[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/19775385/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/20139528/MESO-TP.mergedcluster.txt"

nPatients in clinical file=87, in cluster file=87, common to both=87
[1] 10 87
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
23 26 24 14 
 1  2  3  4 
23 26 24 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
14 20 26 27 
 1  2  3  4 
14 20 26 27 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6 
14  7 13  8  7 14 
 1  2  3  4  5  6 
14  7 13  8  7 14 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
 9 11 10 12  9 12 
 1  2  3  4  5  6 
 9 11 10 12  9 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
26 22 17 21 
 1  2  3  4 
26 22 17 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
22 12 22 13 17 
 1  2  3  4  5 
22 12 22 13 17 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
36 29 22 
 1  2  3 
36 29 22 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
29 25  6 13 14 
 1  2  3  4  5 
29 25  6 13 14 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
37 27 21 
 1  2  3 
37 27 21 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
16 17 21 31 
 1  2  3  4 
16 17 21 31 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 87 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ASIAN   BLACK OR AFRICAN AMERICAN WHITE  
freq.values   "1"     "1"                       "85"   
freq.contrast "86"    "86"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 17:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 87 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "RESIDUAL_TUMOR"             
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
14 26 32 13 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 26 32 13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 26 32 13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 26 32 13 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
44 10 26  3 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   44    10    29 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
44 10 26  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   44    10    29 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=5, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  6 17
  subtype2  3 23
  subtype3  3 20
  subtype4  3 11
subtype1 subtype2 subtype3 subtype4 
      23       26       23       14 
subtype1 subtype2 subtype3 subtype4 
      17       23       20       11 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-3U-A98H TCGA-3U-A98I 
       56.38        42.81        55.36        20.71        38.01        22.06 
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        66.54 
TCGA-TS-A7OU TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV 
       55.07        22.65        15.02        32.28        26.14         1.55 
TCGA-UD-AAC1 TCGA-YS-AA4M TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
       25.94         2.76        33.70        24.30        42.71 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3U-A98F TCGA-LK-A4O2 TCGA-LK-A4O5 
       11.87        29.10        27.16        17.62         1.87        12.72 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR 
       11.51        18.81         5.19        19.99        13.61        29.42 
TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF 
       23.90        19.79        41.46         9.30        19.43        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E 
       10.78        15.42         8.32        14.99        13.35        14.27 
TCGA-UT-A88G TCGA-ZN-A9VQ 
        2.50        16.41 

$subtype3
TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3U-A98D TCGA-LK-A4NW TCGA-LK-A4NY TCGA-MQ-A4LJ 
       12.66        13.61         4.67        17.95         5.52        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LQ 
       17.33         3.52        24.89         0.66        28.96         9.76 
TCGA-SH-A7BD TCGA-TS-A7P1 TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88C 
       15.09        18.51        27.72         6.48        23.64        28.37 
TCGA-UT-A88D TCGA-XT-AASU TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VW 
       24.85         4.67         3.68         3.12         2.76 

$subtype4
TCGA-3H-AB3X TCGA-3U-A98J TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A6BR TCGA-SC-A6LP 
       48.99        24.36         6.08        14.73        62.27         2.56 
TCGA-SC-AA5Z TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-UT-A97Y 
       21.40         7.99        14.76         8.38        27.75         4.73 
TCGA-YS-A95B TCGA-YS-A95C 
        1.28         4.37 

subtype1 subtype2 subtype3 subtype4 
    1.55     1.87     0.66     1.28 
subtype1 subtype2 subtype3 subtype4 
   91.73    41.46    28.96    62.27 
subtype1 subtype2 subtype3 subtype4 
  31.200   14.630   13.610   11.555 
[1] "1.6 - 91.7 (31.2)" "1.9 - 41.5 (14.6)" "0.7 - 29.0 (13.6)"
[4] "1.3 - 62.3 (11.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        0        6         9        6
  subtype2       3        0        0        4        17        2
  subtype3       2        0        1        4        12        5
  subtype4       1        1        0        2         7        3
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        3        2        1
  STAGE IA         1        0        0        1
  STAGE IB         0        0        1        0
  STAGE II         6        4        4        2
  STAGE III        9       17       12        7
  STAGE IV         6        2        5        3
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3  9  5  5
  subtype2  4  6 13  2
  subtype3  3  9  8  4
  subtype4  4  2  6  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        4        3        4
  T2        9        6        9        2
  T3        5       13        8        6
  T4        5        2        4        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"
          vv
clus       N0 N1 N2+N3
  subtype1 13  2     8
  subtype2 14  3     9
  subtype3 11  2     7
  subtype4  6  3     5
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          13       14       11        6
  N1           2        3        2        3
  N2+N3        8        9        7        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"
D1V6, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 18  0
  subtype3 16  2
  subtype4 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   18    0
  subtype3   16    2
  subtype4   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       12       18       16       11
  1        1        0        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"
D1V7, binary
          cls
clus        0  1
  subtype1  2 21
  subtype2  5 21
  subtype3  4 20
  subtype4  5  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   21
  subtype2    5   21
  subtype3    4   20
  subtype4    5    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        5        4        5
  MALE         21       21       20        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"
D1V8, binary
          cls
clus        0  1
  subtype1 18  4
  subtype2 16  9
  subtype3 12  9
  subtype4 11  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    4
  subtype2   16    9
  subtype3   12    9
  subtype4   11    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        18       16       12       11
  YES        4        9        9        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     6                                    2
  subtype2                     6                                    0
  subtype3                     8                                    3
  subtype4                     3                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       14                        1
  subtype2                       20                        0
  subtype3                       13                        0
  subtype4                       10                        1
D1V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       6        6        8        3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        0        3        0
  EPITHELIOID MESOTHELIOMA                   14       20       13       10
  SARCOMATOID MESOTHELIOMA                    1        0        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  4  1  3  0
  subtype2  3  2  5  4
  subtype3  8  0  4  3
  subtype4  2  0  3  4
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        4        3        8        2
  R1        1        2        0        0
  R2        3        5        4        3
  RX        0        4        3        4
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  5  9
  subtype2  2 17
  subtype3  5 21
  subtype4  3 24
subtype1 subtype2 subtype3 subtype4 
      14       19       26       27 
subtype1 subtype2 subtype3 subtype4 
       9       17       21       24 
$subtype1
TCGA-3H-AB3K TCGA-3U-A98E TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-MQ-A4LC TCGA-MQ-A6BQ 
       56.38        55.36        17.95         1.87        91.73        66.54 
TCGA-SC-A6LR TCGA-TS-A7OU TCGA-UD-AABZ TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-YS-A95C 
       29.42        55.07         6.48        14.99        13.35         4.37 
TCGA-ZN-A9VS TCGA-ZN-A9VU 
       33.70        24.30 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4O5 
       11.87        12.66        13.61         4.67        22.06        12.72 
TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7P0 TCGA-TS-A7P1 
       17.33         0.66         7.99        14.76        41.46        18.51 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AAC4 TCGA-ZN-A9VP 
        9.30        19.43        11.77        10.78        23.64         3.12 
TCGA-ZN-A9VW 
        2.76 

