23
  1        4        5        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 17  6
  subtype2 13 10
  subtype3  5  2
  subtype4 13 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    6
  subtype2   13   10
  subtype3    5    2
  subtype4   13   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       13        5       13
  MALE          6       10        2       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  2 10
  subtype2  3  8
  subtype3  2  3
  subtype4  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   10
  subtype2    3    8
  subtype3    2    3
  subtype4    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        2        0
  NOT HISPANIC OR LATINO       10        8        3        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 23 15
  subtype2  7  8
  subtype3 22  3
subtype1 subtype2 subtype3 
      38       15       25 
subtype1 subtype2 subtype3 
      15        8        3 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        69.21        17.79        10.16        41.26        22.03 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 
        4.90        12.59        32.68        17.36        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       46.49        87.88       120.30        50.14        35.87         4.11 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       23.80        18.25        39.58         5.23        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OF 
       52.24        61.08        64.08        29.00        23.31         6.81 
TCGA-PK-A5H8 TCGA-PK-A5H9 
      106.52        10.09 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JM 
       55.13        19.04        38.89        18.12        41.39        18.48 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K5 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L3 
       18.15        33.83         8.32       153.63        12.85       128.12 
TCGA-OR-A5LJ TCGA-P6-A5OG TCGA-PK-A5HB 
       36.33        12.59        42.51 

$subtype3
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       57.53        91.46        46.82        29.23        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       16.04        50.66        63.25        31.23         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LH 
       93.44        27.62        20.65        21.21        16.01        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       73.05        53.03        62.99        52.04        21.01        12.00 
TCGA-PK-A5HA 
       27.29 

subtype1 subtype2 subtype3 
    4.11     8.32     6.94 
subtype1 subtype2 subtype3 
  120.30   153.63   121.25 
subtype1 subtype2 subtype3 
  29.655   33.830   46.820 
[1] "4.1 - 120.3 (29.7)" "8.3 - 153.6 (33.8)" "6.9 - 121.2 (46.8)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3       12        12        9
  subtype2       1        4         2        7
  subtype3       4       17         2        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3        1        4
  STAGE II        12        4       17
  STAGE III       12        2        2
  STAGE IV         9        7        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"
          vv
clus       T1 T2 T3 T4
  subtype1  3 16  4 13
  subtype2  1  5  3  5
  subtype3  4 17  2  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        1        4
  T2       16        5       17
  T3        4        3        2
  T4       13        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"
D5V5, binary
          cls
clus        0  1
  subtype1 29  7
  subtype2 11  3
  subtype3 24  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    7
  subtype2   11    3
  subtype3   24    0
   clus
vv  subtype1 subtype2 subtype3
  0       29       11       24
  1        7        3        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 12  3
  subtype3 12 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   12    3
  subtype3   12   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       25       12       12
  MALE         13        3       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  5 18
  subtype2  3  5
  subtype3  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   18
  subtype2    3    5
  subtype3    0    5
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        3        0
  NOT HISPANIC OR LATINO       18        5        5
[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 10  7
  subtype2 18  7
  subtype3 12  0
  subtype4 10 10
  subtype5  2  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       25       12       20        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       7        7        0       10        2 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JC 
       44.55        63.85        15.45        12.00        30.31        57.53 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JX TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KW 
       10.16        41.26        31.23        93.44        17.36        50.14 
TCGA-OR-A5KZ TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-P6-A5OF 
        4.11        52.24        61.08        64.08         6.81 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JM 
       55.13        38.89        18.12        91.46        41.39        18.48 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       22.16       121.25        16.04        50.66        63.25        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L6 
        6.94        33.83        89.52       153.63        12.85        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG 
       21.21        78.41        73.05        52.04        21.01        12.59 
TCGA-PK-A5HA 
       27.29 

$subtype3
TCGA-OR-A5J6 TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5KO TCGA-OR-A5L4 
       79.82        46.82        22.03        29.23        46.49        23.80 
TCGA-OR-A5L5 TCGA-OR-A5LA TCGA-OR-A5LN TCGA-OR-A5LT TCGA-PK-A5H8 TCGA-PK-A5H9 
       27.62        16.01        62.99        12.00       106.52        10.09 

$subtype4
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JP TCGA-OR-A5JS 
       16.11        19.04        69.21        17.79         4.90        12.59 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       32.68         8.32        11.31        87.88       120.30        35.87 
TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LJ 
      128.12        18.25         5.23        39.35        21.76        36.33 
TCGA-OR-A5LS TCGA-PK-A5HB 
       29.00        42.51 

