[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"        "-oTMESO-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/MESO-TP/11541580/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/11588671/MESO-TP.mergedcluster.txt"

nPatients in clinical file=39, in cluster file=87, common to both=39
[1]  8 39
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
 7 12 14  6 
 1  2  3  4 
 7 12 14  6 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
 7  6 12 14 
 1  2  3  4 
 7  6 12 14 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
13  7 10  9 
 1  2  3  4 
13  7 10  9 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
 9 14  8  8 
 1  2  3  4 
 9 14  8  8 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
13 11  8 
 1  2  3 
13 11  8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 3 11  8  4  6 
 1  2  3  4  5 
 3 11  8  4  6 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
12  8 10 
 1  2  3 
12  8 10 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
3 7 3 6 6 5 
1 2 3 4 5 6 
3 7 3 6 6 5 
[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] "KARNOFSKYPERFORMANCESCORE"             
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 39 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
          NA           NA           NA           NA           NA           NA 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
         371           49          108           NA           NA           NA 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
        1316         1575          414            7           NA          200 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
          NA           NA           NA          256           NA           NA 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
          NA           NA          723          652           NA           NA 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=23,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 39 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=23, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 7 17 13  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    7    17    15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 7 17 13  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    7    17    15 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
25  6  5 
[1] "table(vv)"
vv
N0 N1 N2 
25  6  5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
25  6  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
25  6  5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  1  6
  subtype2  4  8
  subtype3  2 12
  subtype4  3  3
subtype1 subtype2 subtype3 subtype4 
       7       12       14        6 
subtype1 subtype2 subtype3 subtype4 
       6        8       12        3 
$subtype1
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BL TCGA-MQ-A6BQ 
        8.02        31.20        80.84        91.73        10.95        43.27 
TCGA-YS-AA4M 
        2.76 

$subtype2
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BS 
        1.87        12.20         3.55        18.81         5.19        13.61 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
        6.58        23.90        14.99        13.35        14.27         2.50 

$subtype3
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN 
       17.95         5.52        23.31        17.33         3.52        24.89 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88C 
        0.23        28.96        15.09         6.48        23.64        23.77 
TCGA-UT-A88D TCGA-XT-AASU 
       21.44         4.67 

$subtype4
TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BR TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UT-A97Y 
        6.08         1.61        51.78         7.99         8.42         4.73 

subtype1 subtype2 subtype3 subtype4 
    2.76     1.87     0.23     1.61 
subtype1 subtype2 subtype3 subtype4 
   91.73    23.90    28.96    51.78 
subtype1 subtype2 subtype3 subtype4 
  31.200   12.775   17.640    7.035 
[1] "2.8 - 91.7 (31.2)" "1.9 - 23.9 (12.8)" "0.2 - 29.0 (17.6)"
[4] "1.6 - 51.8 (7.0)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        0        4         1        1
  subtype2       1        0        0        4         7        0
  subtype3       0        0        1        2         8        3
  subtype4       1        1        0        1         3        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        1        0        1
  STAGE IA         0        0        0        1
  STAGE IB         0        0        1        0
  STAGE II         4        4        2        1
  STAGE III        1        7        8        3
  STAGE IV         1        0        3        0
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  2  5     0
  subtype2  1  5     6
  subtype3  1  6     7
  subtype4  3  1     2
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1           2        1        1        3
  T2           5        5        6        1
  T3+T4        0        6        7        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  6  1  0
  subtype2  9  1  2
  subtype3  6  2  3
  subtype4  4  2  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        6        9        6        4
  N1        1        1        2        2
  N2        0        2        3        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  5  1  1
  subtype2 11  0  1
  subtype3 10  1  3
  subtype4  5  0  1
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        5       11       10        5
  M1        1        0        1        0
  MX        1        1        3        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  0  7
  subtype2  3  9
  subtype3  3 11
  subtype4  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    7
  subtype2    3    9
  subtype3    3   11
  subtype4    4    2
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        0        3        3        4
  MALE          7        9       11        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  1  6
  subtype2  2  4
  subtype3  3  9
  subtype4  4 10
subtype1 subtype2 subtype3 subtype4 
       7        6       12       14 
subtype1 subtype2 subtype3 subtype4 
       6        4        9       10 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A4LC TCGA-MQ-A6BQ TCGA-UD-AABZ TCGA-UD-AAC6 
       17.95         1.87        91.73        43.27         6.48        14.99 
TCGA-UD-AAC7 
       13.35 