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-LK-A4NY TCGA-LK-A4NZ 
       29.10        27.16        48.99        17.62         5.52         8.02 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-SC-A6LM 
       11.51        18.81        23.31        24.89        19.99        28.96 
TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7PB 
       13.61        15.09        19.79        27.75        22.65        32.28 
TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-A95B TCGA-ZN-A9VO 
       27.72         8.32        14.27         2.50         1.28         3.68 
TCGA-ZN-A9VQ TCGA-ZN-A9VV 
       16.41        42.71 

$subtype4
TCGA-3H-AB3O TCGA-3U-A98G TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4O0 TCGA-LK-A4O4 
       42.81        20.71        38.01        24.36         6.08        31.20 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BR 
       14.73        80.84         5.19         3.52        10.95        62.27 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OY TCGA-TS-A7P8 
        2.56         9.76        21.40        23.90         8.38        15.02 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A88D 
       26.14         1.55        15.42        25.94        28.37        24.85 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

subtype1 subtype2 subtype3 subtype4 
    1.87     0.66     1.28     1.55 
subtype1 subtype2 subtype3 subtype4 
   91.73    41.46    48.99    80.84 
subtype1 subtype2 subtype3 subtype4 
   26.86    12.66    19.30    15.42 
[1] "1.9 - 91.7 (26.9)" "0.7 - 41.5 (12.7)" "1.3 - 49.0 (19.3)"
[4] "1.6 - 80.8 (15.4)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        0        7         4        3
  subtype2       2        0        1        3        11        3
  subtype3       3        0        0        3        15        5
  subtype4       2        2        0        3        15        5
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        2        3        2
  STAGE IA         0        0        0        2
  STAGE IB         0        1        0        0
  STAGE II         7        3        3        3
  STAGE III        4       11       15       15
  STAGE IV         3        3        5        5
[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  7  2  3
  subtype2  3  6  7  3
  subtype3  3  7 12  4
  subtype4  6  6 11  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        3        3        6
  T2        7        6        7        6
  T3        2        7       12       11
  T4        3        3        4        3
[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       N0 N1 N2+N3
  subtype1 10  0     4
  subtype2  9  1     8
  subtype3 13  4     8
  subtype4 12  5     9
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          10        9       13       12
  N1           0        1        4        5
  N2+N3        4        8        8        9
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 11  0
  subtype3 17  2
  subtype4 19  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   11    0
  subtype3   17    2
  subtype4   19    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       10       11       17       19
  1        0        0        2        1
[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"
D2V7, binary
          cls
clus        0  1
  subtype1  2 12
  subtype2  2 18
  subtype3  6 20
  subtype4  6 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   12
  subtype2    2   18
  subtype3    6   20
  subtype4    6   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        2        6        6
  MALE         12       18       20       21
[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"
D2V8, binary
          cls
clus        0  1
  subtype1  6  7
  subtype2 16  2
  subtype3 16  9
  subtype4 19  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    7
  subtype2   16    2
  subtype3   16    9
  subtype4   19    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       16       16       19
  YES        7        2        9        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"
D2V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     1                                    2
  subtype2                     7                                    1
  subtype3                     7                                    1
  subtype4                     8                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       11                        0
  subtype2                       12                        0
  subtype3                       18                        0
  subtype4                       16                        2
D2V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       1        7        7        8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        1        1        1
  EPITHELIOID MESOTHELIOMA                   11       12       18       16
  SARCOMATOID MESOTHELIOMA                    0        0        0        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"
          vv
clus       R0 R1 R2 RX
  subtype1  2  1  4  2
  subtype2  1  1  3  0
  subtype3  5  1  4  5
  subtype4  9  0  4  4
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        2        1        5        9
  R1        1        1        1        0
  R2        4        3        4        4
  RX        2        0        5        4
[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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  1 13
  subtype2  1  6
  subtype3  1 12
  subtype4  0  8
  subtype5  0  7
  subtype6  4 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      14        7       13        8        7       14 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      13        6       12        8        7       10 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98G TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       56.38        27.16        20.71        38.01        22.06        24.36 
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A6BS TCGA-TS-A7P8 
       17.95        31.20        80.84        23.31        19.99        15.02 
TCGA-UD-AAC6 TCGA-YS-A95C 
       14.99         4.37 

$subtype2
TCGA-3H-AB3L TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-SC-A6LR TCGA-TS-A7OY TCGA-TS-A7P0 
       11.87         6.08        12.72        29.42         8.38        41.46 
TCGA-TS-A8AV 
        1.55 

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-LK-A4NZ TCGA-LK-A4O6 TCGA-SC-A6LN TCGA-SC-AA5Z 
       29.10        12.66         8.02        14.73        13.61        21.40 
TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AY TCGA-UD-AABY 
       27.75        22.65        19.43        32.28        15.42        27.72 
TCGA-UT-A97Y 
        4.73 

$subtype4
TCGA-3H-AB3O TCGA-3H-AB3T TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A9CT 
       42.81        13.61        28.96         9.76        23.90        14.76 
TCGA-TS-A8AF TCGA-YS-A95B 
       11.77         1.28 

$subtype5
TCGA-3U-A98D TCGA-MQ-A4LV TCGA-TS-A7P1 TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC4 
        4.67         3.52        18.51        10.78         6.48        23.64 
TCGA-XT-AASU 
        4.67 