$subtype5
TCGA-OR-A5K6 TCGA-OR-A5LB TCGA-OR-A5LL TCGA-OU-A5PI 
       37.15        39.58        53.03        23.31 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.11     6.94    10.09     4.90    23.31 
subtype1 subtype2 subtype3 subtype4 subtype5 
   93.44   153.63   106.52   128.12    53.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  41.260   33.830   28.425   25.380   38.365 
[1] "4.1 - 93.4 (41.3)"   "6.9 - 153.6 (33.8)"  "10.1 - 106.5 (28.4)"
[4] "4.9 - 128.1 (25.4)"  "23.3 - 53.0 (38.4)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        5         7        4
  subtype2       1       17         0        6
  subtype3       4        3         2        1
  subtype4       3        6         7        3
  subtype5       0        2         0        2
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        4        3        0
  STAGE II         5       17        3        6        2
  STAGE III        7        0        2        7        0
  STAGE IV         4        6        1        3        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"
          vv
clus       T1 T2 T3 T4
  subtype1  0  6  4  6
  subtype2  1 17  1  5
  subtype3  4  3  1  2
  subtype4  3  9  3  4
  subtype5  0  3  0  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        1        4        3        0
  T2        6       17        3        9        3
  T3        4        1        1        3        0
  T4        6        5        2        4        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"
D6V5, binary
          cls
clus        0  1
  subtype1 13  3
  subtype2 23  2
  subtype3 10  0
  subtype4 15  4
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    3
  subtype2   23    2
  subtype3   10    0
  subtype4   15    4
  subtype5    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       23       10       15        3
  1        3        2        0        4        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"
D6V6, binary
          cls
clus        0  1
  subtype1  7 10
  subtype2 16  9
  subtype3  9  3
  subtype4 14  6
  subtype5  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   10
  subtype2   16    9
  subtype3    9    3
  subtype4   14    6
  subtype5    3    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        7       16        9       14        3
  MALE         10        9        3        6        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"
D6V7, binary
          cls
clus       0 1
  subtype1 3 4
  subtype2 2 6
  subtype3 1 6
  subtype4 2 9
  subtype5 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    4
  subtype2    2    6
  subtype3    1    6
  subtype4    2    9
  subtype5    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        1        2        0
  NOT HISPANIC OR LATINO        4        6        6        9        3
[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 24 15
  subtype2  7 10
  subtype3 21  1
subtype1 subtype2 subtype3 
      39       17       22 
subtype1 subtype2 subtype3 
      15       10        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        69.21        17.79        10.16        41.26        22.03 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
        4.90        12.59        32.68        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        46.49        87.88       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
        4.11        23.80        18.25        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       21.76        52.24        61.08        64.08        29.00        23.31 
TCGA-P6-A5OF TCGA-PK-A5H8 TCGA-PK-A5H9 
        6.81       106.52        10.09 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JM 
       55.13        19.04        38.89        18.12        41.39        18.48 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L3 
       63.25        18.15        33.83       153.63        12.85       128.12 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5HB 
       78.41        36.33        53.03        12.59        42.51 

$subtype3
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       57.53        91.46        46.82        29.23        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       16.04        50.66        31.23         6.94        89.52        93.44 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LK TCGA-OR-A5LN 
       27.62        20.65        21.21        16.01        73.05        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5HA 
       52.04        21.01        12.00        27.29 

subtype1 subtype2 subtype3 
    4.11    12.59     6.94 
subtype1 subtype2 subtype3 
  120.30   153.63   121.25 
subtype1 subtype2 subtype3 
   29.00    38.89    30.23 
[1] "4.1 - 120.3 (29.0)"  "12.6 - 153.6 (38.9)" "6.9 - 121.2 (30.2)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3       12        13        9
  subtype2       1        7         1        7
  subtype3       4       14         2        0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3        1        4
  STAGE II        12        7       14
  STAGE III       13        1        2
  STAGE IV         9        7        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"
          vv
clus       T1 T2 T3 T4
  subtype1  3 16  5 13
  subtype2  1  8  2  5
  subtype3  4 14  2  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        1        4
  T2       16        8       14
  T3        5        2        2
  T4       13        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"
D7V5, binary
          cls
clus        0  1
  subtype1 30  7
  subtype2 13  3
  subtype3 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    7
  subtype2   13    3
  subtype3   21    0
   clus
vv  subtype1 subtype2 subtype3
  0       30       13       21
  1        7        3        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 26 13
  subtype2 13  4
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   13
  subtype2   13    4
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26       13       10
  MALE         13        4       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1  5 18
  subtype2  3  6
  subtype3  0  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   18
  subtype2    3    6
  subtype3    0    4
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        3        0
  NOT HISPANIC OR LATINO       18        6        4
[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(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  3  6
  subtype2 18  5
  subtype3  9  0
  subtype4  9  9
  subtype5  4  5
  subtype6  9  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       23        9       18        9       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        5        0        9        5        1 
$subtype1
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5KW 
       44.55        63.85        15.45        12.00        30.31        50.14 
TCGA-OR-A5KZ TCGA-OR-A5LO TCGA-P6-A5OF 
        4.11        64.08         6.81 