$subtype2
TCGA-LK-A4O5 TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC4 
       12.20        17.33         0.23         7.99         8.42        23.64 

$subtype3
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BN 
        5.52         8.02         3.55        18.81        23.31        24.89 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-UT-A88E TCGA-UT-A88G 
       13.61        28.96         6.58        15.09        14.27         2.50 

$subtype4
TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LM TCGA-MQ-A4LV 
        6.08        31.20         1.61        80.84         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y 
       10.95        51.78        23.90        23.77        21.44         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

subtype1 subtype2 subtype3 subtype4 
    1.87     0.23     2.50     1.61 
subtype1 subtype2 subtype3 subtype4 
   91.73    23.64    28.96    80.84 
subtype1 subtype2 subtype3 subtype4 
  14.990   10.310   13.940    8.515 
[1] "1.9 - 91.7 (15.0)" "0.2 - 23.6 (10.3)" "2.5 - 29.0 (13.9)"
[4] "1.6 - 80.8 (8.5)" 
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        0        5         1        1
  subtype2       0        0        1        1         4        0
  subtype3       1        0        0        3         6        2
  subtype4       2        1        0        2         8        1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        0        1        2
  STAGE IA         0        0        0        1
  STAGE IB         0        1        0        0
  STAGE II         5        1        3        2
  STAGE III        1        4        6        8
  STAGE IV         1        0        2        1
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  0  5     2
  subtype2  1  2     3
  subtype3  1  7     4
  subtype4  5  3     6
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1           0        1        1        5
  T2           5        2        7        3
  T3+T4        2        3        4        6
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  6  0  1
  subtype2  4  0  1
  subtype3  7  3  1
  subtype4  8  3  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        6        4        7        8
  N1        0        0        3        3
  N2        1        1        1        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  6  0  1
  subtype2  5  0  1
  subtype3  9  1  2
  subtype4 11  1  2
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        6        5        9       11
  M1        0        0        1        1
  MX        1        1        2        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  1  6
  subtype2  2  4
  subtype3  4  8
  subtype4  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    2    4
  subtype3    4    8
  subtype4    3   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        4        3
  MALE          6        4        8       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"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  4  9
  subtype2  3  4
  subtype3  0 10
  subtype4  3  6
subtype1 subtype2 subtype3 subtype4 
      13        7       10        9 
subtype1 subtype2 subtype3 subtype4 
       9        4       10        6 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN 
       17.95         8.02        12.20        80.84        91.73        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
       43.27        13.61        15.09        23.64        14.99        23.77 
TCGA-UT-A88E 
       14.27 

$subtype2
TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A7BC 
        5.52         3.55        18.81        23.31        51.78        23.90 
TCGA-SH-A9CT 
        8.42 

$subtype3
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
        6.08         1.87        31.20         5.19         3.52        10.95 
TCGA-NQ-A57I TCGA-UD-AAC7 TCGA-XT-AASU TCGA-YS-AA4M 
        0.23        13.35         4.67         2.76 

$subtype4
TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH TCGA-UD-AABZ 
        1.61        17.33        28.96         6.58         7.99         6.48 
TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y 
       21.44         2.50         4.73 

subtype1 subtype2 subtype3 subtype4 
    8.02     3.55     0.23     1.61 
subtype1 subtype2 subtype3 subtype4 
   91.73    51.78    31.20    28.96 
subtype1 subtype2 subtype3 subtype4 
   17.95    18.81     4.93     6.58 
[1] "8.0 - 91.7 (17.9)" "3.5 - 51.8 (18.8)" "0.2 - 31.2 (4.9)" 
[4] "1.6 - 29.0 (6.6)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0        5         4        2
  subtype2       0        0        0        2         5        0
  subtype3       0        1        1        2         5        1
  subtype4       1        0        0        2         5        1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        0        1
  STAGE IA         0        0        1        0
  STAGE IB         0        0        1        0
  STAGE II         5        2        2        2
  STAGE III        4        5        5        5
  STAGE IV         2        0        1        1
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  2  8     3
  subtype2  1  3     3
  subtype3  3  3     4
  subtype4  1  3     5
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1           2        1        3        1
  T2           8        3        3        3
  T3+T4        3        3        4        5
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  9  1  3
  subtype2  3  3  1
  subtype3  7  1  0
  subtype4  6  1  1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        9        3        7        6
  N1        1        3        1        1
  N2        3        1        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  9  1  3
  subtype2  6  0  1
  subtype3  7  1  2
  subtype4  9  0  0
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        9        6        7        9
  M1        1        0        1        0
  MX        3        1        2        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1  2 11
  subtype2  3  4
  subtype3  1  9
  subtype4  4  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   11
  subtype2    3    4
  subtype3    1    9
  subtype4    4    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        3        1        4
  MALE         11        4        9        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  3  6
  subtype2  4 10
  subtype3  0  8
  subtype4  3  5
subtype1 subtype2 subtype3 subtype4 
       9       14        8        8 
subtype1 subtype2 subtype3 subtype4 
       6       10        8        5 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       17.95         8.02        80.84        91.73        24.89        43.27 
TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-UT-A88C 
       13.61        15.09        23.77 