$subtype6
TCGA-3U-A98E TCGA-3U-A98F TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LI 
       55.36        17.62         5.52         1.87        11.51        18.81 
TCGA-MQ-A4LP TCGA-SH-A9CU TCGA-TS-A7OU TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-ZN-A9VQ 
       17.33        19.79        55.07        25.94        13.35        16.41 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       42.71         2.76 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.37     1.55     4.73     1.28     3.52     1.87 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   80.84    41.46    32.28    42.81    23.64    55.36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.685   11.870   19.430   14.185    6.480   17.475 
[1] "4.4 - 80.8 (22.7)" "1.6 - 41.5 (11.9)" "4.7 - 32.3 (19.4)"
[4] "1.3 - 42.8 (14.2)" "3.5 - 23.6 (6.5)"  "1.9 - 55.4 (17.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE III STAGE IV
  subtype1       1        0        3         6        4
  subtype2       0        1        0         5        1
  subtype3       1        0        2         9        1
  subtype4       1        0        1         4        2
  subtype5       1        0        1         4        1
  subtype6       1        0        2         7        4
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          1        0        1        1        1        1
  STAGE IA         0        1        0        0        0        0
  STAGE II         3        0        2        1        1        2
  STAGE III        6        5        9        4        4        7
  STAGE IV         4        1        1        2        1        4
[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  2  5  2  4
  subtype2  2  1  3  0
  subtype3  1  3  8  1
  subtype4  1  2  3  2
  subtype5  1  3  2  1
  subtype6  1  3  6  4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        2        2        1        1        1        1
  T2        5        1        3        2        3        3
  T3        2        3        8        3        2        6
  T4        4        0        1        2        1        4
[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       N0 N1 N2+N3
  subtype1  6  3     5
  subtype2  3  0     4
  subtype3  4  3     6
  subtype4  3  0     4
  subtype5  3  1     2
  subtype6  9  1     4
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0           6        3        4        3        3        9
  N1           3        0        3        0        1        1
  N2+N3        5        4        6        4        2        4
[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"
D3V6, binary
          cls
clus        0
  subtype1 12
  subtype2  4
  subtype3  8
  subtype4  7
  subtype5  4
  subtype6 10
[1] "NOT AVAILABLE: table only has an event [0]"
D3V7, binary
          cls
clus        0  1
  subtype1  0 14
  subtype2  1  6
  subtype3  4  9
  subtype4  3  5
  subtype5  0  7
  subtype6  5  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   14
  subtype2    1    6
  subtype3    4    9
  subtype4    3    5
  subtype5    0    7
  subtype6    5    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        0        1        4        3        0        5
  MALE         14        6        9        5        7        9
[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"
D3V8, binary
          cls
clus        0  1
  subtype1 11  2
  subtype2  6  1
  subtype3 10  3
  subtype4  3  5
  subtype5  6  1
  subtype6  9  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    2
  subtype2    6    1
  subtype3   10    3
  subtype4    3    5
  subtype5    6    1
  subtype6    9    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        11        6       10        3        6        9
  YES        2        1        3        5        1        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"
D3V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        1        1        2        1        3 
[1] "subtype6" "subtype6" "subtype6"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     4                                    2
  subtype2                     0                                    0
  subtype3                     3                                    1
  subtype4                     1                                    0
  subtype5                     3                                    1
  subtype6                     6                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                        8                        0
  subtype2                        5                        2
  subtype3                        9                        0
  subtype4                        7                        0
  subtype5                        3                        0
  subtype6                        8                        0
D3V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       4        0        3        1
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        0        1        0
  EPITHELIOID MESOTHELIOMA                    8        5        9        7
  SARCOMATOID MESOTHELIOMA                    0        2        0        0
                                      clus
vv                                     subtype5 subtype6
  BIPHASIC MESOTHELIOMA                       3        6
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        0
  EPITHELIOID MESOTHELIOMA                    3        8
  SARCOMATOID MESOTHELIOMA                    0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  1  1
  subtype2  1  1  1  0
  subtype3  1  0  2  3
  subtype4  1  0  3  0
  subtype5  2  0  1  1
  subtype6  2  1  3  1
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0        5        1        1        1        2        2
  R1        0        1        0        0        0        1
  R2        1        1        2        3        1        3
  RX        1        0        3        0        1        1
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  0  9
  subtype2  0 11
  subtype3  1  9
  subtype4  2 10
  subtype5  4  5
  subtype6  0 12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       11       10       12        9       12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       11        9       10        5       12 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98H TCGA-LK-A4NW TCGA-MQ-A4KX TCGA-SH-A7BC 
       56.38        27.16        38.01        17.95        80.84        23.90 
TCGA-TS-A7P8 TCGA-UD-AAC6 TCGA-YS-A95C 
       15.02        14.99         4.37 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3T TCGA-LK-A4O7 TCGA-SC-A6LM TCGA-SC-A6LQ 
       11.87        42.81        13.61        11.51        28.96         9.76 
TCGA-SH-A9CT TCGA-TS-A8AF TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-YS-A95B 
       14.76        11.77        25.94        23.64         1.28 

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-LK-A4NZ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR 
       29.10        12.66         8.02        19.99        13.61        29.42 
TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A8AY TCGA-UT-A97Y 
       27.75        22.65        15.42         4.73 

$subtype4
TCGA-3U-A98D TCGA-3U-A98G TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4O4 TCGA-LK-A4O6 
        4.67        20.71        22.06        24.36        31.20        14.73 
TCGA-MQ-A4LJ TCGA-SC-AA5Z TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-UD-AABY 
       23.31        21.40        19.43        32.28        10.78        27.72 

$subtype5
TCGA-3U-A98E TCGA-3U-A98F TCGA-LK-A4NY TCGA-MQ-A4LP TCGA-SH-A9CU TCGA-TS-A7OU 
       55.36        17.62         5.52        17.33        19.79        55.07 
TCGA-TS-A7P0 TCGA-ZN-A9VQ TCGA-ZN-A9VV 
       41.46        16.41        42.71 