$subtype2
TCGA-OR-A5J2 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JM TCGA-OR-A5JQ 
       55.13        38.89        91.46        41.39        18.48        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        16.04        50.66        63.25        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5L9 
       33.83        89.52       153.63        12.85        20.65        21.21 
TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5HA 
       78.41        73.05        52.04        21.01        27.29 

$subtype3
TCGA-OR-A5J6 TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5L4 
       79.82        41.26        22.03        17.36        46.49        23.80 
TCGA-OR-A5LG TCGA-OR-A5LM TCGA-PK-A5H8 
       52.24        61.08       106.52 

$subtype4
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JE TCGA-OR-A5JJ TCGA-OR-A5JP TCGA-OR-A5JS 
       16.11        19.04        69.21        10.16         4.90        12.59 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L8 
       32.68         8.32        11.31       120.30        35.87        18.25 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LJ TCGA-OR-A5LS TCGA-PK-A5HB 
        5.23        39.35        21.76        36.33        29.00        42.51 

$subtype5
TCGA-OR-A5JB TCGA-OR-A5JG TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5L3 TCGA-OR-A5LB 
       18.12        17.79        37.15        87.88       128.12        39.58 
TCGA-OR-A5LL TCGA-OU-A5PI TCGA-P6-A5OG 
       53.03        23.31        12.59 

$subtype6
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JX TCGA-OR-A5K3 TCGA-OR-A5L5 
       57.53        46.82        29.23        31.23        93.44        27.62 
TCGA-OR-A5LA TCGA-OR-A5LN TCGA-OR-A5LT TCGA-PK-A5H9 
       16.01        62.99        12.00        10.09 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.11     6.94    17.36     4.90    12.59    10.09 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   64.08   153.63   106.52   120.30   128.12    93.44 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   30.31    38.89    46.49    20.40    37.15    30.23 
[1] "4.1 - 64.1 (30.3)"   "6.9 - 153.6 (38.9)"  "17.4 - 106.5 (46.5)"
[4] "4.9 - 120.3 (20.4)"  "12.6 - 128.1 (37.1)" "10.1 - 93.4 (30.2)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        3         4        2
  subtype2       1       17         0        4
  subtype3       1        2         3        2
  subtype4       1        6         7        3
  subtype5       2        2         0        5
  subtype6       3        3         2        0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          0        1        1        1        2        3
  STAGE II         3       17        2        6        2        3
  STAGE III        4        0        3        7        0        2
  STAGE IV         2        4        2        3        5        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  4  2  3
  subtype2  1 17  1  3
  subtype3  1  2  1  4
  subtype4  1  9  3  4
  subtype5  2  3  0  4
  subtype6  3  3  2  0
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        0        1        1        1        2        3
  T2        4       17        2        9        3        3
  T3        2        1        1        3        0        2
  T4        3        3        4        4        4        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1  7  2
  subtype2 21  2
  subtype3  8  0
  subtype4 13  4
  subtype5  7  2
  subtype6  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2   21    2
  subtype3    8    0
  subtype4   13    4
  subtype5    7    2
  subtype6    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0        7       21        8       13        7        8
  1        2        2        0        4        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1  6  3
  subtype2 15  8
  subtype3  5  4
  subtype4 12  6
  subtype5  6  3
  subtype6  5  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2   15    8
  subtype3    5    4
  subtype4   12    6
  subtype5    6    3
  subtype6    5    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        6       15        5       12        6        5
  MALE          3        8        4        6        3        5
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 2 5
  subtype3 1 4
  subtype4 2 7
  subtype5 0 6
  subtype6 0 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    2    5
  subtype3    1    4
  subtype4    2    7
  subtype5    0    6
  subtype6    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        2        1        2        0        0
  NOT HISPANIC OR LATINO        3        5        4        7        6        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