$subtype2
TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        5.52         1.87        12.20         3.55        18.81        23.31 
TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 
       51.78        23.90         8.42         6.48        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88E 
       13.35        14.27 

$subtype3
TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I 
        6.08        31.20         5.19         3.52        10.95         0.23 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

$subtype4
TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH TCGA-UT-A88D 
        1.61        17.33        28.96         6.58         7.99        21.44 
TCGA-UT-A88G TCGA-UT-A97Y 
        2.50         4.73 

subtype1 subtype2 subtype3 subtype4 
    8.02     1.87     0.23     1.61 
subtype1 subtype2 subtype3 subtype4 
   91.73    51.78    31.20    28.96 
subtype1 subtype2 subtype3 subtype4 
  23.770   13.810    4.930    7.285 
[1] "8.0 - 91.7 (23.8)" "1.9 - 51.8 (13.8)" "0.2 - 31.2 (4.9)" 
[4] "1.6 - 29.0 (7.3)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        0        4         2        2
  subtype2       1        0        0        5         8        0
  subtype3       0        1        1        1         4        1
  subtype4       1        0        0        1         5        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        1        0        1
  STAGE IA         0        0        1        0
  STAGE IB         0        0        1        0
  STAGE II         4        5        1        1
  STAGE III        2        8        4        5
  STAGE IV         2        0        1        1
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  1  6     2
  subtype2  2  7     5
  subtype3  3  2     3
  subtype4  1  2     5
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1           1        2        3        1
  T2           6        7        2        2
  T3+T4        2        5        3        5
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  6  1  2
  subtype2  9  3  2
  subtype3  5  1  0
  subtype4  5  1  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        6        9        5        5
  N1        1        3        1        1
  N2        2        2        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  5  1  3
  subtype2 13  0  1
  subtype3  5  1  2
  subtype4  8  0  0
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        5       13        5        8
  M1        1        0        1        0
  MX        3        1        2        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus       0 1
  subtype1 1 8
  subtype2 5 9
  subtype3 0 8
  subtype4 4 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    8
  subtype2    5    9
  subtype3    0    8
  subtype4    4    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        5        0        4
  MALE          8        9        8        4
[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  2 11
  subtype2  5  6
  subtype3  2  6
subtype1 subtype2 subtype3 
      13       11        8 
subtype1 subtype2 subtype3 
      11        6        6 
$subtype1
TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC 
        1.61         5.19         3.52         0.23        28.96        23.90 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU 
        6.48        23.64        14.99        21.44         4.73         4.67 
TCGA-YS-AA4M 
        2.76 

$subtype2
TCGA-LK-A4NW TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BR 
       17.95         3.55        18.81        23.31        17.33        51.78 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BD TCGA-UT-A88C TCGA-UT-A88E 
       13.61         6.58        15.09        23.77        14.27 

$subtype3
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SH-A7BH TCGA-SH-A9CT 
        1.87        31.20        12.20        10.95         7.99         8.42 
TCGA-UD-AAC7 TCGA-UT-A88G 
       13.35         2.50 