$subtype6
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LV TCGA-TS-A7OY 
        6.08         1.87        12.72        18.81         3.52         8.38 
TCGA-TS-A7P1 TCGA-TS-A8AV TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-XT-AASU TCGA-ZN-A9VW 
       18.51         1.55         6.48        13.35         4.67         2.76 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.37     1.28     4.73     4.67     5.52     1.55 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   80.84    42.81    29.42    32.28    55.36    18.81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.900   13.610   17.705   21.730   19.790    6.280 
[1] "4.4 - 80.8 (23.9)" "1.3 - 42.8 (13.6)" "4.7 - 29.4 (17.7)"
[4] "4.7 - 32.3 (21.7)" "5.5 - 55.4 (19.8)" "1.6 - 18.8 (6.3)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE III STAGE IV
  subtype1       1        0        2         4        2
  subtype2       1        0        1         7        2
  subtype3       1        0        3         6        0
  subtype4       0        0        0         8        4
  subtype5       1        0        0         5        3
  subtype6       1        1        3         5        2
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          1        1        1        0        1        1
  STAGE IA         0        0        0        0        0        1
  STAGE II         2        1        3        0        0        3
  STAGE III        4        7        6        8        5        5
  STAGE IV         2        2        0        4        3        2
[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  2  2  2  2
  subtype2  1  4  3  2
  subtype3  2  4  4  0
  subtype4  0  3  5  4
  subtype5  1  0  5  3
  subtype6  2  4  5  1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        2        1        2        0        1        2
  T2        2        4        4        3        0        4
  T3        2        3        4        5        5        5
  T4        2        2        0        4        3        1
[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       N0 N1 N2+N3
  subtype1  4  1     4
  subtype2  3  1     6
  subtype3  4  2     4
  subtype4  2  4     6
  subtype5  6  0     3
  subtype6  9  0     2
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0           4        3        4        2        6        9
  N1           1        1        2        4        0        0
  N2+N3        4        6        4        6        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"
D4V6, binary
          cls
clus        0
  subtype1  8
  subtype2 10
  subtype3  6
  subtype4  9
  subtype5  5
  subtype6  7
[1] "NOT AVAILABLE: table only has an event [0]"
D4V7, binary
          cls
clus        0  1
  subtype1  0  9
  subtype2  4  7
  subtype3  3  7
  subtype4  1 11
  subtype5  2  7
  subtype6  3  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    4    7
  subtype3    3    7
  subtype4    1   11
  subtype5    2    7
  subtype6    3    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        0        4        3        1        2        3
  MALE          9        7        7       11        7        9
[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"
D4V8, binary
          cls
clus        0  1
  subtype1  6  3
  subtype2  6  5
  subtype3  7  3
  subtype4 10  1
  subtype5  6  2
  subtype6 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2    6    5
  subtype3    7    3
  subtype4   10    1
  subtype5    6    2
  subtype6   10    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         6        6        7       10        6       10
  YES        3        5        3        1        2        2
[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"
D4V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"               "subtype6"              
clus
subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        1        3        1 
[1] "subtype5" "subtype5" "subtype5"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     2                                    2
  subtype2                     1                                    1
  subtype3                     1                                    0
  subtype4                     5                                    1
  subtype5                     5                                    0
  subtype6                     3                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                        5                        0
  subtype2                        9                        0
  subtype3                        9                        0
  subtype4                        6                        0
  subtype5                        4                        0
  subtype6                        7                        2
D4V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       2        1        1        5
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        1        0        1
  EPITHELIOID MESOTHELIOMA                    5        9        9        6
  SARCOMATOID MESOTHELIOMA                    0        0        0        0
                                      clus
vv                                     subtype5 subtype6
  BIPHASIC MESOTHELIOMA                       5        3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        0        0
  EPITHELIOID MESOTHELIOMA                    4        7
  SARCOMATOID MESOTHELIOMA                    0        2
[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       R0 R1 R2 RX
  subtype1  2  0  2  1
  subtype2  2  0  4  0
  subtype3  2  0  2  1
  subtype4  2  0  1  2
  subtype5  1  0  0  1
  subtype6  3  2  2  1
D4V11, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5        6        5        5        2        8 
 [1] "subtype4" "subtype1" "subtype3" "subtype6" "subtype6" "subtype4"
 [7] "subtype6" "subtype4" "subtype2" "subtype1" "subtype6" "subtype6"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype4"
[19] "subtype1" "subtype4" "subtype6" "subtype2" "subtype2" "subtype1"
[25] "subtype6" "subtype3" "subtype6" "subtype2" "subtype1"
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype6
  R0        2        2        2        2        3
  R1        0        0        0        0        2
  R2        2        4        2        1        2
  RX        1        0        1        2        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  5 21
  subtype2  6 15
  subtype3  1 16
  subtype4  3 18
subtype1 subtype2 subtype3 subtype4 
      26       21       17       21 
subtype1 subtype2 subtype3 subtype4 
      21       15       16       18 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-3U-A98E TCGA-3U-A98H TCGA-LK-A4NW 
       56.38        11.87        27.16        55.36        38.01        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        8.02        12.72        80.84        91.73        24.89        66.54 
TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB TCGA-TS-A8AS 
       19.99         9.76        15.09        55.07        32.28        26.14 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-A95C TCGA-ZN-A9VO 
       23.64        14.99        28.37        14.27         4.37         3.68 
TCGA-ZN-A9VS TCGA-ZN-A9VU 
       33.70        24.30 

$subtype2
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O7 
       29.10        48.99         4.67        24.36         5.52        11.51 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC 
       18.81        23.31        62.27        29.42        21.40        23.90 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY 
       14.76        19.79        41.46         9.30        15.02        15.42 
TCGA-UD-AAC1 TCGA-YS-A95B TCGA-ZN-A9VP 
       25.94         1.28         3.12 

$subtype3
TCGA-3H-AB3O TCGA-3H-AB3T TCGA-3U-A98I TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       42.81        13.61        22.06         6.08         1.87        31.20 
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SC-A6LP TCGA-TS-A7OY 
        5.19         3.52        10.95         0.66         2.56         8.38 
TCGA-TS-A8AV TCGA-UD-AAC7 TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VW 
        1.55        13.35         4.67         2.76         2.76 

$subtype4
TCGA-3H-AB3S TCGA-3U-A98F TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN 
       12.66        17.62        14.73        17.33        28.96        13.61 
TCGA-SH-A7BH TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AF 
        7.99        27.75        18.51        22.65        19.43        11.77 
TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UT-A88D TCGA-UT-A88G 
       10.78        27.72         6.48         8.32        24.85         2.50 
TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        4.73        16.41        42.71 