subtype1 subtype2 subtype3 
    0.23     3.55     1.87 
subtype1 subtype2 subtype3 
   28.96    51.78    31.20 
subtype1 subtype2 subtype3 
   5.190   17.330    9.685 
[1] "0.2 - 29.0 (5.2)"  "3.5 - 51.8 (17.3)" "1.9 - 31.2 (9.7)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        3         6        2
  subtype2       1        0        2         6        2
  subtype3       0        0        3         5        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          1        1        0
  STAGE IB         1        0        0
  STAGE II         3        2        3
  STAGE III        6        6        5
  STAGE IV         2        2        0
[1] 5 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  4     6
  subtype2  2  5     4
  subtype3  0  4     4
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           3        2        0
  T2           4        5        4
  T3+T4        6        4        4
[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       N0 N1 N2
  subtype1  7  1  2
  subtype2  5  3  3
  subtype3  7  1  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0        7        5        7
  N1        1        3        1
  N2        2        3        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       M0 M1 MX
  subtype1 10  1  2
  subtype2  8  1  2
  subtype3  8  0  0
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       10        8        8
  M1        1        1        0
  MX        2        2        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"
D5V7, binary
          cls
clus        0  1
  subtype1  3 10
  subtype2  2  9
  subtype3  3  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   10
  subtype2    2    9
  subtype3    3    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        2        3
  MALE         10        9        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 0 3
  subtype2 5 6
  subtype3 3 5
  subtype4 0 4
  subtype5 1 5
subtype1 subtype2 subtype3 subtype4 subtype5 
       3       11        8        4        6 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        6        5        4        5 
$subtype1
TCGA-MQ-A4LV TCGA-UD-AAC4 TCGA-UD-AAC6 
        3.52        23.64        14.99 

$subtype2
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR 
       17.95        31.20         3.55        18.81        23.31        51.78 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UT-A88G 
       13.61         6.58         7.99         8.42         2.50 

$subtype3
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A6BL TCGA-UD-AAC7 TCGA-UT-A88D 
        1.87        12.20         1.61        10.95        13.35        21.44 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

$subtype4
TCGA-MQ-A4LM TCGA-NQ-A57I TCGA-SH-A7BC TCGA-UT-A97Y 
        5.19         0.23        23.90         4.73 

$subtype5
TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SH-A7BD TCGA-UD-AABZ TCGA-UT-A88C TCGA-UT-A88E 
       17.33        28.96        15.09         6.48        23.77        14.27 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.52     2.50     1.61     0.23     6.48 
subtype1 subtype2 subtype3 subtype4 subtype5 
   23.64    51.78    21.44    23.90    28.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
   14.99    13.61     7.81     4.96    16.21 
[1] "3.5 - 23.6 (15.0)" "2.5 - 51.8 (13.6)" "1.6 - 21.4 (7.8)" 
[4] "0.2 - 23.9 (5.0)"  "6.5 - 29.0 (16.2)"
D6V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        1         2        0
  subtype2       0        0        3         7        1
  subtype3       0        0        3         4        1
  subtype4       1        1        0         2        0
  subtype5       1        0        1         2        2
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        0        0        1        1
  STAGE IB         0        0        0        1        0
  STAGE II         1        3        3        0        1
  STAGE III        2        7        4        2        2
  STAGE IV         0        1        1        0        2
[1] 5 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  2     1
  subtype2  1  6     4
  subtype3  1  3     4
  subtype4  2  0     2
  subtype5  1  2     3
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T1           0        1        1        2        1
  T2           2        6        3        0        2
  T3+T4        1        4        4        2        3
[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       N0 N1 N2
  subtype1  2  0  1
  subtype2  5  4  2
  subtype3  6  1  0
  subtype4  2  0  1
  subtype5  4  0  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        2        5        6        2        4
  N1        0        4        1        0        0
  N2        1        2        0        1        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  3  0  0
  subtype2  9  0  2
  subtype3  6  1  1
  subtype4  3  0  1
  subtype5  5  1  0
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0        3        9        6        3        5
  M1        0        0        1        0        1
  MX        0        2        1        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"
D6V7, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 3 8
  subtype3 3 5
  subtype4 1 3
  subtype5 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    3    8
  subtype3    3    5
  subtype4    1    3
  subtype5    1    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        0        3        3        1        1
  MALE          3        8        5        3        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 5 7
  subtype2 1 7
  subtype3 3 7
subtype1 subtype2 subtype3 
      12        8       10 
subtype1 subtype2 subtype3 
       7        7        7 
$subtype1
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A6BR TCGA-MQ-A6BS 
        1.87        12.20         3.55        18.81        51.78        13.61 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
       15.09         8.42         6.48        13.35        14.27         2.50 

$subtype2
TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SC-A6LM TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D 
       17.33         0.23        28.96        23.64        14.99        21.44 
TCGA-UT-A97Y TCGA-XT-AASU 
        4.73         4.67 