subtype1 subtype2 subtype3 subtype4 
    3.68     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 
   91.73    62.27    42.81    42.71 
subtype1 subtype2 subtype3 subtype4 
  24.595   19.790    5.190   16.410 
[1] "3.7 - 91.7 (24.6)" "1.3 - 62.3 (19.8)" "0.7 - 42.8 (5.2)" 
[4] "2.5 - 42.7 (16.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        1        0        7        10        6
  subtype2       0        0        0        3        16        3
  subtype3       1        1        1        3         7        4
  subtype4       4        0        0        3        12        2
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        1        4
  STAGE IA         1        0        1        0
  STAGE IB         0        0        1        0
  STAGE II         7        3        3        3
  STAGE III       10       16        7       12
  STAGE IV         6        3        4        2
[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  4 10  6  5
  subtype2  2  6 10  3
  subtype3  4  5  6  2
  subtype4  4  5 10  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        2        4        4
  T2       10        6        5        5
  T3        6       10        6       10
  T4        5        3        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"
          vv
clus       N0 N1 N2+N3
  subtype1 15  1    10
  subtype2  5  5    11
  subtype3 11  1     3
  subtype4 12  3     5
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          15        5       11       12
  N1           1        5        1        3
  N2+N3       10       11        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"
D5V6, binary
          cls
clus        0  1
  subtype1 16  2
  subtype2 16  0
  subtype3 11  1
  subtype4 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    2
  subtype2   16    0
  subtype3   11    1
  subtype4   13    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       16       16       11       13
  1        2        0        1        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"
D5V7, binary
          cls
clus        0  1
  subtype1  4 22
  subtype2  7 15
  subtype3  1 16
  subtype4  4 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   22
  subtype2    7   15
  subtype3    1   16
  subtype4    4   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        7        1        4
  MALE         22       15       16       17
[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"
D5V8, binary
          cls
clus        0  1
  subtype1 17  8
  subtype2 13  7
  subtype3 13  3
  subtype4 13  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    8
  subtype2   13    7
  subtype3   13    3
  subtype4   13    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       13       13       13
  YES        8        7        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"
D5V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        5        2        5 
 [1] "subtype1" "subtype2" "subtype4" "subtype4" "subtype2" "subtype4"
 [7] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype2"
[13] "subtype4" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     3                                    3
  subtype2                     2                                    0
  subtype3                     9                                    1
  subtype4                     8                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       20                        0
  subtype2                       20                        0
  subtype3                        5                        2
  subtype4                       12                        0
D5V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       3        2        9        8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        3        0        1        1
  EPITHELIOID MESOTHELIOMA                   20       20        5       12
  SARCOMATOID MESOTHELIOMA                    0        0        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       R0 R1 R2 RX
  subtype1  7  2  4  2
  subtype2  3  1  5  2
  subtype3  4  0  4  1
  subtype4  2  0  2  6
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        7        3        4        2
  R1        2        1        0        0
  R2        4        5        4        2
  RX        2        2        1        6
[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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  6 16
  subtype2  0 12
  subtype3  6 15
  subtype4  0 13
  subtype5  3 14
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       12       21       13       17 
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       12       15       13       14 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98E TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NZ 
       56.38        27.16        55.36        38.01        17.95         8.02 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LQ 
       80.84        91.73        24.89        66.54        19.99         9.76 
TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB TCGA-TS-A8AS TCGA-UT-A88C 
       29.42        15.09        55.07        32.28        26.14        28.37 
TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
        4.37         3.68        33.70        24.30 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3S TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-TS-A7P1 
       11.87        12.66         1.87        12.72        11.51        18.51 
TCGA-TS-A8AF TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E 
       11.77         6.48        23.64        14.99        13.35        14.27 

$subtype3
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY 
       29.10        48.99         4.67        22.06        24.36         5.52 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A9CT 
       18.81        23.31        62.27        21.40        23.90        14.76 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AY 
       19.79         8.38        41.46         9.30        15.02        15.42 
TCGA-UD-AAC1 TCGA-YS-A95B TCGA-ZN-A9VP 
       25.94         1.28         3.12 

$subtype4
TCGA-3H-AB3O TCGA-3H-AB3T TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-MQ-A4LM TCGA-MQ-A4LV 
       42.81        13.61         6.08        31.20         5.19         3.52 
TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SC-A6LP TCGA-TS-A8AV TCGA-XT-AASU TCGA-YS-AA4M 
       10.95         0.66         2.56         1.55         4.67         2.76 
TCGA-ZN-A9VW 
        2.76 

$subtype5
TCGA-3U-A98F TCGA-LK-A4O6 TCGA-MQ-A4LP TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH 
       17.62        14.73        17.33        28.96        13.61         7.99 
TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 
       27.75        22.65        19.43        10.78        27.72         8.32 
TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VQ TCGA-ZN-A9VV 
       24.85         2.50         4.73        16.41        42.71 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.68     1.87     1.28     0.66     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.73    23.64    62.27    42.81    42.71 
subtype1 subtype2 subtype3 subtype4 subtype5 
  27.765   12.690   19.790    4.670   17.330 
[1] "3.7 - 91.7 (27.8)" "1.9 - 23.6 (12.7)" "1.3 - 62.3 (19.8)"
[4] "0.7 - 42.8 (4.7)"  "2.5 - 42.7 (17.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        1        0        6         8        6
  subtype2       2        0        0        4         6        0
  subtype3       0        0        0        3        14        5
  subtype4       1        1        1        2         6        2
  subtype5       3        0        0        1        11        2
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        2        0        1        3
  STAGE IA         1        0        0        1        0
  STAGE IB         0        0        0        1        0
  STAGE II         6        4        3        2        1
  STAGE III        8        6       14        6       11
  STAGE IV         6        0        5        2        2
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  4  8  5  5
  subtype2  2  6  3  0
  subtype3  1  6 10  4
  subtype4  4  4  4  1
  subtype5  3  2 10  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4        2        1        4        3
  T2        8        6        6        4        2
  T3        5        3       10        4       10
  T4        5        0        4        1        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 12  1     9
  subtype2  8  1     3
  subtype3  5  4    12
  subtype4  9  1     1
  subtype5  9  3     4
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          12        8        5        9        9
  N1           1        1        4        1        3
  N2+N3        9        3       12        1        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 12  2
  subtype2 10  0
  subtype3 15  0
  subtype4  8  1
  subtype5 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    2
  subtype2   10    0
  subtype3   15    0
  subtype4    8    1
  subtype5   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       12       10       15        8       11
  1        2        0        0        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1  3 19
  subtype2  2 10
  subtype3  7 15
  subtype4  0 13
  subtype5  4 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   19
  subtype2    2   10
  subtype3    7   15
  subtype4    0   13
  subtype5    4   13
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        3        2        7        0        4
  MALE         19       10       15       13       13
[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"
D6V8, binary
          cls
clus        0  1
  subtype1 13  8
  subtype2  7  5
  subtype3 15  5
  subtype4 10  2
  subtype5 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    8
  subtype2    7    5
  subtype3   15    5
  subtype4   10    2
  subtype5   11    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        13        7       15       10       11
  YES        8        5        5        2        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"
D6V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype3 subtype4 subtype5 
       6        4        2        5 
 [1] "subtype1" "subtype3" "subtype5" "subtype5" "subtype1" "subtype5"
 [7] "subtype3" "subtype3" "subtype1" "subtype5" "subtype1" "subtype3"
[13] "subtype5" "subtype1" "subtype1"
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     2                                    2
  subtype2                     1                                    1
  subtype3                     3                                    0
  subtype4                     8                                    1
  subtype5                     8                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       18                        0
  subtype2                       10                        0
  subtype3                       19                        0
  subtype4                        2                        2
  subtype5                        8                        0
D6V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       2        1        3        8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        2        1        0        1
  EPITHELIOID MESOTHELIOMA                   18       10       19        2
  SARCOMATOID MESOTHELIOMA                    0        0        0        2
                                      clus
vv                                     subtype5
  BIPHASIC MESOTHELIOMA                       8
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1
  EPITHELIOID MESOTHELIOMA                    8
  SARCOMATOID MESOTHELIOMA                    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       R0 R1 R2 RX
  subtype1  7  1  3  1
  subtype2  1  1  4  2
  subtype3  2  1  4  2
  subtype4  4  0  2  1
  subtype5  2  0  2  5
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7        1        2        4        2
  R1        1        1        1        0        0
  R2        3        4        4        2        2
  RX        1        2        2        1        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  6 30
  subtype2  7 21
  subtype3  2 20
subtype1 subtype2 subtype3 
      36       28       22 
subtype1 subtype2 subtype3 
      30       21       20 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3U-A98F TCGA-3U-A98G 
       56.38        11.87        12.66        13.61        17.62        20.71 
TCGA-3U-A98I TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LM 
       22.06        14.73         5.19         3.52         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OU TCGA-TS-A7P1 
        2.56         9.76        21.40        23.90        55.07        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AS 
       22.65         9.30        19.43        32.28        11.77        26.14 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D 
        1.55        27.72         6.48        23.64        14.99        24.85 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV 
        4.73         4.67         2.76        16.41        24.30        42.71 

$subtype2
TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3U-A98E TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O7 
       29.10        27.16        55.36        17.95         5.52        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BN 
       80.84        91.73        18.81        23.31        17.33        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LR TCGA-SH-A7BD 
       66.54        62.27        19.99        13.61        29.42        15.09 
TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AY TCGA-UT-A88C TCGA-UT-A88E 
       19.79        41.46        15.02        15.42        28.37        14.27 
TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VS 
        1.28         4.37         3.68        33.70 

$subtype3
TCGA-3H-AB3O TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NZ 
       42.81        48.99         4.67        38.01        24.36         8.02 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SH-A7BH 
        6.08         1.87        31.20        12.72        10.95         7.99 
TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A8AI TCGA-UD-AAC1 TCGA-UD-AAC5 
       14.76         8.38        27.75        10.78        25.94         8.32 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-ZN-A9VP TCGA-ZN-A9VW 
       13.35         2.50         3.12         2.76 

subtype1 subtype2 subtype3 
    0.66     1.28     1.87 
subtype1 subtype2 subtype3 
   56.38    91.73    48.99 
subtype1 subtype2 subtype3 
  17.015   19.890   10.865 
[1] "0.7 - 56.4 (17.0)" "1.3 - 91.7 (19.9)" "1.9 - 49.0 (10.9)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       4        1        1        7        17        6
  subtype2       2        0        0        5        16        6
  subtype3       1        1        0        4        12        4
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          4        2        1
  STAGE IA         1        0        1
  STAGE IB         1        0        0
  STAGE II         7        5        4
  STAGE III       17       16       12
  STAGE IV         6        6        4
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  7 10 13  5
  subtype2  5  9  9  5
  subtype3  2  7 10  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7        5        2
  T2       10        9        7
  T3       13        9       10
  T4        5        5        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 19  1    13
  subtype2 12  6    10
  subtype3 13  3     6
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          19       12       13
  N1           1        6        3
  N2+N3       13       10        6
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 21  1
  subtype2 19  2
  subtype3 17  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    1
  subtype2   19    2
  subtype3   17    0
   clus
vv  subtype1 subtype2 subtype3
  0       21       19       17
  1        1        2        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"
D7V7, binary
          cls
clus        0  1
  subtype1  4 32
  subtype2  8 21
  subtype3  4 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   32
  subtype2    8   21
  subtype3    4   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        8        4
  MALE         32       21       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 23 12
  subtype2 16  9
  subtype3 18  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   12
  subtype2   16    9
  subtype3   18    4
     clus
vv    subtype1 subtype2 subtype3
  NO        23       16       18
  YES       12        9        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"
D7V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                    14                                    4
  subtype2                     3                                    1
  subtype3                     6                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       17                        1
  subtype2                       25                        0
  subtype3                       15                        1
D7V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3
  BIPHASIC MESOTHELIOMA                      14        3        6
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        4        1        0
  EPITHELIOID MESOTHELIOMA                   17       25       15
  SARCOMATOID MESOTHELIOMA                    1        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  7  5
  subtype2 10  2  3  4
  subtype3  2  1  5  2
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        5       10        2
  R1        0        2        1
  R2        7        3        5
  RX        5        4        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  5 24
  subtype2  4 20
  subtype3  0  6
  subtype4  2 11
  subtype5  4 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       24        6       13       14 
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       20        6       11       10 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98G 
       56.38        11.87        13.61         4.67        17.62        20.71 
TCGA-3U-A98I TCGA-3U-A98J TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LP 
       22.06        24.36         5.19         3.52         0.66         2.56 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P6 
       21.40        23.90        55.07        27.75        18.51         9.30 
TCGA-TS-A7P7 TCGA-TS-A8AI TCGA-TS-A8AV TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88D 
       19.43        10.78         1.55        23.64        14.99        24.85 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU 
        4.73         4.67         2.76        16.41        24.30 

$subtype2
TCGA-3H-AB3M TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 
       29.10        38.01        17.95         5.52         8.02        31.20 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SC-A6LR 
       11.51        18.81        23.31        62.27        13.61        29.42 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AY 
        7.99        14.76        19.79        41.46        15.02        15.42 
TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VP TCGA-ZN-A9VW 
       25.94        13.35         2.50         4.37         3.12         2.76 

$subtype3
TCGA-3H-AB3O TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-TS-A7OY 
       42.81         6.08         1.87        12.72        10.95         8.38 

$subtype4
TCGA-3H-AB3S TCGA-3H-AB3X TCGA-LK-A4O6 TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-TS-A7P3 
       12.66        48.99        14.73        19.99         9.76        22.65 
TCGA-TS-A8AF TCGA-TS-A8AS TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-YS-A95B 
       11.77        26.14        27.72         6.48         8.32         1.28 
TCGA-ZN-A9VV 
       42.71 