$subtype3
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A6BL 
       17.95        31.20         1.61        23.31         5.19        10.95 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UT-A88C TCGA-YS-AA4M 
        6.58        23.90        23.77         2.76 

subtype1 subtype2 subtype3 
    1.87     0.23     1.61 
subtype1 subtype2 subtype3 
   51.78    28.96    31.20 
subtype1 subtype2 subtype3 
  12.775   16.160   14.450 
[1] "1.9 - 51.8 (12.8)" "0.2 - 29.0 (16.2)" "1.6 - 31.2 (14.4)"
D7V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        5         5        1
  subtype2       1        1        2         3        1
  subtype3       0        0        1         7        2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          1        1        0
  STAGE IB         0        1        0
  STAGE II         5        2        1
  STAGE III        5        3        7
  STAGE IV         1        1        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  2  6     4
  subtype2  2  3     3
  subtype3  1  4     5
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           2        2        1
  T2           6        3        4
  T3+T4        4        3        5
[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       N0 N1 N2
  subtype1 10  2  0
  subtype2  4  0  1
  subtype3  3  3  4
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       10        4        3
  N1        2        0        3
  N2        0        1        4
[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       M0 M1 MX
  subtype1  9  1  2
  subtype2  6  0  2
  subtype3  9  1  0
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        9        6        9
  M1        1        0        1
  MX        2        2        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"
D7V7, binary
          cls
clus       0 1
  subtype1 4 8
  subtype2 2 6
  subtype3 1 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    8
  subtype2    2    6
  subtype3    1    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        2        1
  MALE          8        6        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 1 2
  subtype2 3 4
  subtype3 2 1
  subtype4 2 4
  subtype5 1 5
  subtype6 0 5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        7        3        6        6        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        4        1        4        5        5 
$subtype1
TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-UT-A88E 
       13.61        15.09        14.27 

$subtype2
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A9CT TCGA-UD-AAC7 
        3.55        18.81        23.31        51.78         8.42        13.35 
TCGA-UT-A88G 
        2.50 

$subtype3
TCGA-MQ-A6BL TCGA-UT-A88C TCGA-UT-A88D 
       10.95        23.77        21.44 

$subtype4
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-SC-A6LN TCGA-SH-A7BC 
       17.95         1.87        31.20        12.20         6.58        23.90 

$subtype5
TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-NQ-A57I TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        1.61         5.19         0.23         4.73         4.67         2.76 

$subtype6
TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 
       17.33        28.96         6.48        23.64        14.99 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   13.61     2.50    10.95     1.87     0.23     6.48 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   15.09    51.78    23.77    31.20     5.19    28.96 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  14.270   13.350   21.440   15.075    3.715   17.330 
[1] "13.6 - 15.1 (14.3)" "2.5 - 51.8 (13.3)"  "10.9 - 23.8 (21.4)"
[4] "1.9 - 31.2 (15.1)"  "0.2 - 5.2 (3.7)"    "6.5 - 29.0 (17.3)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        1         0        1
  subtype2       0        0        3         4        0
  subtype3       0        0        2         1        0
  subtype4       0        0        0         5        1
  subtype5       1        1        0         3        1
  subtype6       0        0        2         2        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          1        0        0        0        1        0
  STAGE IB         0        0        0        0        1        0
  STAGE II         1        3        2        0        0        2
  STAGE III        0        4        1        5        3        2
  STAGE IV         1        0        0        1        1        1
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  1  2     0
  subtype2  1  4     2
  subtype3  0  2     1
  subtype4  0  2     4
  subtype5  3  0     3
  subtype6  0  3     2
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1           1        1        0        0        3        0
  T2           2        4        2        2        0        3
  T3+T4        0        2        1        4        3        2
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  3  0  0
  subtype2  4  3  0
  subtype3  2  0  1
  subtype4  2  1  3
  subtype5  3  1  0
  subtype6  3  0  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        3        4        2        2        3        3
  N1        0        3        0        1        1        0
  N2        0        0        1        3        0        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  1  1  1
  subtype2  6  0  1
  subtype3  3  0  0
  subtype4  6  0  0
  subtype5  3  1  2
  subtype6  5  0  0
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0        1        6        3        6        3        5
  M1        1        0        0        0        1        0
  MX        1        1        0        0        2        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 2 5
  subtype3 0 3
  subtype4 2 4
  subtype5 2 4
  subtype6 1 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    2    5
  subtype3    0    3
  subtype4    2    4
  subtype5    2    4
  subtype6    1    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        0        2        0        2        2        1
  MALE          3        5        3        4        4        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