$subtype5
TCGA-3H-AB3U TCGA-3U-A98E TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LP TCGA-MQ-A6BN 
       27.16        55.36        80.84        91.73        17.33        24.89 
TCGA-MQ-A6BQ TCGA-SC-A6LM TCGA-SH-A7BD TCGA-TS-A7PB TCGA-UT-A88C TCGA-UT-A88E 
       66.54        28.96        15.09        32.28        28.37        14.27 
TCGA-ZN-A9VO TCGA-ZN-A9VS 
        3.68        33.70 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     2.50     1.87     1.28     3.68 
subtype1 subtype2 subtype3 subtype4 subtype5 
   56.38    62.27    42.81    48.99    91.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.410   15.220    9.665   14.730   28.665 
[1] "0.7 - 56.4 (16.4)" "2.5 - 62.3 (15.2)" "1.9 - 42.8 (9.7)" 
[4] "1.3 - 49.0 (14.7)" "3.7 - 91.7 (28.7)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       4        0        1        5        13        6
  subtype2       0        0        0        5        16        4
  subtype3       0        1        0        1         3        1
  subtype4       1        1        0        3         7        1
  subtype5       2        0        0        2         6        4
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          4        0        0        1        2
  STAGE IA         0        0        1        1        0
  STAGE IB         1        0        0        0        0
  STAGE II         5        5        1        3        2
  STAGE III       13       16        3        7        6
  STAGE IV         6        4        1        1        4
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  6  8  9  5
  subtype2  3  9  8  4
  subtype3  1  1  4  0
  subtype4  2  4  6  1
  subtype5  2  4  5  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        3        1        2        2
  T2        8        9        1        4        4
  T3        9        8        4        6        5
  T4        5        4        0        1        3
[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       N0 N1 N2+N3
  subtype1 15  2    10
  subtype2  9  6     9
  subtype3  5  0     1
  subtype4  7  1     5
  subtype5  8  1     4
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          15        9        5        7        8
  N1           2        6        0        1        1
  N2+N3       10        9        1        5        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 17  1
  subtype2 19  0
  subtype3  5  0
  subtype4  8  0
  subtype5  8  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    1
  subtype2   19    0
  subtype3    5    0
  subtype4    8    0
  subtype5    8    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       17       19        5        8        8
  1        1        0        0        0        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"
D8V7, binary
          cls
clus        0  1
  subtype1  1 28
  subtype2  7 18
  subtype3  2  4
  subtype4  3 10
  subtype5  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   28
  subtype2    7   18
  subtype3    2    4
  subtype4    3   10
  subtype5    3   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1        7        2        3        3
  MALE         28       18        4       10       11
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 20  8
  subtype2 17  6
  subtype3  5  1
  subtype4  8  5
  subtype5  7  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    8
  subtype2   17    6
  subtype3    5    1
  subtype4    8    5
  subtype5    7    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        20       17        5        8        7
  YES        8        6        1        5        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"
D8V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                    12                                    3
  subtype2                     6                                    1
  subtype3                     1                                    0
  subtype4                     2                                    1
  subtype5                     2                                    0
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       13                        1
  subtype2                       18                        0
  subtype3                        4                        1
  subtype4                       10                        0
  subtype5                       12                        0
D8V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                      12        6        1        2
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        3        1        0        1
  EPITHELIOID MESOTHELIOMA                   13       18        4       10
  SARCOMATOID MESOTHELIOMA                    1        0        1        0
                                      clus
vv                                     subtype5
  BIPHASIC MESOTHELIOMA                       2
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        0
  EPITHELIOID MESOTHELIOMA                   12
  SARCOMATOID MESOTHELIOMA                    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       R0 R1 R2 RX
  subtype1  4  0  6  2
  subtype2  6  1  5  4
  subtype3  1  1  1  0
  subtype4  2  0  1  4
  subtype5  4  1  2  1
D8V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        4        6        1        2        4
  R1        0        1        1        0        1
  R2        6        5        1        1        2
  RX        2        4        0        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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1  9 27
  subtype2  5 22
  subtype3  1 20
subtype1 subtype2 subtype3 
      36       27       21 
subtype1 subtype2 subtype3 
      27       22       20 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98E 
       56.38        29.10        12.66        27.16        48.99        55.36 
TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX 
       24.36         5.52         8.02        12.72        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       91.73        18.81        23.31        24.89        66.54        62.27 
TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P0 
       19.99        15.09        14.76        19.79        55.07        41.46 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
       15.42         6.48        25.94        13.35        14.27         2.50 
TCGA-YS-A95C TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         3.68         3.12        33.70        24.30         2.76 

$subtype2
TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98F TCGA-3U-A98G TCGA-3U-A98I TCGA-MQ-A4LP 
       11.87        13.61        17.62        20.71        22.06        17.33 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-AA5Z TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
        0.66        28.96        21.40        27.75        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AAC4 TCGA-UD-AAC5 
       19.43        32.28        11.77        27.72        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       14.99        28.37        24.85         4.73         4.67         1.28 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VV 
        2.76        16.41        42.71 

$subtype3
TCGA-3H-AB3O TCGA-3U-A98D TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 
       42.81         4.67        38.01        17.95         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-SC-A6LN TCGA-SC-A6LP 
       31.20        14.73         5.19        10.95        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-TS-A7OY TCGA-TS-A7P6 TCGA-TS-A7P8 
        9.76        29.42        23.90         8.38         9.30        15.02 
TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       10.78        26.14         1.55 

subtype1 subtype2 subtype3 
    2.50     0.66     1.55 
subtype1 subtype2 subtype3 
   91.73    42.71    42.81 
subtype1 subtype2 subtype3 
   19.89    18.51    10.95 
[1] "2.5 - 91.7 (19.9)" "0.7 - 42.7 (18.5)" "1.6 - 42.8 (10.9)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0       12        17        6
  subtype2       5        0        1        2        13        6
  subtype3       0        2        0        2        13        4
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          2        5        0
  STAGE IA         0        0        2
  STAGE IB         0        1        0
  STAGE II        12        2        2
  STAGE III       17       13       13
  STAGE IV         6        6        4
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  4 16 12  5
  subtype2  7  4 10  5
  subtype3  3  6  8  3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        7        3
  T2       16        4        6
  T3       12       10        8
  T4        5        5        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 23  5     8
  subtype2 12  1    11
  subtype3  7  4    10
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          23       12        7
  N1           5        1        4
  N2+N3        8       11       10
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 24  2
  subtype2 16  1
  subtype3 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    2
  subtype2   16    1
  subtype3   15    0
   clus
vv  subtype1 subtype2 subtype3
  0       24       16       15
  1        2        1        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"
D9V7, binary
          cls
clus        0  1
  subtype1  9 28
  subtype2  3 24
  subtype3  3 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   28
  subtype2    3   24
  subtype3    3   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        3        3
  MALE         28       24       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1 22 12
  subtype2 18  8
  subtype3 15  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   12
  subtype2   18    8
  subtype3   15    5
     clus
vv    subtype1 subtype2 subtype3
  NO        22       18       15
  YES       12        8        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"
D9V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     3                                    1
  subtype2                    11                                    3
  subtype3                     7                                    1
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       33                        0
  subtype2                       13                        0
  subtype3                       11                        2
D9V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3
  BIPHASIC MESOTHELIOMA                       3       11        7
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        3        1
  EPITHELIOID MESOTHELIOMA                   33       13       11
  SARCOMATOID MESOTHELIOMA                    0        0        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1  8  3  4  5
  subtype2  4  0  7  3
  subtype3  4  0  3  3
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        8        4        4
  R1        3        0        0
  R2        4        7        3
  RX        5        3        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1  5 11
  subtype2  3 13
  subtype3  3 18
  subtype4  4 27
subtype1 subtype2 subtype3 subtype4 
      16       16       21       31 
subtype1 subtype2 subtype3 subtype4 
      11       13       18       27 
$subtype1
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-3U-A98E TCGA-MQ-A4KX TCGA-MQ-A4LC 
       56.38        11.87        27.16        55.36        80.84        91.73 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7PB 
       24.89        66.54        19.99        15.09        55.07        32.28 
TCGA-UT-A88E TCGA-ZN-A9VO TCGA-ZN-A9VS TCGA-ZN-A9VU 
       14.27         3.68        33.70        24.30 

$subtype2
TCGA-3H-AB3M TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       29.10        24.36         5.52        11.51        18.81        23.31 
TCGA-MQ-A6BR TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A8AY TCGA-UD-AAC1 
       62.27        14.76        19.79        41.46        15.42        25.94 
TCGA-UT-A88G TCGA-YS-A95C TCGA-ZN-A9VP TCGA-ZN-A9VW 
        2.50         4.37         3.12         2.76 

$subtype3
TCGA-3H-AB3O TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NZ 
       42.81        48.99         4.67        38.01        17.95         8.02 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A6BL TCGA-SC-A6LQ 
        6.08         1.87        31.20        12.72        10.95         9.76 
TCGA-SC-A6LR TCGA-TS-A7OY TCGA-TS-A7P8 TCGA-TS-A8AI TCGA-TS-A8AS TCGA-UD-AAC5 
       29.42         8.38        15.02        10.78        26.14         8.32 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D 
       13.35        28.37        24.85 

$subtype4
TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3U-A98F TCGA-3U-A98G TCGA-3U-A98I TCGA-LK-A4O6 
       12.66        13.61        17.62        20.71        22.06        14.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
        5.19        17.33         0.66        28.96        13.61         2.56 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
       21.40        23.90        27.75        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 
       19.43        11.77         1.55        27.72         6.48        23.64 
TCGA-UD-AAC6 TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-AA4M TCGA-ZN-A9VQ 
       14.99         4.73         4.67         1.28         2.76        16.41 
TCGA-ZN-A9VV 
       42.71 

subtype1 subtype2 subtype3 subtype4 
    3.68     2.50     1.87     0.66 
subtype1 subtype2 subtype3 subtype4 
   91.73    62.27    48.99    42.71 
subtype1 subtype2 subtype3 subtype4 
  29.720   17.115   13.350   14.990 
[1] "3.7 - 91.7 (29.7)" "2.5 - 62.3 (17.1)" "1.9 - 49.0 (13.3)"
[4] "0.7 - 42.7 (15.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV
  subtype1       2        0        0        5         5        4
  subtype2       0        0        0        3        12        2
  subtype3       1        2        0        4        10        4
  subtype4       4        0        1        4        16        6
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        0        1        4
  STAGE IA         0        0        2        0
  STAGE IB         0        0        0        1
  STAGE II         5        3        4        4
  STAGE III        5       12       10       16
  STAGE IV         4        2        4        6
[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  7  3  3
  subtype2  2  5  8  2
  subtype3  4  6  7  3
  subtype4  6  8 12  5
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        2        2        4        6
  T2        7        5        6        8
  T3        3        8        7       12
  T4        3        2        3        5
[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       N0 N1 N2+N3
  subtype1 11  1     4
  subtype2  6  4     6
  subtype3 11  3     7
  subtype4 14  2    12
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11        6       11       14
  N1           1        4        3        2
  N2+N3        4        6        7       12
[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"
D10V6, binary
          cls
clus        0  1
  subtype1  7  2
  subtype2 12  0
  subtype3 17  0
  subtype4 19  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2   12    0
  subtype3   17    0
  subtype4   19    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7       12       17       19
  1        2        0        0        1
[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"
D10V7, binary
          cls
clus        0  1
  subtype1  2 14
  subtype2  6 11
  subtype3  3 18
  subtype4  4 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   14
  subtype2    6   11
  subtype3    3   18
  subtype4    4   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        6        3        4
  MALE         14       11       18       27
[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"
D10V8, binary
          cls
clus        0  1
  subtype1 10  5
  subtype2 12  3
  subtype3 13  8
  subtype4 20  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    5
  subtype2   12    3
  subtype3   13    8
  subtype4   20    9
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        10       12       13       20
  YES        5        3        8        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"
D10V9, continuous
          vv
clus       BIPHASIC MESOTHELIOMA DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  subtype1                     1                                    1
  subtype2                     3                                    0
  subtype3                     3                                    1
  subtype4                    14                                    3
          vv
clus       EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  subtype1                       14                        0
  subtype2                       14                        0
  subtype3                       16                        1
  subtype4                       13                        1
D10V10, multiclass
                                      clus
vv                                     subtype1 subtype2 subtype3 subtype4
  BIPHASIC MESOTHELIOMA                       1        3        3       14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS        1        0        1        3
  EPITHELIOID MESOTHELIOMA                   14       14       16       13
  SARCOMATOID MESOTHELIOMA                    0        0        1        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       R0 R1 R2 RX
  subtype1  4  1  1  1
  subtype2  4  1  1  3
  subtype3  5  1  4  2
  subtype4  3  0  8  5
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        4        4        5        3
  R1        1        1        1        0
  R2        1        1        4        8
  RX        1        3        2        5
[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"
